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DNA Origami–Graphene Hybrid Nanopore for DNA Detection

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Department of Mechanical Science and Engineering, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
*E-mail: [email protected]
Cite this: ACS Appl. Mater. Interfaces 2017, 9, 1, 92–100
Publication Date (Web):December 1, 2016
https://doi.org/10.1021/acsami.6b11001

Copyright © 2016 American Chemical Society. This publication is licensed under these Terms of Use.

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Abstract

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DNA origami nanostructures can be used to functionalize solid-state nanopores for single molecule studies. In this study, we characterized a nanopore in a DNA origami–graphene heterostructure for DNA detection. The DNA origami nanopore is functionalized with a specific nucleotide type at the edge of the pore. Using extensive molecular dynamics (MD) simulations, we computed and analyzed the ionic conductivity of nanopores in heterostructures carpeted with one or two layers of DNA origami on graphene. We demonstrate that a nanopore in DNA origami–graphene gives rise to distinguishable dwell times for the four DNA base types, whereas for a nanopore in bare graphene, the dwell time is almost the same for all types of bases. The specific interactions (hydrogen bonds) between DNA origami and the translocating DNA strand yield different residence times and ionic currents. We also conclude that the speed of DNA translocation decreases due to the friction between the dangling bases at the pore mouth and the sequencing DNA strands.

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Introduction

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Biological and solid-state nanopores have great potential for DNA sequencing as they provide label-free and fast single-molecule detection. (1, 2) In nanopore devices, the ionic current modulated during DNA translocation reveals the nucleotide type. (3, 4) Noise in the electric current readout can mask the detection signal, making detection erroneous and difficult. (5-7) To overcome this challenge, practical solutions such as using thin 2D material membranes, (8-16) slowing down DNA translocation, (17-19) employing flexible biological nanopores, (20) pore functionalization, and hybrid nanopores were developed. (21-23) Among these solutions, hybrid nanopores constructed with biological and synthetic materials and chemically and synthetically functionalized pores offer two advantages. First, they can be programmed to yield specific interactions improving the noisy currents or even yielding ancillary detection signals. (24, 25) Second, functionalization may be tuned and engineered with nanometer scale precision at the pore mouth. (26, 27)
Programmable nanoboxes, (28-32) plates, (24) and channels in bilayers (33, 34) are some of the structures constructed using DNA origami techniques. It has been shown that DNA origami (28) can be used for selective detection of biomolecules. (24, 35) The self-assembly property and nanometer precision engineering of DNA origami nanostructures are attractive for creating heterostructure and hybrid nanopores. (24, 35) Using experimental techniques, DNA origami was inserted into a silicon nitride nanopore and used for detection of λ-DNA. (24) In another work, (24, 35) DNA origami nanoplate with some single-stranded DNA (ssDNA) overhangs attached to the pore mouth were deposited on the surface of a solid-state nanopore, and the hybrid nanopore was used for selective detection of proteins and ssDNAs. The “bait–prey” mechanism (24) was used by taking advantage of DNA origami plate on a nanopore to create specific interactions with a translocating target molecule. (24) The specific interactions between the nanopore and the prey molecule increase the translocation time and give rise to a distinguishable signal for selective detection, facilitating single-molecule studies and protein recognition. (36) Molecular dynamics simulations were also used to explore and investigate the stability and structural properties of DNA origami shapes. (37) Recently, the dependence of conductivity on the number of DNA origami layers with different applied biases was characterized. (38) In addition, the packing of origami plates in the presence of Mg2+ ions was explored. (38)
With advances in fabrication technologies, deposition and alignment of DNA origami on top of substrates and patterned surfaces, (39-43) chemically modified graphene, (44) and MoS2 (45) are feasible. Considering these advances and the benefits that DNA origami offer to nanopore functionalization, (46) we investigate DNA translocation through a nanopore in a heterostructure of graphene and DNA origami nanoplate. It is notable that molecular scale interactions between DNA origami and translocating DNA are largely unknown. Furthermore, the stability and structure of DNA origami at the pore edge during DNA translocation needs to be understood. In this work, the DNA origami nanopore is functionalized by dangling T bases; i.e., a DNA origami nanopore with unpaired T bases at the edge of the pore is placed on top of a graphene nanopore. In this study, the graphene substrate was primarily used to restrict the DNA origami motion under a positive applied bias, even though the electronic structure changes in graphene during DNA translocation can provide additional sensing signals. The sticky behavior of DNA to graphene decreases the movement of DNA origami on top of the graphene and maintains the initial alignment of the nanopores. The (hybrid) nanopores with zero, one and two layers of DNA origami were characterized and used for the detection of DNA bases. The interactions between the hybrid nanopore and translocating DNA, the dwell time of each base type, and the stability of hybrid nanopores were investigated.

Methods

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We performed all-atom molecular dynamics (MD) simulations with NAMD 2.6 using the petascale Blue Waters machine. (47) Visual molecular dynamics (VMD) (48) is used for the visualization of a typical simulation setup consisting of the DNA origami nanoplate, graphene nanopore, ssDNA, water, and ions (∼118 000–120 000 atoms, as shown in Figure 1a). A pore with a diameter of 2.1 nm is drilled in the center of a 10 nm × 10 nm single-layer graphene (Figure 1b). In all simulations, the carbon atoms of the graphene sheet inside a ring of radius 1.6 nm around the pore have been restrained by a harmonic potential (with a spring constant of k = 5 kcal/(mol Å2)), and the remaining atoms of the graphene sheet were fixed.

Figure 1

Figure 1. (a) Simulation box consisting of a single-layer DNA origami (depicted in red), graphene sheet, water, ions, and translocating ssDNA (depicted in blue). (b) Bare graphene nanopore. (c) Single-layer DNA origami nanopore on top of a graphene nanopore.

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A single layer of 8.7 nm × 9.3 nm × 2.6 nm square lattice DNA origami nanoplate has been designed and generated using caDNAno software. (49) Using caDNAno, (49) the sequence of bases was properly assigned to place a number of A–T base pairs in the middle of the plate. The DNA origami nanoplate is then placed on top of the graphene nanopore. At the location of the graphene pore, the structure of the DNA origami was modified to create an aperture in the DNA origami nanoplate by deleting eight A bases of staple strands and leaving eight unpaired T bases in the scaffold strand. The generated DNA origami pore has roughly a circular shape with a diameter of 1.8 nm. By following the same procedure as for a single-layer DNA origami, a double-layer square lattice DNA origami nanoplate of dimensions 9.0 nm × 11.1 nm × 4.4 nm that includes a semicircular aperture with a diameter of 1.7 nm has also been designed and generated. For the double-layer DNA origami hybrid nanopore, a larger graphene nanoplate that measures 12 nm × 12 nm with a pore diameter of 2.1 nm is used. The dangling unpaired T bases of the DNA origami coat the edge of the graphene nanopore (Figure 1c) (see the Supporting Information for more details on construction of the DNA origami nanopore).
To perform simulations on the translocation of different nucleotide types through the hybrid nanopore with single-layer DNA origami, four different systems were constructed: one for each poly(dA), poly(dC), poly(dG), and poly(dT). Each ssDNA consists of 20 bases. In addition, the same simulation systems were built for translocation of ssDNAs consisting of 30 bases through the double-layer DNA origami hybrid nanopore. In each case, the three first bases of the ssDNA were located inside the hybrid nanopore. Then, the entire structure was solvated in an aqueous 1.0 M NaCl solution.
Water molecules were treated to be rigid using the SHAKE algorithm. (50) The CHARMM27 force field (51) parameters were used for nucleic acids, TIP3P water molecules, graphene, and ions. The periodic boundary condition is applied in all the three directions. The cut-off distance for Lennard-Jones and short-range electrostatic interactions is 12.5 Å. The long-range electrostatic interactions were computed by using the particle–mesh–Ewald (PME) method. (52) The integration time step is 1 fs.
Before equilibration, energy minimization was performed for each system for 25 000 steps. Upon minimization, equilibration was performed for 5 ns with harmonically restrained nucleic acids (for both DNA origami and ssDNA with kspring = 100 kcal/(mol Å2)). Following that, we maintained the ssDNA with harmonic constraint (with kspring = 1 kcal/(mol Å2)) and performed equilibration for 2 ns, while the DNA origami nanoplate was free to move with no constraint. Next, another equilibration simulation was performed for 1 ns with no constraint on nucleic acids. All of these equilibration steps were done under NPT ensemble, while pressure was kept constant at 1 atm using the Nosé–Hoover Langevin piston method, (53, 54) and the temperature was maintained at the constant value of 300 K by Langevin thermostat. (55) Before applying an external electric field, the system was further equilibrated for 2 ns with NVT ensemble at 300 K.
All ionic current simulations were performed under NVT ensemble at 300 K. An electric field was applied along the z direction (ssDNA axis). During all ionic current simulations, DNA origami nanoplate was completely free to move. The external electric fields are reported in terms of a transmembrane voltage difference V = −ELz, where E is the electric field strength and Lz is the length of the simulation system along the z direction. (56) We monitored the time-dependent ionic current, I(t), through the pore. We computed the ionic current through the nanopore by using the definition of current, I = dq/dt, as , where the sum is over all the ions; δt is chosen to be 4 ps; zi and qi are the z-coordinate and charge of ion i, respectively; and n is the total number of ions. The ionic current data was block-averaged over intervals of 100 ps. (56)

Results and Discussion

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To characterize the conductivity of hybrid nanopores with one and two layers of DNA origami, single-layer DNA origami, and the bare graphene nanopores, we computed the ionic current associated with these pores for different biases (these systems do not contain translocating ssDNA). For the single-layer DNA origami nanopore case, a graphene sheet with a larger nanopore is used to keep the DNA origami in place because of the applied electric field. Because DNA origami is negatively charged, we did not study the negative branch of the I–V curve as applying negative biases causes the detachment of DNA origami from the surface of the graphene sheet. (See the Supporting Information for detailed studies on detachment of the DNA origami from graphene under negative applied biases). For each bias point in Figure 2a, we performed a simulation for a duration of 40 ns, and we block-averaged the ionic currents over the simulation time. Although the DNA origami has a porous structure that lets ions permeate through (leakage current), in the hybrid nanopores, these porous areas of DNA origami are blocked by the graphene surface. Consequently, the current is primarily due to the ions passing through the pore. In the case of a single-layer DNA origami nanopore, we only accounted for the current through the nanopore of the nanoplate and not through the gaps and free spaces between DNA strands. For the same bias, the bare graphene nanopore has the largest ionic current followed by a single-layer DNA origami nanopore and then the single-layer DNA origami hybrid nanopore followed by the double-layer DNA origami hybrid nanopore (Figure 2a). For a bias of 0.25 V, the currents for double-layer DNA origami hybrid, single-layer DNA origami hybrid, single-layer DNA origami, and bare (pristine) graphene nanopores are 0.104, 0.52, 1.26, and 1.50 nA, respectively (Figure 2a). The characteristic plots for all the pores denote a linear correlation between the current and the applied bias. The resistance of the bare graphene pore is 0.285 V/nA and for the single-layer DNA origami hybrid nanopore is 0.667 V/nA. Because the DNA origami and the graphene nanopores are connected in series, the resistance of the origami nanopore turns out to be 0.382 V/nA (see the Supporting Information for more details on calculating the resistance of the nanopores). The resistances of the hybrid nanopores are higher than the graphene nanopore, which can be attributed to the higher thickness and polarization of the hybrid pores (35, 46) (see the Supporting Information to find the I–V curve of single-layer DNA origami hybrid nanopore solvated in 1 M KCl aqueous solution.)

Figure 2

Figure 2. Characteristics of the hybrid nanopores under external biases. (a) I–V curves for the four types of nanopores. Lines are linear fits with the corresponding color for the symbols. (b) Conductance of different pores and their comparison with theoretical predictions. (c) Center-to-center distance of the DNA origami pore to the graphene pore in the x–y plane. Interaction between the DNA origami and the external positive bias does not disarrange the alignment of the hybrid nanopore.

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We computed the conductance of each nanopore (Figure 2b). The conductance is defined as G = I/V. The highest and lowest conductance is associated with the bare graphene and the double-layer DNA origami hybrid nanopore, respectively. Wannanu et al. (57) proposed the following equation for the conductance(1)where κ is the conductivity of the solution, lpore is the effective thickness of the nanopore, and d is the diameter of the nanopore. The conductivity of the buffer κ is calculated by performing ionic current simulations for a 1 M NaCl solution cell (see the Supporting Information for more details on calculating the conductivity of the buffer). Kowalczyk et al. (58) showed that this model is accurate enough to predict the conductance of nanopores with a thickness of ∼8.5 nm, while it overestimates the conductance of thinner membranes. (58) We evaluated and compared the results from eq 1 to our results obtained from MD simulations (Figure 2b). The higher values from eq 1 in comparison with the simulations results can be due to the small thickness of our nanopores. The pore thickness of bare graphene, single-layer DNA origami, single-layer DNA origami hybrid, and double-layer DNA origami hybrid nanopores is 0.34, 2.6, 2.94, and 5.44 nm, respectively.
When an electric field is applied, the DNA origami can move on top of the graphene nanoplate. To characterize the motion of the DNA origami under different biases, we monitored the distance from the center of the graphene pore to the center of the DNA origami pore in the x–y plane for a single-layer DNA origami hybrid nanopore. Figure 2c shows the center-to-center distance averaged over the simulation time for different external biases. Under a positive external bias, the initial alignment of the hybrid nanopore is not significantly changed because the motion of the DNA origami is compensated by the stickiness of DNA origami to graphene. However, under a large negative applied bias, DNA origami detaches from graphene and the interaction between DNA origami and graphene becomes weaker (see the Supporting Information for detailed studies on the detachment of DNA origami from graphene under negative applied biases), and the DNA origami moves on top of the graphene under a negative bias (Figure 2c). The motion of DNA origami under a negative bias can be overcome by sandwiching DNA origami between two graphene nanoplates, i.e., on top and bottom and creating a nanopore in the sandwiched structure (see the Supporting Information for studies on sandwiched DNA origami graphene hybrid nanopore.)
The previous studies (59, 60) have shown that by increasing the external bias beyond a critical value, DNA origami can be pulled inside the solid-state nanopore. In our hybrid nanopores, the pores in graphene and DNA origami have almost the same size, and we did not observe any significant pull in phenomenon for external biases below 2 V. In fact, we did not observe pull in phenomenon in our simulations as the DNA strands that are located near the edges of the pore are completely supported by the graphene sheet.
We characterized the instantaneous electrostatic potential map for the distribution of ions, approximated by Gaussian spheres, (61, 62) in the single-layer DNA origami hybrid nanopore system under an external bias of 2 V. The instantaneous potential is averaged over 9.5 ns of the simulation time to get the mean resulting transmembrane bias. Figure 3a shows the resulting bias for the system in the x–z plane. The electrostatic potential map near the graphene nanopore is slightly affected by the presence of negatively charged DNA origami. Also, we averaged the total potential over the pore along x and y axes to find the resulting transmembrane bias in the pore along the direction of the external bias, i.e., the z axis (Figure 3b). This plot shows that the potential drops primarily across the nanopore from zero to −2 V and does not change significantly in the electrolyte (far from the nanopore).

Figure 3

Figure 3. (a) Electrostatic potential map of the single-layer DNA origami hybrid nanopore under an external applied bias of 2 V. Ions and other point charges are approximated by Gaussian spheres with an inverse width of β = 0.25 Å–1. (b) The resulting mean bias across the pore along the z direction, averaged over x and y directions. The cyan and yellow regions approximately show, respectively, the area where the graphene nanopore and the DNA origami nanopore occupy along the z direction during the simulation time. The potential is primarily changing across the graphene nanopore.

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The presence of the T bases at the mouth of the pore induces specific interactions with the translocating DNA, especially with its complementary base, i.e., base A. These interactions usually lower the ssDNAs translocation speed and give rise to specific signatures for DNA detection. To investigate the translocation speed of ssDNA in hybrid nanopores and bare graphene, we simulated a poly(dA)20 in a bare graphene nanopore (Figure 4a), 4 poly ssDNAs with 20 bases (A, C, G, and T bases) in single-layer and double-layer DNA origami hybrid nanopores (Figure 4b,c). All of these simulations were performed for a bias of 2.0 V. The most rapid electrophoretic translocation is observed for the bare graphene nanopore, in which 20 DNA bases (type A) passed through the pore in 5 ns (Figure 4d). The lowest translocation is observed for poly(dA)30 through the double-layer DNA origami hybrid nanopore, in which only five bases translocated in 26 ns (Figure 4e). For the single-layer DNA origami hybrid nanopore, poly(dG)20 has the fastest translocation speed followed by poly(dC)20 and poly(dT)20, and poly(dA)20 has the smallest translocation speed. For poly(dA)20, only 15 bases successfully translocated, and the five last bases were stuck in the pore for more than 30 ns. All the base types reside in the double-layer DNA origami hybrid nanopore for a longer time compared to the single-layer DNA origami hybrid nanopore although the capture of A bases is still more stable compared to the other base types (Figure 4e).

Figure 4

Figure 4. (a) Simulation system of DNA translocating through a bare graphene nanopore. The all-atom model contains a graphene nanopore, ssDNA (depicted in blue), water, and ions. (b) Simulation system of DNA translocating through a single-layer DNA origami hybrid nanopore. The all-atom model contains a single-layer DNA origami (depicted in red)–graphene nanopore, ssDNA (depicted in blue), water, and ions. (c) Simulation system of DNA translocating through a double-layer DNA origami hybrid nanopore. The all-atom model contains a double-layer DNA origami (depicted in red)–graphene nanopore, ssDNA (depicted in blue), water, and ions. (d) Translocation history of ssDNA in pristine graphene and single-layer DNA origami hybrid nanopores. (e) Translocation history of ssDNA in double-layer DNA origami hybrid nanopore. (f) Statistical distribution of the dwell times for different base types translocating through single-layer DNA origami hybrid nanopore under an external bias of 2 V. (g) Average residence time of base in single-layer DNA origami hybrid and bare graphene nanopores.

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To find the statistical distribution of dwell times, we performed 20 simulations for each translocating ssDNA type, poly(dA)20, poly(dC)20, poly(dG)20, and poly(dT)20 (80 simulations in total), through a single-layer DNA origami hybrid nanopore under an external bias of 2 V with different initial velocities and a total simulation time of ∼1.2 μs. Figure 4f shows that most of the A bases reside inside the pore for longer times compared to the other base types. The expected value of the residence time of base type A is approximately 3 ns, and for base types C, G, and T is 1.6, 0.75, and 0.64 ns, respectively. Although the nonhybridized dangling bases of DNA origami nanopore only allow for efficient interactions with A bases, C bases also have long residence time compared to G and T bases. The reason can be explained by the overall (VdW and electrostatic) interactions between ssDNA and nanopore especially the instantaneous hydrogen bonding between poly(dC) and G bases of G–C base pairs near the nanopore. These interactions are a result of the specific configuration of DNA origami base pairs (see the Supporting Information for detailed studies about the interactions between ssDNAs and nanopore). We also averaged the residence time of bases at the pore mouth and found that the A base resides in the single-layer DNA origami hybrid nanopore about nine times longer than in the bare graphene nanopore (Figure 4g). Furthermore, in the case of single-layer DNA origami hybrid nanopore, A bases dwell in the pore about two times longer than T and C and three times longer than G (Figure 4g). While the residence time of different base types is nearly the same for the graphene nanopore, it varies significantly depending on the base type translocating through the hybrid nanopore. This feature of the hybrid nanopore can be used as an ancillary detection signal for DNA base sensing. Although the dwell time can help distinguish the signal, it cannot be a standalone signature for detection (specifically, if the levels of currents for each base are close to each other).
To obtain more insight into the interactions between the hybrid pore and the translocating DNA strand, we computed the average number of hydrogen bonds (HB) between ssDNA and DNA origami in the nanopore region for the single-layer DNA origami hybrid nanopore. The snapshots of hydrogen bonding during translocation of DNA are shown in Figure 5a,b. The bases of poly(dA)20 create the largest number of hydrogen bonds with the DNA origami, while the bases of poly(dT)20 have the smallest number of hydrogen bonds during the simulation time. Bases of poly(dC)20 and poly(dG)20 create almost the same number of hydrogen bonds during the simulation time (Figure 5c). The A (translocating base type)–T (unpaired dangling bases of the pore) base pairing gives rise to the highest attraction between poly(dA)20 and the hybrid nanopore and the highest number of HBs. However, for translocation of poly(dT), we observed the lowest number of HBs because of the mismatch between ssDNA T bases and the unpaired dangling T bases of the pore (Figure 5c).

Figure 5

Figure 5. (a) Snapshot of hydrogen bonds between poly(dA) and DNA origami (the black dashed lines represent HBs). (b) Snapshot of hydrogen bonds between poly(dT) and DNA origami (the black dashed lines represent HBs). (c) Average number of HBs between ssDNA and DNA origami nanoplates. (d) Time-dependent interaction energy between poly(dA) and DNA origami nanoplate (black). Translocation plot of poly(dA) through hybrid nanopore (red).

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To understand the change in the interaction energy during translocation of ssDNA, we computed the interaction energy between the atoms of the translocating poly(dA) and the DNA origami nanoplate in the single-layer DNA origami hybrid nanopore (Figure 5d). There is a high correlation between the interaction energy and the stepwise translocation history (Figure 5d). For example, some bases were stuck in the time window of 7–10 and 14–16 ns (long-lasting flat steps are the signatures of bases being stuck; Figure 5d), and at the same time, we observed a peak (local maxima) in the interaction energy (190 and 210 kcal/mol, respectively). In other words, at time instances in which the DNA origami and the translocating DNA are strongly interacting with each other, the electrophoretic forces could not overcome the friction between the DNA origami and the translocating DNA, which gives rise to a higher residence time. At the time instances in which successive translocation occurs, the average of interaction energies is lower and around 110 kcal/mol.
Figure 6a illustrates the schematic of the system used for ionic current simulations. To explore the ionic current characteristic of the single-layer DNA origami hybrid nanopore, we averaged the current associated with the translocation of each poly ssDNA type (Figure 6b). Bases A and G are distinguishable by their ionic currents, while for bases C and T, the ionic currents are about the same (Figure 6b). In measurements with the nanopore technology, the translocation of DNA chain is performed hundreds of times and the ionic current and the dwell time (bandwidth) of each translocation event are recorded. The combination of dwell time and ionic current in the statistical distribution (data clusters built upon dwell time and ionic current for each base) are used to distinguish nucleotides.

Figure 6

Figure 6. (a) Schematic of the ionic current simulation system showing the interaction of the complementary bases (A–T). (b) Ionic currents for different bases computed from the translocation of poly ssDNAs through the single-layer DNA origami hybrid nanopore. (c) Density of different bases of the DNA origami nanoplate in the vicinity of the pore vs simulation time for translocation of poly(dA) through the single-layer DNA origami hybrid nanopore. (d) Average density of different bases of the DNA origami nanoplate in the vicinity of the pore during poly ssDNAs translocations through the single-layer DNA origami hybrid nanopore.

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To understand the stability and arrangement of the dangling unpaired T bases at the pore entrance, we monitored the number of bases of DNA origami nanoplate, which reside around the pore for the translocation of poly(dA)20 through the single-layer DNA origami hybrid nanopore (see the Supporting Information for translocation of other poly ssDNAs). The geometrical space that we examined the bases is within an infinitely long cylinder concentric with the pore center and with a radius of 22.4 Å. The most-prevalent base type of the DNA origami nanoplate around the pore is T, which resides around the pore in a stable manner (Figure 6c). The number of the other base types (i.e., A, C, and G) prevalent at the pore vicinity is approximately one-third of the number of base type T, which implies that the initially functionalized DNA origami with unpaired T bases is stable even in the presence of thermal noise, water and ion permeation, and DNA electrophoretic translocation (Figure 6c).
To investigate the status of pore functionalization during the translocation of other poly ssDNAs, we averaged the number of different base types of the DNA origami residing in the geometrical space, as defined above, over the entire period of DNA translocation (Figure 6d). A total of 10–13 T bases reside around the pore, but only 4–6 bases of A, C, and G types stay near the pore. Interestingly, bases of poly(dA) and poly(dC) attract the T bases of DNA origami nanoplate more than poly(dG) and poly(dT) do (Figure 6d, green line). As a result, more number of T bases of DNA origami line the pore during the simulation of poly(dA) and poly(dC). For the translocation of A bases, the higher number of hydrogen bonds combined with the high density of complementary T bases around the pore create specific interactions resulting in a higher dwell time for base A.
The higher residence time of the single base at the pore would be beneficial for DNA read-out. Longer residence time and slower speed of DNA translocation can ensure a higher resolution signal acquisition. In nanopores, usually, the speed of translocation is fast even at low biases of around 100 mV that the MHz bandwidth of current amplifiers may not be able to resolve the single base readouts. Among the solutions that were proposed for speed reduction are the use of high-viscosity buffer solution, (17) lower temperature, (63) flexible MscL nanopores, (20) pore functionalization, (64) and ionic liquid systems. (65) The presence of DNA origami on top of a graphene nanopore not only creates an additional signature for recognition but also reduces the speed of translocation. To quantify and compare the speed of translocation of poly(dA) in hybrid and bare graphene nanopores, we performed simulations of up to 70 ns at different biases (Figure 7). At biases between 2 and 4 V, the translocation rate for the hybrid pore is 5–7 times slower than that for the bare graphene pore (Figure 7). At lower biases, DNA bases reside for a longer time inside the pore, and hence, the probability increases to form hydrogen bond with the hybrid pore. This gives rise to a longer dwell time.

Figure 7

Figure 7. Comparison of poly(dA) translocation rate through the single-layer DNA origami hybrid nanopore and the bare graphene nanopore.

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Conclusions

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We demonstrated that the hybrid DNA origami–graphene nanopore can yield a distinguishable dwell time for DNA bases. A total of four different nanopores (i.e., bare graphene, single-layer DNA origami, single-layer DNA origami hybrid, and double-layer DNA origami hybrid nanopores) were characterized in terms of ionic current, conductance, and resistance. The functionalization of a DNA origami nanopore with T bases remains intact during the electrophoretic translocation of ssDNA bases. The combination of distinguishable dwell time and ionic current along with the slower speed of translocation make the hybrid DNA origami–graphene nanopore attractive for selective DNA detection. The hydrogen bonds between translocating ssDNA and DNA origami at the pore contribute to the distinguishable dwell time.

Supporting Information

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The Supporting Information is available free of charge on the ACS Publications website at DOI: 10.1021/acsami.6b11001.

  • Calculation of resistivity and conductivity of different nanopore architectures, the design and structure of single-layer and double-layer DNA origami nanopore, density of bases around the pore mouth, motion of DNA origami on top of graphene under external biases, sandwiched DNA origami–graphene hybrid nanopore analysis and I–V curve of hybrid nanopore solvated in 1 M KCl aqueous solution. (PDF)

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Most electronic Supporting Information files are available without a subscription to ACS Web Editions. Such files may be downloaded by article for research use (if there is a public use license linked to the relevant article, that license may permit other uses). Permission may be obtained from ACS for other uses through requests via the RightsLink permission system: http://pubs.acs.org/page/copyright/permissions.html.

Author Information

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  • Corresponding Author
    • Narayana R. Aluru - Department of Mechanical Science and Engineering, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States;  Email: [email protected]
  • Authors
    • Amir Barati Farimani - Department of Mechanical Science and Engineering, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States;  Orcidhttp://orcid.org/0000-0002-2952-8576
    • Payam Dibaeinia - Department of Mechanical Science and Engineering, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
  • Notes
    The authors declare no competing financial interest.

Acknowledgment

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This work is supported by AFOSR under grant no. FA9550-12-1-0464 and by NSF under grant nos. 1264282, 1420882, 1506619, and 1545907. The authors gratefully acknowledge the use of the parallel computing resource Blue Waters provided by the University of Illinois and the National Center for Supercomputing Applications (NCSA).

References

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    A review. Nanopore anal. is an emerging technique that involves using a voltage to drive mols. through a nanoscale pore in a membrane between two electrolytes, and monitoring how the ionic current through the nanopore changes as single mols. pass through it. This approach allows charged polymers (including single-stranded DNA, double-stranded DNA and RNA) to be analyzed with subnanometer resoln. and without the need for labels or amplification. Recent advances suggest that nanopore-based sensors could be competitive with other third-generation DNA sequencing technologies, and may be able to rapidly and reliably sequence the human genome for under $1,000. In this article the authors review the use of nanopore technol. in DNA sequencing, genetics and medical diagnostics.
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  2. 2
    Keyser, U. F. Controlling Molecular Transport through Nanopores J. R. Soc., Interface 2011, 8, 1369– 1378 DOI: 10.1098/rsif.2011.0222
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    2
    Controlling molecular transport through nanopores
    Keyser, Ulrich F.
    Journal of the Royal Society, Interface (2011), 8 (63), 1369-1378CODEN: JRSICU; ISSN:1742-5689. (Royal Society)
    A review. Nanopores are emerging as powerful tools for the detection and identification of macromols. in aq. soln. In this review, we discuss the recent development of active and passive controls over mol. transport through nanopores with emphasis on biosensing applications. We give an overview of the solns. developed to enhance the sensitivity and specificity of the resistive-pulse technique based on biol. and solid-state nanopores.
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  3. 3
    Kasianowicz, J. J.; Brandin, E.; Branton, D.; Deamer, D. W. Characterization of Individual Polynucleotide Molecules Using a Membrane Channel Proc. Natl. Acad. Sci. U. S. A. 1996, 93, 13770– 13773 DOI: 10.1073/pnas.93.24.13770
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    3
    Characterization of individual polynucleotide molecules using a membrane channel
    Kasianowicz, John J.; Brandin, Eric; Branton, Daniel; Deamer, David
    Proceedings of the National Academy of Sciences of the United States of America (1996), 93 (24), 13770-13773CODEN: PNASA6; ISSN:0027-8424. (National Academy of Sciences)
    We show that an elec. field can drive single-stranded RNA and DNA mols. through a 2.6-nm diam. ion channel in a lipid bilayer membrane. Because the channel diam. can accommodate only a single strand of RNA or DNA, each polymer traverses the membrane as an extended chain that partially blocks the channel. The passage of each mol. is detected as a transient decrease of ionic current whose duration is proportional to polymer length. Channel blockades can therefore be used to measure polynucleotide length. With further improvements,the method could in principle provide direct, high-speed detection of the sequence of bases in single mols. of DNA or RNA.
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  4. 4
    Bayley, H.; Cremer, P. S. Stochastic Sensors Inspired by Biology Nature 2001, 413, 226– 230 DOI: 10.1038/35093038
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    4
    Stochastic sensors inspired by biology
    Bayley, Hagan; Cremer, Paul S.
    Nature (London, United Kingdom) (2001), 413 (6852), 226-230CODEN: NATUAS; ISSN:0028-0836. (Nature Publishing Group)
    A review with ∼54 refs. Sensory systems use a variety of membrane-bound receptors, including responsive ion channels, to discriminate between a multitude of stimuli. Here we describe how engineered membrane pores can be used to make rapid and sensitive biosensors with potential applications that range from the detection of biol. warfare agents to pharmaceutical screening. Notably, use of the engineered pores in stochastic sensing, a single-mol. detection technol., reveals the identity of an analyte as well as its concn.
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    Deamer, D. W.; Branton, D. Characterization of Nucleic Acids by Nanopore Analysis Acc. Chem. Res. 2002, 35, 817– 825 DOI: 10.1021/ar000138m
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    5
    Characterization of Nucleic Acids by Nanopore Analysis
    Deamer, David W.; Branton, Daniel
    Accounts of Chemical Research (2002), 35 (10), 817-825CODEN: ACHRE4; ISSN:0001-4842. (American Chemical Society)
    Single-stranded DNA and RNA mols. in soln. can be driven through a nanoscopic pore by an applied elec. field. As each mol. occupies the pore, a characteristic blockade of ionic current is produced. Information about length, compn., structure, and dynamic motion of the mol. can be deduced from modulations of the current blockade.
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  6. 6
    Dekker, C. Solid-State Nanopores Nat. Nanotechnol. 2007, 2, 209– 215 DOI: 10.1038/nnano.2007.27
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    6
    Solid-state nanopores
    Dekker, Cees
    Nature Nanotechnology (2007), 2 (4), 209-215CODEN: NNAABX; ISSN:1748-3387. (Nature Publishing Group)
    A review. The passage of individual mols. through nanosized pores in membranes is central to many processes in biol. Previously, expts. have been restricted to naturally occurring nanopores, but advances in technol. now allow artificial solid-state nanopores to be fabricated in insulating membranes. By monitoring ion currents and forces as mols. pass through a solid-state nanopore, it is possible to investigate a wide range of phenomena involving DNA, RNA and proteins. The solid-state nanopore proves to be a surprisingly versatile new single-mol. tool for biophysics and biotechnol.
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  7. 7
    Branton, D.; Deamer, D. W.; Marziali, A.; Bayley, H.; Benner, S. A.; Butler, T.; Di Ventra, M.; Garaj, S.; Hibbs, A.; Huang, X. H.; Jovanovich, S. B.; Krstic, P. S.; Lindsay, S.; Ling, X. S. S.; Mastrangelo, C. H.; Meller, A.; Oliver, J. S.; Pershin, Y. V.; Ramsey, J. M.; Riehn, R.; Soni, G. V.; Tabard-Cossa, V.; Wanunu, M.; Wiggin, M.; Schloss, J. A. The Potential and Challenges of Nanopore Sequencing Nat. Biotechnol. 2008, 26, 1146– 1153 DOI: 10.1038/nbt.1495
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    7
    The potential and challenges of nanopore sequencing
    Branton, Daniel; Deamer, David W.; Marziali, Andre; Bayley, Hagan; Benner, Steven A.; Butler, Thomas; Di Ventra, Massimiliano; Garaj, Slaven; Hibbs, Andrew; Huang, Xiaohua; Jovanovich, Stevan B.; Krstic, Predrag S.; Lindsay, Stuart; Ling, Xinsheng Sean; Mastrangelo, Carlos H.; Meller, Amit; Oliver, John S.; Pershin, Yuriy V.; Ramsey, J. Michael; Riehn, Robert; Soni, Gautam V.; Tabard-Cossa, Vincent; Wanunu, Meni; Wiggin, Matthew; Schloss, Jeffery A.
    Nature Biotechnology (2008), 26 (10), 1146-1153CODEN: NABIF9; ISSN:1087-0156. (Nature Publishing Group)
    A review. A nanopore-based device provides single-mol. detection and anal. capabilities that are achieved by electrophoretically driving mols. in soln. through a nano-scale pore. The nanopore provides a highly confined space within which single nucleic acid polymers can be analyzed at high throughput by one of a variety of means, and the perfect processivity that can be enforced in a narrow pore ensures that the native order of the nucleobases in a polynucleotide is reflected in the sequence of signals that is detected. Kilobase length polymers (single-stranded genomic DNA or RNA) or small mols. (e.g., nucleosides) can be identified and characterized without amplification or labeling, a unique anal. capability that makes inexpensive, rapid DNA sequencing a possibility. Further research and development to overcome current challenges to nanopore identification of each successive nucleotide in a DNA strand offers the prospect of 'third generation' instruments that will sequence a diploid mammalian genome for ∼$1,000 in ∼24 h.
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  8. 8
    Farimani, A. B.; Min, K.; Aluru, N. R. DNA Base Detection Using a Single-Layer MoS2 ACS Nano 2014, 8, 7914– 22 DOI: 10.1021/nn5029295
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    8
    DNA base detection using a single-layer MoS2
    Farimani, Amir Barati; Min, Kyoungmin; Aluru, Narayana R.
    ACS Nano (2014), 8 (8), 7914-7922CODEN: ANCAC3; ISSN:1936-0851. (American Chemical Society)
    Nanopore-based DNA sequencing has led to fast and high-resoln. recognition and detection of DNA bases. Solid-state and biol. nanopores have low signal-to-noise ratio (SNR) (< 10) and are generally too thick (> 5 nm) to be able to read at single-base resoln. A nanopore in graphene, a 2-D material with sub-nanometer thickness, has a SNR of ∼3 under DNA ionic current. In this report, using atomistic and quantum simulations, we find that a single-layer MoS2 is an extraordinary material (with a SNR > 15) for DNA sequencing by two competing technologies (i.e., nanopore and nanochannel). A MoS2 nanopore shows four distinct ionic current signals for single-nucleobase detection with low noise. In addn., a single-layer MoS2 shows a characteristic change/response in the total d. of states for each base. The band gap of MoS2 is significantly changed compared to other nanomaterials (e.g., graphene, h-BN, and silicon nanowire) when bases are placed on top of the pristine MoS2 and armchair MoS2 nanoribbon, thus making MoS2 a promising material for base detection via transverse current tunneling measurement. MoS2 nanopore benefits from a craftable pore architecture (combination of Mo and S atoms at the edge) which can be engineered to obtain the optimum sequencing signals.
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  9. 9
    Liu, K.; Feng, J. D.; Kis, A.; Radenovic, A. Atomically Thin Molybdenum Disulfide Nanopores with High Sensitivity for DNA Trans Location ACS Nano 2014, 8, 2504– 2511 DOI: 10.1021/nn406102h
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    There is no corresponding record for this reference.
  10. 10
    Schneider, G. F.; Kowalczyk, S. W.; Calado, V. E.; Pandraud, G.; Zandbergen, H. W.; Vandersypen, L. M. K.; Dekker, C. DNA Translocation through Graphene Nanopores Nano Lett. 2010, 10, 3163– 3167 DOI: 10.1021/nl102069z
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    10
    DNA Translocation through Graphene Nanopores
    Schneider, Gregory F.; Kowalczyk, Stefan W.; Calado, Victor E.; Pandraud, Gregory; Zandbergen, Henny W.; Vandersypen, Lieven M. K.; Dekker, Cees
    Nano Letters (2010), 10 (8), 3163-3167CODEN: NALEFD; ISSN:1530-6984. (American Chemical Society)
    Nanopores - nanosized holes that can transport ions and mols. - are very promising devices for genomic screening, in particular DNA sequencing. Solid-state nanopores currently suffer from the drawback, however, that the channel constituting the pore is long, ∼100 times the distance between two bases in a DNA mol. (0.5 nm for single-stranded DNA). This paper provides proof of concept that it is possible to realize and use ultrathin nanopores fabricated in graphene monolayers for single-mol. DNA translocation. The pores are obtained by placing a graphene flake over a microsize hole in a silicon nitride membrane and drilling a nanosize hole in the graphene using an electron beam. As individual DNA mols. translocate through the pore, characteristic temporary conductance changes are obsd. in the ionic current through the nanopore, setting the stage for future single-mol. genomic screening devices.
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  11. 11
    Traversi, F.; Raillon, C.; Benameur, S. M.; Liu, K.; Khlybov, S.; Tosun, M.; Krasnozhon, D.; Kis, A.; Radenovic, A. Detecting the Translocation of DNA through a Nanopore Using Graphene Nanoribbons Nat. Nanotechnol. 2013, 8, 939– 945 DOI: 10.1038/nnano.2013.240
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    11
    Detecting the translocation of DNA through a nanopore using graphene nanoribbons
    Traversi, F.; Raillon, C.; Benameur, S. M.; Liu, K.; Khlybov, S.; Tosun, M.; Krasnozhon, D.; Kis, A.; Radenovic, A.
    Nature Nanotechnology (2013), 8 (12), 939-945CODEN: NNAABX; ISSN:1748-3387. (Nature Publishing Group)
    Solid-state nanopores can act as single-mol. sensors and could potentially be used to rapidly sequence DNA mols. However, nanopores are typically fabricated in insulating membranes that are as thick as 15 bases, which makes it difficult for the devices to read individual bases. Graphene is only 0.335 nm thick (equiv. to the spacing between two bases in a DNA chain) and could therefore provide a suitable membrane for sequencing applications. Here, we show that a solid-state nanopore can be integrated with a graphene nanoribbon transistor to create a sensor for DNA translocation. As DNA mols. move through the pore, the device can simultaneously measure drops in ionic current and changes in local voltage in the transistor, which can both be used to detect the mols. We examine the correlation between these two signals and use the ionic current measurements as a real-time control of the graphene-based sensing device.
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  12. 12
    Saha, K. K.; Drndic, M.; Nikolic, B. K. DNA Base-Specific Modulation of Microampere Transverse Edge Currents through a Metallic Graphene Nanoribbon with a Nanopore Nano Lett. 2012, 12, 50– 55 DOI: 10.1021/nl202870y
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    12
    DNA base-specific modulation of microampere transverse edge currents through a metallic graphene nanoribbon with a nanopore
    Saha, Kamal K.; Drndic, Marija; Nikolic, Branislav K.
    Nano Letters (2012), 12 (1), 50-55CODEN: NALEFD; ISSN:1530-6984. (American Chemical Society)
    We study two-terminal devices for DNA sequencing that consist of a metallic graphene nanoribbon with zigzag edges (ZGNR) and a nanopore in its interior through which the DNA mol. is translocated. Using the nonequil. Green functions combined with d. functional theory, we demonstrate that each of the four DNA nucleobases inserted into the nanopore, whose edge carbon atoms are passivated by either hydrogen or nitrogen, will lead to a unique change in the device conductance. Unlike other recent biosensors based on transverse electronic transport through translocated DNA, which utilize small (of the order of pA) tunneling current across a nanogap or a nanopore yielding a poor signal-to-noise ratio, our device concept relies on the fact that in ZGNRs local c.d. is peaked around the edges so that drilling a nanopore away from the edges will not diminish the conductance. Inserting a nucleobase into the nanopore affects the charge d. in the surrounding area, thereby modulating edge conduction currents whose magnitude is of the order of microampere at bias voltage 0.1 V. The proposed biosensors are not limited to ZGNRs and they could be realized with other nanowires supporting transverse edge currents, such as chiral GNRs or wires made of two-dimensional topol. insulators.
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  13. 13
    Merchant, C. A.; Healy, K.; Wanunu, M.; Ray, V.; Peterman, N.; Bartel, J.; Fischbein, M. D.; Venta, K.; Luo, Z. T.; Johnson, A. T. C.; Drndic, M. DNA Translocation through Graphene Nanopores Nano Lett. 2010, 10, 2915– 2921 DOI: 10.1021/nl101046t
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    13
    DNA Translocation through Graphene Nanopores
    Merchant, Christopher A.; Healy, Ken; Wanunu, Meni; Ray, Vishva; Peterman, Neil; Bartel, John; Fischbein, Michael D.; Venta, Kimberly; Luo, Zhengtang; Johnson, A. T. Charlie; Drndic, Marija
    Nano Letters (2010), 10 (8), 2915-2921CODEN: NALEFD; ISSN:1530-6984. (American Chemical Society)
    The authors report on DNA translocations through nanopores created in graphene membranes. Devices consist of 1-5 nm thick graphene membranes with electron-beam sculpted nanopores from 5 to 10 nm in diam. Due to the thin nature of the graphene membranes, the authors observe larger blocked currents than for traditional solid-state nanopores. However, ionic current noise levels are several orders of magnitude larger than those for silicon nitride nanopores. These fluctuations are reduced with the at.-layer deposition of 5 nm of titanium dioxide over the device. Unlike traditional solid-state nanopore materials that are insulating, graphene is an excellent elec. conductor. Use of graphene as a membrane material opens the door to a new class of nanopore devices in which electronic sensing and control are performed directly at the pore.
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  14. 14
    Merchant, C. A.; Drndic, M. Graphene Nanopore Devices for DNA Sensing Methods Mol. Biol. (N. Y., NY, U. S.) 2012, 870, 211– 226 DOI: 10.1007/978-1-61779-773-6_12
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    There is no corresponding record for this reference.
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    Heerema, S. J.; Dekker, C. Graphene Nanodevices for DNA Sequencing Nat. Nanotechnol. 2016, 11, 127– 136 DOI: 10.1038/nnano.2015.307
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    15
    Graphene nanodevices for DNA sequencing
    Heerema, Stephanie J.; Dekker, Cees
    Nature Nanotechnology (2016), 11 (2), 127-136CODEN: NNAABX; ISSN:1748-3387. (Nature Publishing Group)
    A review. Fast, cheap, and reliable DNA sequencing could be one of the most disruptive innovations of this decade, as it will pave the way for personalized medicine. In pursuit of such technol., a variety of nanotechnol.-based approaches have been explored and established, including sequencing with nanopores. Owing to its unique structure and properties, graphene provides interesting opportunities for the development of a new sequencing technol. In recent years, a wide range of creative ideas for graphene sequencers have been theor. proposed and the first exptl. demonstrations have begun to appear. Here, we review the different approaches to using graphene nanodevices for DNA sequencing, which involve DNA passing through graphene nanopores, nanogaps, and nanoribbons, and the physisorption of DNA on graphene nanostructures. We discuss the advantages and problems of each of these key techniques, and provide a perspective on the use of graphene in future DNA sequencing technol.
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  16. 16
    Garaj, S.; Liu, S.; Golovchenko, J. A.; Branton, D. Molecule-Hugging Graphene Nanopores Proc. Natl. Acad. Sci. U. S. A. 2013, 110, 12192– 12196 DOI: 10.1073/pnas.1220012110
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    16
    Molecule-hugging graphene nanopores
    Garaj, Slaven; Liu, Song; Golovchenko, Jene A.; Branton, Daniel
    Proceedings of the National Academy of Sciences of the United States of America (2013), 110 (30), 12192-12196,S12192/1-S12192/3CODEN: PNASA6; ISSN:0027-8424. (National Academy of Sciences)
    It has recently been recognized that solid-state nanopores in single-at.-layer graphene membranes can be used to electronically detect and characterize single long charged polymer mols. We have now fabricated nanopores in single-layer graphene that are closely matched to the diam. of a double-stranded DNA mol. Ionic current signals during electrophoretically driven translocation of DNA through these nanopores were exptl. explored and theor. modeled. Our expts. show that these nanopores have unusually high sensitivity (0.65 nA/Å) to extremely small changes in the translocating mol.'s outer diam. Such atomically short graphene nanopores can also resolve nanoscale-spaced mol. structures along the length of a polymer, but do so with greatest sensitivity only when the pore and mol. diams. are closely matched. Modeling confirms that our most closely matched pores have an inherent resoln. of ≤0.6 nm along the length of the mol.
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  17. 17
    Fologea, D.; Uplinger, J.; Thomas, B.; McNabb, D. S.; Li, J. L. Slowing DNA Translocation in a Solid-State Nanopore Nano Lett. 2005, 5, 1734– 1737 DOI: 10.1021/nl051063o
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    17
    Slowing DNA Translocation in a Solid-State Nanopore
    Fologea, Daniel; Uplinger, James; Thomas, Brian; McNabb, David S.; Li, Jiali
    Nano Letters (2005), 5 (9), 1734-1737CODEN: NALEFD; ISSN:1530-6984. (American Chemical Society)
    Reducing a DNA mol.'s translocation speed in a solid-state nanopore is a key step toward rapid single mol. identification. Here we demonstrate that DNA translocation speeds can be reduced by an order of magnitude over previous results. By controlling the electrolyte temp., salt concn., viscosity, and the elec. bias voltage across the nanopore, we obtain a 3 base/μs translocation speed for 3 kbp double-stranded DNA in a 4-8 nm diam. silicon nitride pore. Our results also indicate that the ionic cond. inside such a nanopore is smaller than it is in bulk.
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  18. 18
    Kowalczyk, S. W.; Wells, D. B.; Aksimentiev, A.; Dekker, C. Slowing Down DNA Translocation through a Nanopore in Lithium Chloride Nano Lett. 2012, 12, 1038– 1044 DOI: 10.1021/nl204273h
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    18
    Slowing down DNA Translocation through a Nanopore in Lithium Chloride
    Kowalczyk, Stefan W.; Wells, David B.; Aksimentiev, Aleksei; Dekker, Cees
    Nano Letters (2012), 12 (2), 1038-1044CODEN: NALEFD; ISSN:1530-6984. (American Chemical Society)
    The charge of a DNA mol. is a crucial parameter in many DNA detection and manipulation schemes such as gel electrophoresis and lab-on-a-chip applications. Here, we study the partial redn. of the DNA charge due to counterion binding by means of nanopore translocation expts. and all-atom mol. dynamics (MD) simulations. Surprisingly, we find that the translocation time of a DNA mol. through a solid-state nanopore strongly increases as the counterions decrease in size from K+ to Na+ to Li+, both for double-stranded DNA (dsDNA) and single-stranded DNA (ssDNA). MD simulations elucidate the microscopic origin of this effect: Li+ and Na+ bind DNA stronger than K+. These fundamental insights into the counterion binding to DNA also provide a practical method for achieving at least 10-fold enhanced resoln. in nanopore applications.
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  19. 19
    Wanunu, M.; Sutin, J.; McNally, B.; Chow, A.; Meller, A. DNA Translocation Governed by Interactions with Solid-State Nanopores Biophys. J. 2008, 95, 4716– 4725 DOI: 10.1529/biophysj.108.140475
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    19
    DNA translocation governed by interactions with solid-state nanopores
    Wanunu, Meni; Sutin, Jason; McNally, Ben; Chow, Andrew; Meller, Amit
    Biophysical Journal (2008), 95 (10), 4716-4725CODEN: BIOJAU; ISSN:0006-3495. (Biophysical Society)
    We investigate the voltage-driven translocation dynamics of individual DNA mols. through solid-state nanopores in the diam. range 2.7-5 nm. Our studies reveal an order of magnitude increase in the translocation times when the pore diam. is decreased from 5 to 2.7 nm, and steep temp. dependence, nearly threefold larger than would be expected if the dynamics were governed by viscous drag. As previously predicted for an interaction-dominated translocation process, we observe exponential voltage dependence on translocation times. Mean translocation times scale with DNA length by two power laws: for short DNA mols., in the range 150-3500 bp, we find an exponent of 1.40, whereas for longer mols., an exponent of 2.28 dominates. Surprisingly, we find a transition in the fraction of ion current blocked by DNA, from a length-independent regime for short DNA mols. to a regime where the longer the DNA, the more current is blocked. Temp. dependence studies reveal that for increasing DNA lengths, addnl. interactions are responsible for the slower DNA dynamics. Our results can be rationalized by considering DNA/pore interactions as the predominant factor detg. DNA translocation dynamics in small pores. These interactions markedly slow down the translocation rate, enabling higher temporal resoln. than obsd. with larger pores. These findings shed light on the transport properties of DNA in small pores, relevant for future nanopore applications, such as DNA sequencing and genotyping.
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  20. 20
    Farimani, A. B.; Heiranian, M.; Aluru, N. R. Electromechanical Signatures for DNA Sequencing through a Mechanosensitive Nanopore J. Phys. Chem. Lett. 2015, 6, 650– 657 DOI: 10.1021/jz5025417
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    20
    Electromechanical signatures for DNA sequencing through a mechanosensitive nanopore
    Farimani, A. Barati; Heiranian, M.; Aluru, N. R.
    Journal of Physical Chemistry Letters (2015), 6 (4), 650-657CODEN: JPCLCD; ISSN:1948-7185. (American Chemical Society)
    Biol. nanopores have been extensively used for DNA base detection since these pores are widely available and tunable through mutations. Distinguishing bases of nucleic acids by passing them through nanopores has so far primarily relied on elec. signals-specifically, ionic currents through the nanopores. However, the low signal-to-noise ratio makes detection of ionic currents difficult. In this study, we show that the initially closed mechanosensitive channel of large conductance (MscL) protein pore opens for single-stranded DNA (ssDNA) translocation under an applied elec. field. As each nucleotide translocates through the pore, a unique mech. signal is obsd.-specifically, the tension in the membrane contg. the MscL pore is different for each nucleotide. In addn. to the membrane tension, we found that the ionic current is also different for the four nucleotide types. The initially closed MscL adapts its opening for nucleotide translocation due to the flexibility of the pore. This unique operation of MscL provides single nucleotide resoln. in both elec. and mech. signals. Finally, we also show that the speed of DNA translocation is roughly 1 order of magnitude slower in MscL compared to Mycobacterium smegmatis porin A (MspA), suggesting MscL to be an attractive protein pore for DNA sequencing.
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  21. 21
    Luan, B. Q.; Stolovitzky, G.; Martyna, G. Slowing and Controlling the Translocation of DNA in a Solid-State Nanopore Nanoscale 2012, 4, 1068– 1077 DOI: 10.1039/C1NR11201E
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    21
    Slowing and controlling the translocation of DNA in a solid-state nanopore
    Luan, Binquan; Stolovitzky, Gustavo; Martyna, Glenn
    Nanoscale (2012), 4 (4), 1068-1077CODEN: NANOHL; ISSN:2040-3372. (Royal Society of Chemistry)
    A review. DNA sequencing methods based on nanopores could potentially represent a low-cost and high-throughput pathway to practical genomics, by replacing current sequencing methods based on synthesis that are limited in speed and cost. The success of nanopore sequencing techniques requires the soln. to two fundamental problems: (1) sensing each nucleotide of a DNA strand, in sequence, as it passes through a nanopore; (2) delivering each nucleotide in a DNA strand, in turn, to a sensing site within the nanopore in a controlled manner. It has been demonstrated that a DNA nucleotide can be sensed using elec. signals, such as ionic current changes caused by nucleotide blockage at a constriction region in a protein pore or a tunneling current through the nucleotide-bridged gap of two nanoelectrodes built near a solid-state nanopore. However, it is not yet clear how each nucleotide in a DNA strand can be delivered in turn to a sensing site and held there for a sufficient time to ensure high fidelity sensing. This latter problem has been addressed by modifying macroscopic properties, such as a solvent viscosity, ion concn. or temp. Also, the DNA transistor, a solid state nanopore dressed with a series of metal-dielec. layers has been proposed as a soln. Mol. dynamics simulations provide the means to study and to understand DNA transport in nanopores microscopically. In this article, we review computational studies on how to slow down and control the DNA translocation through a solid-state nanopore.
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  22. 22
    Butler, T. Z.; Pavlenok, M.; Derrington, I. M.; Niederweis, M.; Gundlach, J. H. Single-Molecule DNA Detection with an Engineered Mspa Protein Nanopore Proc. Natl. Acad. Sci. U. S. A. 2008, 105, 20647– 20652 DOI: 10.1073/pnas.0807514106
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    22
    Single-molecule DNA detection with an engineered MspA protein nanopore
    Butler, Tom Z.; Pavlenok, Mikhail; Derrington, Ian M.; Niederweis, Michael; Gundlach, Jens H.
    Proceedings of the National Academy of Sciences of the United States of America (2008), 105 (52), 20647-20652CODEN: PNASA6; ISSN:0027-8424. (National Academy of Sciences)
    Nanopores hold great promise as single-mol. anal. devices and biophys. model systems because the ionic current blockades they produce contain information about the identity, concn., structure, and dynamics of target mols. The porin MspA of Mycobacterium smegmatis has remarkable stability against environmental stresses and can be rationally modified based on its crystal structure. Further, MspA has a short and narrow channel constriction that is promising for DNA sequencing because it may enable improved characterization of short segments of a ssDNA mol. that is threaded through the pore. By eliminating the neg. charge in the channel constriction, we designed and constructed an MspA mutant capable of electronically detecting and characterizing single mols. of ssDNA as they are electrophoretically driven through the pore. A second mutant with addnl. exchanges of neg.-charged residues for pos.-charged residues in the vestibule region exhibited a factor of ≈ 20 higher interaction rates, required only half as much voltage to observe interaction, and allowed ssDNA to reside in the vestibule ≈ 100 times longer than the first mutant. Our results introduce MspA as a nanopore for nucleic acid anal. and highlight its potential as an engineerable platform for single-mol. detection and characterization applications.
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  23. 23
    Sint, K.; Wang, B.; Kral, P. Selective Ion Passage through Functionalized Graphene Nanopores J. Am. Chem. Soc. 2008, 130, 16448– 16449 DOI: 10.1021/ja804409f
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    23
    Selective Ion Passage through Functionalized Graphene Nanopores
    Sint, Kyaw; Wang, Boyang; Kral, Petr
    Journal of the American Chemical Society (2008), 130 (49), 16448-16449CODEN: JACSAT; ISSN:0002-7863. (American Chemical Society)
    We design functionalized nanopores in graphene monolayers and show by mol. dynamics simulations that they provide highly selective passage of hydrated ions. Only ions that can be partly stripped of their hydration shells can pass through these ultrasmall pores with diams. of ∼5 Å. For example, a fluorine-nitrogen-terminated pore allows the passage of Li+, Na+, and K+ cations with the ratio 9:14:33, but it blocks the passage of anions. The hydrogen-terminated pore allows the passage of F-, Cl-, and Br- anions with the ratio 0:17:33, but it blocks the passage of cations. These nanopores could have potential applications in mol. sepn., desalination, and energy storage systems.
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  24. 24
    Wei, R. S.; Martin, T. G.; Rant, U.; Dietz, H. DNA Origami Gatekeepers for Solid-State Nanopores Angew. Chem., Int. Ed. 2012, 51, 4864– 4867 DOI: 10.1002/anie.201200688
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    24
    DNA origami gatekeepers for solid-state nanopores
    Wei, Ruoshan; Martin, Thomas G.; Rant, Ulrich; Dietz, Hendrik
    Angewandte Chemie, International Edition (2012), 51 (20), 4864-4867, S4864/1-S4864/31CODEN: ACIEF5; ISSN:1433-7851. (Wiley-VCH Verlag GmbH & Co. KGaA)
    The authors have presented DNA nanoplates that function with solid-state nanopores, which can be fabricated through std. electron beam lithog. The nanoplates are permeable to small ions, but the passage of macromols. can be controlled by including custom apertures. The chem. addressability of the DNA nanoplates enables bait-prey single-mol. sensing expts., as highlighted here by the sequence-specific detection of DNA snippets and genomic phage DNA. Applications in biomol. interaction screens and for detecting DNA sequences by hybridization are readily conceivable. High-resoln. sensing applications, such as elec. DNA sequencing will require reducing both the leakage current and current fluctuations.
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  25. 25
    Yusko, E. C.; Johnson, J. M.; Majd, S.; Prangkio, P.; Rollings, R. C.; Li, J. L.; Yang, J.; Mayer, M. Controlling Protein Translocation through Nanopores with Bio-Inspired Fluid Walls Nat. Nanotechnol. 2011, 6, 253– 260 DOI: 10.1038/nnano.2011.12
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    25
    Controlling protein translocation through nanopores with bio-inspired fluid walls
    Yusko, Erik C.; Johnson, Jay M.; Majd, Sheereen; Prangkio, Panchika; Rollings, Ryan C.; Li, Jiali; Yang, Jerry; Mayer, Michael
    Nature Nanotechnology (2011), 6 (4), 253-260CODEN: NNAABX; ISSN:1748-3387. (Nature Publishing Group)
    Synthetic nanopores have been used to study individual biomols. in high throughput, but their performance as sensors does not match that of biol. ion channels. Challenges include control of nanopore diams. and surface chem., modification of the translocation times of single-mol. analytes through nanopores, and prevention of nonspecific interactions with pore walls. Here, inspired by the olfactory sensilla of insect antennae, the authors show that coating nanopores with a fluid lipid bilayer tailors their surface chem. and allows fine-tuning and dynamic variation of pore diams. in subnanometer increments. Incorporation of mobile ligands in the lipid bilayer conferred specificity and slowed the translocation of targeted proteins sufficiently to time-resolve translocation events of individual proteins. Lipid coatings also prevented pores from clogging, eliminated nonspecific binding and enabled the translocation of amyloid-beta (Aβ) oligomers and fibrils. Through combined anal. of their translocation time, vol., charge, shape and ligand affinity, different proteins were identified.
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    Martin, C. R.; Siwy, Z. S. Learning Nature’s Way: Biosensing with Synthetic Nanopores Science 2007, 317, 331– 332 DOI: 10.1126/science.1146126
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    26
    Learning Nature's Way: Biosensing with Synthetic Nanopores
    Martin, Charles R.; Siwy, Zuzanna S.
    Science (Washington, DC, United States) (2007), 317 (5836), 331-332CODEN: SCIEAS; ISSN:0036-8075. (American Association for the Advancement of Science)
    A review. Synthetic sensors use mol. recognition events in nanometer-scale pores for selective detection of proteins, nucleotides, and drugs.
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  27. 27
    Iqbal, S. M.; Akin, D.; Bashir, R. Solid-State Nanopore Channels with DNA Selectivity Nat. Nanotechnol. 2007, 2, 243– 248 DOI: 10.1038/nnano.2007.78
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    27
    Solid-state nanopore channels with DNA selectivity
    Iqbal, Samir M.; Akin, Demir; Bashir, Rashid
    Nature Nanotechnology (2007), 2 (4), 243-248CODEN: NNAABX; ISSN:1748-3387. (Nature Publishing Group)
    Solid-state nanopores have emerged as possible candidates for next-generation DNA sequencing devices. In such a device, the DNA sequence would be detd. by measuring how the forces on the DNA mols., and also the ion currents through the nanopore, change as the mols. pass through the nanopore. Unlike their biol. counterparts, solid-state nanopores have the advantage that they can withstand a wide range of analyte solns. and environments. Here we report solid-state nanopore channels that are selective towards single-stranded DNA (ssDNA). Nanopores functionalized with a 'probe' of hair-pin loop DNA can, under an applied elec. field, selectively transport short lengths of 'target' ssDNA that are complementary to the probe. Even a single base mismatch between the probe and the target results in longer translocation pulses and a significantly reduced no. of translocation events. Our single-mol. measurements allow us to measure sep. the mol. flux and the pulse duration, providing a tool to gain fundamental insight into the channel-mol. interactions. The results can be explained in the conceptual framework of diffusive mol. transport with particle-channel interactions.
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    Rothemund, P. W. K. Folding DNA to Create Nanoscale Shapes and Patterns Nature 2006, 440, 297– 302 DOI: 10.1038/nature04586
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    Folding DNA to create nanoscale shapes and patterns
    Rothemund, Paul W. K.
    Nature (London, United Kingdom) (2006), 440 (7082), 297-302CODEN: NATUAS; ISSN:0028-0836. (Nature Publishing Group)
    'Bottom-up fabrication', which exploits the intrinsic properties of atoms and mols. to direct their self-organization, is widely used to make relatively simple nanostructures. A key goal for this approach is to create nanostructures of high complexity, matching that routinely achieved by 'top-down' methods. The self-assembly of DNA mols. provides an attractive route towards this goal. Here the author describe a simple method for folding long, single-stranded DNA mols. into arbitrary two-dimensional shapes. The design for a desired shape is made by raster-filling the shape with a 7-kilobase single-stranded scaffold and by choosing over 200 short oligonucleotide 'staple strands' to hold the scaffold in place. Once synthesized and mixed, the staple and scaffold strands self-assemble in a single step. The resulting DNA structures are roughly 100 nm in diam. and approx. desired shapes such as squares, disks and five-pointed stars with a spatial resoln. of 6 nm. Because each oligonucleotide can serve as a 6-nm pixel, the structures can be programmed to bear complex patterns such as words and images on their surfaces. Finally, individual DNA structures can be programmed to form larger assemblies, including extended periodic lattices and a hexamer of triangles (which constitutes a 30-megadalton mol. complex).
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  29. 29
    Andersen, E. S.; Dong, M.; Nielsen, M. M.; Jahn, K.; Subramani, R.; Mamdouh, W.; Golas, M. M.; Sander, B.; Stark, H.; Oliveira, C. L. P.; Pedersen, J. S.; Birkedal, V.; Besenbacher, F.; Gothelf, K. V.; Kjems, J. Self-Assembly of a Nanoscale DNA Box with a Controllable Lid Nature 2009, 459, 73– 75 DOI: 10.1038/nature07971
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    Self-assembly of a nanoscale DNA box with a controllable lid
    Andersen, Ebbe S.; Dong, Mingdong; Nielsen, Morten M.; Jahn, Kasper; Subramani, Ramesh; Mamdouh, Wael; Golas, Monika M.; Sander, Bjoern; Stark, Holger; Oliveira, Cristiano L. P.; Pedersen, Jan Skov; Birkedal, Victoria; Besenbacher, Flemming; Gothelf, Kurt V.; Kjems, Jorgen
    Nature (London, United Kingdom) (2009), 459 (7243), 73-76CODEN: NATUAS; ISSN:0028-0836. (Nature Publishing Group)
    The unique structural motifs and self-recognition properties of DNA can be exploited to generate self-assembling DNA nanostructures of specific shapes using a 'bottom-up' approach. Several assembly strategies have been developed for building complex three-dimensional (3D) DNA nanostructures. Recently, the DNA 'origami' method was used to build two-dimensional addressable DNA structures of arbitrary shape that can be used as platforms to arrange nanomaterials with high precision and specificity. A long-term goal of this field has been to construct fully addressable 3D DNA nanostructures. Here we extend the DNA origami method into three dimensions by creating an addressable DNA box 42 × 36 × 36 nm3 in size that can be opened in the presence of externally supplied DNA 'keys'. We thoroughly characterize the structure of this DNA box using cryogenic transmission electron microscopy, small-angle X-ray scattering and at. force microscopy, and use fluorescence resonance energy transfer to optically monitor the opening of the lid. Controlled access to the interior compartment of this DNA nanocontainer could yield several interesting applications, for example as a logic sensor for multiple-sequence signals or for the controlled release of nanocargos.
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    Sobczak, J. P. J.; Martin, T. G.; Gerling, T.; Dietz, H. Rapid Folding of DNA into Nanoscale Shapes at Constant Temperature Science 2012, 338, 1458– 1461 DOI: 10.1126/science.1229919
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    30
    Rapid Folding of DNA into Nanoscale Shapes at Constant Temperature
    Sobczak, Jean-Philippe J.; Martin, Thomas G.; Gerling, Thomas; Dietz, Hendrik
    Science (Washington, DC, United States) (2012), 338 (6113), 1458-1461CODEN: SCIEAS; ISSN:0036-8075. (American Association for the Advancement of Science)
    At const. temp., hundreds of DNA strands can cooperatively fold a long template DNA strand within minutes into complex nanoscale objects. Folding occurred out of equil. along nucleation-driven pathways at temps. that could be influenced by the choice of sequences, strand lengths, and chain topol. Unfolding occurred in apparent equil. at higher temps. than those for folding. Folding at optimized const. temps. enabled the rapid prodn. of three-dimensional DNA objects with yields that approached 100%. The results point to similarities with protein folding in spite of chem. and structural differences. The possibility for rapid and high-yield assembly will enable DNA nanotechnol. for practical applications.
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  31. 31
    Falconi, M.; Oteri, F.; Chillemi, G.; Andersen, F. F.; Tordrup, D.; Oliveira, C. L. P.; Pedersen, J. S.; Knudsen, B. R.; Desideri, A. Deciphering the Structural Properties That Confer Stability to a DNA Nanocage ACS Nano 2009, 3, 1813– 1822 DOI: 10.1021/nn900468y
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    Zadegan, R. M.; Jepsen, M. D. E.; Thomsen, K. E.; Okholm, A. H.; Schaffert, D. H.; Andersen, E. S.; Birkedal, V.; Kjems, J. Construction of a 4 Zeptoliters Switchable 3d DNA Box Origami ACS Nano 2012, 6, 10050– 10053 DOI: 10.1021/nn303767b
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    Construction of a 4 Zeptoliters Switchable 3D DNA Box Origami
    Zadegan, Reza M.; Jepsen, Mette D. E.; Thomsen, Karen E.; Okholm, Anders H.; Schaffert, David H.; Andersen, Ebbe S.; Birkedal, Victoria; Kjems, Joergen
    ACS Nano (2012), 6 (11), 10050-10053CODEN: ANCAC3; ISSN:1936-0851. (American Chemical Society)
    The DNA origami technique is a recently developed self-assembly method that allows construction of 3D objects at the nanoscale for various applications. In the current study we report the prodn. of a 18 × 18 × 24 nm3 hollow DNA box origami structure with a switchable lid. The structure was efficiently produced and characterized by at. force microscopy, transmission electron microscopy, and Foerster resonance energy transfer spectroscopy. The DNA box has a unique reclosing mechanism, which enables it to repeatedly open and close in response to a unique set of DNA keys. This DNA device can potentially be used for a broad range of applications such as controlling the function of single mols., controlled drug delivery, and mol. computing.
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    Langecker, M.; Arnaut, V.; Martin, T. G.; List, J.; Renner, S.; Mayer, M.; Dietz, H.; Simmel, F. C. Synthetic Lipid Membrane Channels Formed by Designed DNA Nanostructures Science 2012, 338, 932– 936 DOI: 10.1126/science.1225624
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    Synthetic Lipid Membrane Channels Formed by Designed DNA Nanostructures
    Langecker, Martin; Arnaut, Vera; Martin, Thomas G.; List, Jonathan; Renner, Stephan; Mayer, Michael; Dietz, Hendrik; Simmel, Friedrich C.
    Science (Washington, DC, United States) (2012), 338 (6109), 932-936CODEN: SCIEAS; ISSN:0036-8075. (American Association for the Advancement of Science)
    We created nanometer-scale transmembrane channels in lipid bilayers by means of self-assembled DNA-based nanostructures. Scaffolded DNA origami was used to create a stem that penetrated and spanned a lipid membrane, as well as a barrel-shaped cap that adhered to the membrane, in part via 26 cholesterol moieties. In single-channel electrophysiol. measurements, we found similarities to the response of natural ion channels, such as conductances on the order of 1 nanosiemens and channel gating. More pronounced gating was seen for mutations in which a single DNA strand of the stem protruded into the channel. Single-mol. translocation expts. show that the synthetic channels can be used to discriminate single DNA mols.
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    Seifert, A.; Gopfrich, K.; Burns, J. R.; Fertig, N.; Keyser, U. F.; Howorka, S. Bilayer-Spanning DNA Nanopores with Voltage-Switching between Open and Closed State ACS Nano 2015, 9, 1117– 1126 DOI: 10.1021/nn5039433
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    34
    Bilayer-Spanning DNA Nanopores with Voltage-Switching between Open and Closed State
    Seifert, Astrid; Goepfrich, Kerstin; Burns, Jonathan R.; Fertig, Niels; Keyser, Ulrich F.; Howorka, Stefan
    ACS Nano (2015), 9 (2), 1117-1126CODEN: ANCAC3; ISSN:1936-0851. (American Chemical Society)
    Membrane-spanning nanopores from folded DNA are a recent example of biomimetic man-made nanostructures that can open up applications in biosensing, drug delivery, and nanofluidics. The authors generate a DNA nanopore based on the archetypal six-helix-bundle architecture and systematically characterize it via single-channel current recordings to address several fundamental scientific questions in this emerging field. The DNA pores exhibit two voltage-dependent conductance states. Low transmembrane voltages favor a stable high-conductance level, which corresponds to an unobstructed DNA pore. The expected inner width of the open channel is confirmed by measuring the conductance change as a function of poly(ethylene glycol) (PEG) size, whereby smaller PEGs are assumed to enter the pore. PEG sizing also clarifies that the main ion-conducting path runs through the membrane-spanning channel lumen as opposed to any proposed gap between the outer pore wall and the lipid bilayer. At higher voltages, the channel shows a main low-conductance state probably caused by elec.-field-induced changes of the DNA pore in its conformation or orientation. This voltage-dependent switching between the open and closed states is obsd. with planar lipid bilayers as well as bilayers mounted on glass nanopipettes. These findings settle a discrepancy between two previously published conductances. By systematically exploring a large space of parameters and answering key questions, the authors' report supports the development of DNA nanopores for nanobiotechnol.
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  35. 35
    Hernandez-Ainsa, S.; Bell, N. A. W.; Thacker, V. V.; Gopfrich, K.; Misiunas, K.; Fuentes-Perez, M. E.; Moreno-Herrero, F.; Keyser, U. F. DNA Origami Nanopores for Controlling DNA Translocation ACS Nano 2013, 7, 6024– 6030 DOI: 10.1021/nn401759r
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    DNA Origami Nanopores for Controlling DNA Translocation
    Hernandez-Ainsa, Silvia; Bell, Nicholas A. W.; Thacker, Vivek V.; Gopfrich, Kerstin; Misiunas, Karolis; Fuentes-Perez, Maria Eugenia; Moreno-Herrero, Fernando; Keyser, Ulrich F.
    ACS Nano (2013), 7 (7), 6024-6030CODEN: ANCAC3; ISSN:1936-0851. (American Chemical Society)
    The authors combine DNA origami structures with glass nanocapillaries to reversibly form hybrid DNA origami nanopores. Trapping of the DNA origami onto the nanocapillary is proven by imaging fluorescently labeled DNA origami structures and simultaneous ionic current measurements of the trapping events. The authors then show two applications highlighting the versatility of these DNA origami nanopores. First, by tuning the pore size the authors can control the folding of dsDNA mols. ("phys. control"). Second, the specific introduction of binding sites in the DNA origami nanopore allows selective detection of ssDNA as a function of the DNA sequence ("chem. control").
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  36. 36
    Wei, R. S.; Gatterdam, V.; Wieneke, R.; Tampe, R.; Rant, U. Stochastic Sensing of Proteins with Receptor-Modified Solid-State Nanopores Nat. Nanotechnol. 2012, 7, 257– 263 DOI: 10.1038/nnano.2012.24
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    36
    Stochastic sensing of proteins with receptor-modified solid-state nanopores
    Wei, Ruoshan; Gatterdam, Volker; Wieneke, Ralph; Tampe, Robert; Rant, Ulrich
    Nature Nanotechnology (2012), 7 (4), 257-263CODEN: NNAABX; ISSN:1748-3387. (Nature Publishing Group)
    Solid-state nanopores are capable of the label-free anal. of single mols. It is possible to add biochem. selectivity by anchoring a mol. receptor inside the nanopore, but it is difficult to maintain single-mol. sensitivity in these modified nanopores. Here, we show that metalized silicon nitride nanopores chem. modified with nitrilotriacetic acid (NTA) receptors can be used for the stochastic sensing of proteins. The reversible binding and unbinding of the proteins to the receptors is obsd. in real time, and the interaction parameters are statistically analyzed from single-mol. binding events. To demonstrate the versatile nature of this approach, we detect His-tagged proteins and discriminate between the subclasses of rodent IgG antibodies.
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    Yoo, J.; Aksimentiev, A. In Situ Structure and Dynamics of DNA Origami Determined through Molecular Dynamics Simulations Proc. Natl. Acad. Sci. U. S. A. 2013, 110, 20099– 20104 DOI: 10.1073/pnas.1316521110
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    In situ structure and dynamics of DNA origami determined through molecular dynamics simulations
    Yoo, Jejoong; Aksimentiev, Aleksei
    Proceedings of the National Academy of Sciences of the United States of America (2013), 110 (50), 20099-20104,S20099/1-S20099/24CODEN: PNASA6; ISSN:0027-8424. (National Academy of Sciences)
    The DNA origami method permits folding of long single-stranded DNA into complex 3-dimensional structures with subnanometer precision. Transmission electron microscopy (TEM), at. force microscopy ATM), and recently cryo-electron microscopic tomog. have been used to characterize the properties of such DNA origami objects; however, their microscopic structures and dynamics have remained unknown. Here, the authors report the results of all-atom mol. dynamics (MD) simulations that characterized the structural and mech. properties of DNA origami objects in unprecedented microscopic detail. When simulated in an aq. environment, the structures of DNA origami objects departed from their idealized targets as a result of steric, electrostatic, and solvent-mediated forces. Whereas the global structural features of such relaxed conformations conformed to the target designs, local deformations were abundant and varied in magnitude along the structures. In contrast to their free-soln. conformation, the Holliday junctions in the DNA origami structures adopted a left-handed antiparallel conformation. The authors found that the DNA origami structures underwent considerable temporal fluctuations on both local and global scales. Anal. of such structural fluctuations revealed the local mech. properties of the DNA origami objects. The lattice type of the structures considerably affected global mech. properties such as bending rigidity. This study demonstrated the potential of all-atom MD simulations to play a considerable role in future development of the DNA origami field by providing accurate, quant. assessment of local and global structural and mech. properties of DNA origami objects.
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  38. 38
    Li, C. Y.; Hemmig, E. A.; Kong, J. L.; Yoo, J.; Hernandez-Ainsa, S.; Keyser, U. F.; Aksimentiev, A. Ionic Conductivity, Structural Deformation, and Programmable Anisotropy of DNA Origami in Electric Field ACS Nano 2015, 9, 1420– 1433 DOI: 10.1021/nn505825z
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    38
    Ionic Conductivity, Structural Deformation, and Programmable Anisotropy of DNA Origami in Electric Field
    Li, Chen-Yu; Hemmig, Elisa A.; Kong, Jinglin; Yoo, Jejoong; Hernandez-Ainsa, Silvia; Keyser, Ulrich F.; Aksimentiev, Aleksei
    ACS Nano (2015), 9 (2), 1420-1433CODEN: ANCAC3; ISSN:1936-0851. (American Chemical Society)
    The DNA origami technique can enable functionalization of inorg. structures for single-mol. elec. current recordings. Several layers of DNA mols., a DNA origami plate, placed on top of a solid-state nanopore is permeable to ions. Here, the authors report a comprehensive characterization of the ionic cond. of DNA origami plates by all-atom mol. dynamics (MD) simulations and nanocapillary elec. current recordings. Using the MD method, the authors characterize the ionic cond. of several origami constructs, revealing the local distribution of ions, the distribution of the electrostatic potential and contribution of different mol. species to the current. The simulations det. the dependence of the ionic cond. on the applied voltage, the no. of DNA layers, the nucleotide content and the lattice type of the plates. Increasing the concn. of Mg2+ ions makes the origami plates more compact, reducing their cond. The conductance of a DNA origami plate on top of a solid-state nanopore is detd. by the two competing effects: bending of the DNA origami plate that reduces the current and sepn. of the DNA origami layers that increases the current. The latter is produced by the electroosmotic flow and is reversible at the time scale of a hundred nanoseconds. The conductance of a DNA origami object depends on its orientation, reaching max. when the elec. field aligns with the direction of the DNA helixes. The authors' work demonstrates feasibility of programming the elec. properties of a self-assembled nanoscale object using DNA.
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  39. 39
    Gao, B.; Sarveswaran, K.; Bernstein, G. H.; Lieberman, M. Guided Deposition of Individual DNA Nanostructures on Silicon Substrates Langmuir 2010, 26, 12680– 12683 DOI: 10.1021/la101343k
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    39
    Guided Deposition of Individual DNA Nanostructures on Silicon Substrates
    Gao, Bo; Sarveswaran, Koshala; Bernstein, Gary H.; Lieberman, Marya
    Langmuir (2010), 26 (15), 12680-12683CODEN: LANGD5; ISSN:0743-7463. (American Chemical Society)
    The authors demonstrate immobilization of DNA nanostructures (37 nm × 8 nm) on silicon by a combination of top-down fabrication and bottom-up self-assembly. Anchor lines and pads were defined using electron beam lithog. and a cationic mol. monolayer. Individual DNA nanostructures bind in 85% yield onto the anchor pads and can be washed and imaged in air. The strength of the binding interaction between a DNA nanostructure and its anchor pad is at least -43 kJ/mol.
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  40. 40
    Teshome, B.; Facsko, S.; Keller, A. Topography-Controlled Alignment of DNA Origami Nanotubes on Nanopatterned Surfaces Nanoscale 2014, 6, 1790– 1796 DOI: 10.1039/C3NR04627C
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  41. 41
    Pearson, A. C.; Pound, E.; Woolley, A. T.; Linford, M. R.; Harb, J. N.; Davis, R. C. Chemical Alignment of DNA Origami to Block Copolymer Patterned Arrays of 5 Nm Gold Nanoparticles Nano Lett. 2011, 11, 1981– 1987 DOI: 10.1021/nl200306w
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  42. 42
    Gu, H. Z.; Chao, J.; Xiao, S. J.; Seeman, N. C. Dynamic Patterning Programmed by DNA Tiles Captured on a DNA Origami Substrate Nat. Nanotechnol. 2009, 4, 245– 248 DOI: 10.1038/nnano.2009.5
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    42
    Dynamic patterning programmed by DNA tiles captured on a DNA origami substrate
    Gu, Hongzhou; Chao, Jie; Xiao, Shou-Jun; Seeman, Nadrian C.
    Nature Nanotechnology (2009), 4 (4), 245-248CODEN: NNAABX; ISSN:1748-3387. (Nature Publishing Group)
    The aim of nanotechnol. is to put specific at. and mol. species where we want them, when we want them there. Achieving such dynamic and functional control could lead to programmable chem. synthesis and nanoscale systems that are responsive to their environments. Structural DNA nanotechnol. offers a powerful route to this goal by combining stable branched DNA motifs with cohesive ends to produce programmed nanomech. devices and fixed or modified patterned lattices. Here, we demonstrate a dynamic form of patterning in which a pattern component is captured between two independently programmed DNA devices. A simple and robust error-correction protocol has been developed that yields programmed targets in all cases. This capture system can lead to dynamic control either on patterns or on programmed elements; this capability enables computation or a change of structural state as a function of information in the surroundings of the system.
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  43. 43
    Kershner, R. J.; Bozano, L. D.; Micheel, C. M.; Hung, A. M.; Fornof, A. R.; Cha, J. N.; Rettner, C. T.; Bersani, M.; Frommer, J.; Rothemund, P. W. K.; Wallraff, G. M. Placement and Orientation of Individual DNA Shapes on Lithographically Patterned Surfaces Nat. Nanotechnol. 2009, 4, 557– 561 DOI: 10.1038/nnano.2009.220
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    43
    Placement and orientation of individual DNA shapes on lithographically patterned surfaces
    Kershner, Ryan J.; Bozano, Luisa D.; Micheel, Christine M.; Hung, Albert M.; Fornof, Ann R.; Cha, Jennifer N.; Rettner, Charles T.; Bersani, Marco; Frommer, Jane; Rothemund, Paul W. K.; Wallraff, Gregory M.
    Nature Nanotechnology (2009), 4 (9), 557-561CODEN: NNAABX; ISSN:1748-3387. (Nature Publishing Group)
    Artificial DNA nanostructures show promise for the organization of functional materials to create nanoelectronic or nano-optical devices. DNA origami, in which a long single strand of DNA is folded into a shape using shorter staple strands', can display 6-nm-resoln. patterns of binding sites, in principle allowing complex arrangements of carbon nanotubes, silicon nanowires, or quantum dots. However, DNA origami are synthesized in soln. and uncontrolled deposition results in random arrangements; this makes it difficult to measure the properties of attached nanodevices or to integrate them with conventionally fabricated microcircuitry. Here the authors describe the use of electron-beam lithog. and dry oxidative etching to create DNA origami-shaped binding sites on technol. useful materials, such as SiO2 and diamond-like carbon. In buffer with ∼100 mM MgCl2, DNA origami bind with high selectivity and good orientation: 70-95% of sites have individual origami aligned with an angular dispersion ( ± 1 s d.) as low as ±10° (on diamond-like carbon) or ±20° (on SiO2).
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  44. 44
    Yun, J. M.; Kim, K. N.; Kim, J. Y.; Shin, D. O.; Lee, W. J.; Lee, S. H.; Lieberman, M.; Kim, S. O. DNA Origami Nanopatterning on Chemically Modified Graphene Angew. Chem., Int. Ed. 2012, 51, 912– 915 DOI: 10.1002/anie.201106198
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  45. 45
    Zhang, X. N.; Rahman, M.; Neff, D.; Norton, M. L. DNA Origami Deposition on Native and Passivated Molybdenum Disulfide Substrates Beilstein J. Nanotechnol. 2014, 5, 501– 506 DOI: 10.3762/bjnano.5.58
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    DNA origami deposition on native and passivated molybdenum disulfide substrates
    Zhang, Xiaoning; Rahman, Masudur; Neff, David; Norton, Michael L.
    Beilstein Journal of Nanotechnology (2014), 5 (), 501-506, 6 pp.CODEN: BJNEAH; ISSN:2190-4286. (Beilstein-Institut zur Foerderung der Chemischen Wissenschaften)
    Maintaining the structural fidelity of DNA origami structures on substrates is a prerequisite for the successful fabrication of hybrid DNA origami/semiconductor-based biomedical sensor devices. Molybdenum disulfide (MoS2) is an ideal substrate for such future sensors due to its exceptional elec., mech. and structural properties. In this work, we performed the first investigations into the interaction of DNA origami with the MoS2 surface. In contrast to the structure-preserving interaction of DNA origami with mica, another atomically flat surface, it was obsd. that DNA origami structures rapidly lose their structural integrity upon interaction with MoS2. In a further series of studies, pyrene and 1-pyrenemethylamine, were evaluated as surface modifications which might mitigate this effect. While both species were found to form adsorption layers on MoS2 via physisorption, 1-pyrenemethyamine serves as a better protective agent and preserves the structures for significantly longer times. These findings will be benefcial for the fabrication of future DNA origami/MoS2 hybrid electronic structures.
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  46. 46
    Bell, N. A. W.; Keyser, U. F. Nanopores Formed by DNA Origami: A Review FEBS Lett. 2014, 588, 3564– 3570 DOI: 10.1016/j.febslet.2014.06.013
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    46
    Nanopores formed by DNA origami: A review
    Bell, Nicholas A. W.; Keyser, Ulrich F.
    FEBS Letters (2014), 588 (19), 3564-3570CODEN: FEBLAL; ISSN:0014-5793. (Elsevier B.V.)
    A review. Nanopores have emerged over the past two decades to become an important technique in single mol. exptl. physics and biomol. sensing. Recently DNA nanotechnol., in particular DNA origami, has been used for the formation of nanopores in insulating materials. DNA origami is a very attractive technique for the formation of nanopores since it enables the construction of 3D shapes with precise control over geometry and surface functionality. DNA origami has been applied to nanopore research by forming hybrid architectures with solid state nanopores and by direct insertion into lipid bilayers. This review discusses recent exptl. work in this area and provides an outlook for future avenues and challenges.
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  47. 47
    Kale, L.; Skeel, R.; Bhandarkar, M.; Brunner, R.; Gursoy, A.; Krawetz, N.; Phillips, J.; Shinozaki, A.; Varadarajan, K.; Schulten, K. Namd2: Greater Scalability for Parallel Molecular Dynamics J. Comput. Phys. 1999, 151, 283– 312 DOI: 10.1006/jcph.1999.6201
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    NAMD2: Greater Scalability for Parallel Molecular Dynamics
    Kale, Laxmikant; Skeel, Robert; Bhandarkar, Milind; Brunner, Robert; Gursoy, Attila; Krawetz, Neal; Phillips, James; Shinozaki, Aritomo; Varadarajan, Krishnan; Schulten, Klaus
    Journal of Computational Physics (1999), 151 (1), 283-312CODEN: JCTPAH; ISSN:0021-9991. (Academic Press)
    Mol. dynamics programs simulate the behavior of biomol. systems, leading to understanding of their functions. However, the computational complexity of such simulations is enormous. Parallel machines provide the potential to meet this computational challenge. To harness this potential, it is necessary to develop a scalable program. It is also necessary that the program be easily modified by application-domain programmers. The NAMD2 program presented in this paper seeks to provide these desirable features. It uses spatial decompn. combined with force decompn. to enhance scalability. It uses intelligent periodic load balancing, so as to maximally utilize the available compute power. It is modularly organized, and implemented using Charm++, a parallel C++ dialect, so as to enhance its modifiability. It uses a combination of numerical techniques and algorithms to ensure that energy drifts are minimized, ensuring accuracy in long running calcns. NAMD2 uses a portable run-time framework called Converse that also supports interoperability among multiple parallel paradigms. As a result, different components of applications can be written in the most appropriate parallel paradigms. NAMD2 runs on most parallel machines including workstation clusters and has yielded speedups in excess of 180 on 220 processors. This paper also describes the performance obtained on some benchmark applications. (c) 1999 Academic Press.
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  48. 48
    Humphrey, W.; Dalke, A.; Schulten, K. Vmd: Visual Molecular Dynamics J. Mol. Graphics 1996, 14, 33– 38 DOI: 10.1016/0263-7855(96)00018-5
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    VDM: visual molecular dynamics
    Humphrey, William; Dalke, Andrew; Schulten, Klaus
    Journal of Molecular Graphics (1996), 14 (1), 33-8, plates, 27-28CODEN: JMGRDV; ISSN:0263-7855. (Elsevier)
    VMD is a mol. graphics program designed for the display and anal. of mol. assemblies, in particular, biopolymers such as proteins and nucleic acids. VMD can simultaneously display any no. of structures using a wide variety of rendering styles and coloring methods. Mols. are displayed as one or more "representations," in which each representation embodies a particular rendering method and coloring scheme for a selected subset of atoms. The atoms displayed in each representation are chosen using an extensive atom selection syntax, which includes Boolean operators and regular expressions. VMD provides a complete graphical user interface for program control, as well as a text interface using the Tcl embeddable parser to allow for complex scripts with variable substitution, control loops, and function calls. Full session logging is supported, which produces a VMD command script for later playback. High-resoln. raster images of displayed mols. may be produced by generating input scripts for use by a no. of photorealistic image-rendering applications. VMD has also been expressly designed with the ability to animate mol. dynamics (MD) simulation trajectories, imported either from files or from a direct connection to a running MD simulation. VMD is the visualization component of MDScope, a set of tools for interactive problem solving in structural biol., which also includes the parallel MD program NAMD, and the MDCOMM software used to connect the visualization and simulation programs, VMD is written in C++, using an object-oriented design; the program, including source code and extensive documentation, is freely available via anonymous ftp and through the World Wide Web.
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  49. 49
    Douglas, S. M.; Marblestone, A. H.; Teerapittayanon, S.; Vazquez, A.; Church, G. M.; Shih, W. M. Rapid Prototyping of 3d DNA-Origami Shapes with Cadnano Nucleic Acids Res. 2009, 37, 5001– 5006 DOI: 10.1093/nar/gkp436
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    Rapid prototyping of 3D DNA-origami shapes with caDNAno
    Douglas, Shawn M.; Marblestone, Adam H.; Teerapittayanon, Surat; Vazquez, Alejandro; Church, George M.; Shih, William M.
    Nucleic Acids Research (2009), 37 (15), 5001-5006CODEN: NARHAD; ISSN:0305-1048. (Oxford University Press)
    DNA nanotechnol. exploits the programmable specificity afforded by base-pairing to produce self-assembling macromol. objects of custom shape. For building megadalton-scale DNA nanostructures, a long scaffold' strand can be employed to template the assembly of hundreds of oligonucleotide staple' strands into a planar antiparallel array of cross-linked helixes. The authors recently adapted this scaffolded DNA origami' method to producing 3-dimensional shapes formed as pleated layers of double helixes constrained to a honeycomb lattice. However, completing the required design steps can be cumbersome and time-consuming. Here the authors present caDNAno, an open-source software package with a graphical user interface that aids in the design of DNA sequences for folding 3-dimensional honeycomb-pleated shapes rectangular-block motifs were designed, assembled, and analyzed to identify a well-behaved motif that could serve as a building block for future studies. The use of caDNAno significantly reduces the effort required to design 3-dimensional DNA-origami structures. The software is available at http://cadnano.org/, along with example designs and video tutorials demonstrating their construction. The source code is released under the MIT license.
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    Ryckaert, J. P.; Ciccotti, G.; Berendsen, H. J. C. Numerical-Integration of Cartesian Equations of Motion of a System with Constraints - Molecular-Dynamics of N-Alkanes J. Comput. Phys. 1977, 23, 327– 341 DOI: 10.1016/0021-9991(77)90098-5
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    Numerical integration of the Cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes
    Ryckaert, Jean Paul; Ciccotti, Giovanni; Berendsen, Herman J. C.
    Journal of Computational Physics (1977), 23 (3), 327-41CODEN: JCTPAH; ISSN:0021-9991.
    A numerical algorithm integrating the 3N Cartesian equation of motion of a system of N points subject to holonomic constraints is applied to mol. dynamics simulation of a liq. of 64 butane mols.
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    MacKerell, A. D.; Banavali, N. K. All-Atom Empirical Force Field for Nucleic Acids: Ii. Application to Molecular Dynamics Simulations of DNA and Rna in Solution J. Comput. Chem. 2000, 21, 105– 120 DOI: 10.1002/(SICI)1096-987X(20000130)21:2<105::AID-JCC3>3.0.CO;2-P
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    All-atom empirical force field for nucleic acids: II. Application to molecular dynamics simulations of DNA and RNA in solution
    Mackerell, Alexander D.; Banavali, Nilesh K.
    Journal of Computational Chemistry (2000), 21 (2), 105-120CODEN: JCCHDD; ISSN:0192-8651. (John Wiley & Sons, Inc.)
    Mol. dynamics simulations based on empirical force fields can greatly enhance knowledge of DNA and RNA structure and dynamics in soln. Presented are results on simulations of three DNA sequences and one RNA sequence using the new all-atom CHARMM27 force field for nucleic acids presented in the accompanying manuscript (Foloppe, MacKerell, J Comput Chem, this issue). Data are reported on structural, dynamic, and hydration properties including dihedral angle, sugar puckering, and helicoidal parameter probability distributions. Also presented are calcns. of a DNA hexamer in 0 and 75% ethanol starting from both the canonical A and B forms. Anal. of RMS differences with respect to the canonical A and B forms of DNA show a highly anticorrelated behavior indicating that the force field samples the equil. between the A and B forms of DNA. Proper stabilization of B form DNA in aq. soln. and A form DNA in 75% ethanol show that this equil. can be perturbed by environmental contributions. Success of the force field in reproducing a variety of exptl. data for duplex DNA and RNA indicates that it is of general use for computational investigations of nucleic acids as well as nucleic acids in complexes with proteins and lipids.
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    Darden, T.; York, D.; Pedersen, L. Particle Mesh Ewald - an N.Log(N) Method for Ewald Sums in Large Systems J. Chem. Phys. 1993, 98, 10089– 10092 DOI: 10.1063/1.464397
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    Particle mesh Ewald: an N·log(N) method for Ewald sums in large systems
    Darden, Tom; York, Darrin; Pedersen, Lee
    Journal of Chemical Physics (1993), 98 (12), 10089-92CODEN: JCPSA6; ISSN:0021-9606.
    An N·log(N) method for evaluating electrostatic energies and forces of large periodic systems is presented. The method is based on interpolation of the reciprocal space Ewald sums and evaluation of the resulting convolution using fast Fourier transforms. Timings and accuracies are presented for three large cryst. ionic systems.
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    Nose, S. A Unified Formulation of the Constant Temperature Molecular-Dynamics Methods J. Chem. Phys. 1984, 81, 511– 519 DOI: 10.1063/1.447334
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    A unified formulation of the constant-temperature molecular-dynamics methods
    Nose, Shuichi
    Journal of Chemical Physics (1984), 81 (1), 511-19CODEN: JCPSA6; ISSN:0021-9606.
    Three recently proposed const. temp. mol. dynamics methods [N., (1984) (1); W. G. Hoover et al., (1982) (2); D. J. Evans and G. P. Morris, (1983) (2); and J. M. Haile and S. Gupta, 1983) (3)] are examd. anal. via calcg. the equil. distribution functions and comparing them with that of the canonical ensemble. Except for effects due to momentum and angular momentum conservation, method (1) yields the rigorous canonical distribution in both momentum and coordinate space. Method (2) can be made rigorous in coordinate space, and can be derived from method (1) by imposing a specific constraint. Method (3) is not rigorous and gives a deviation of order N-1/2 from the canonical distribution (N the no. of particles). The results for the const. temp.-const. pressure ensemble are similar to the canonical ensemble case.
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    Hoover, W. G. Canonical Dynamics - Equilibrium Phase-Space Distributions Phys. Rev. A: At., Mol., Opt. Phys. 1985, 31, 1695– 1697 DOI: 10.1103/PhysRevA.31.1695
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    Canonical dynamics: Equilibrium phase-space distributions
    Hoover
    Physical review. A, General physics (1985), 31 (3), 1695-1697 ISSN:0556-2791.
    There is no expanded citation for this reference.
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    Brunger, A. T.; Adams, P. D.; Clore, G. M.; DeLano, W. L.; Gros, P.; Grosse-Kunstleve, R. W.; Jiang, J. S.; Kuszewski, J.; Nilges, M.; Pannu, N. S.; Read, R. J.; Rice, L. M.; Simonson, T.; Warren, G. L. Crystallography & Nmr System: A New Software Suite for Macromolecular Structure Determination Acta Crystallogr., Sect. D: Biol. Crystallogr. 1998, 54, 905– 921 DOI: 10.1107/S0907444998003254
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    Crystallography & NMR System: a new software suite for macromolecular structure determination
    Brunger, Axel T.; Adams, Paul D.; Clore, G. Marius; DeLano, Warren L.; Gros, Piet; Grosse-Kunstleve, Ralf W.; Jiang, Jian-Sheng; Kuszewski, John; Nilges, Michael; Pannu, Navraj S.; Read, Randy J.; Rice, Luke M.; Simonson, Thomas; Warren, Gregory L.
    Acta Crystallographica, Section D: Biological Crystallography (1998), D54 (5), 905-921CODEN: ABCRE6; ISSN:0907-4449. (Munksgaard International Publishers Ltd.)
    A new software suite, called Crystallog. & NMR System (CNS), has been developed for macromol. structure detn. by x-ray crystallog. or soln. NMR (NMR) spectroscopy. In contrast to existing structure-detn. programs the architecture of CNS is highly flexible, allowing for extension to other structure-detn. methods, such as electron microscopy and solid-state NMR spectroscopy. CNS has a hierarchical structure: a high-level hypertext markup language (HTML) user interface, task-oriented user input files, module files, a symbolic structure-detn. language (CNS language), and low-level source code. Each layer is accessible to the user. The novice user may just use the HTML interface, while the more advanced user may use any of the other layers. The source code will be distributed, thus source-code modification is possible. The CNS language is sufficiently powerful and flexible that many new algorithms can be easily implemented in the CNS language without changes to the source code. The CNS language allows the user to perform operations on data structures, such as structure factors, electron-d. maps, and at. properties. The power of the CNS language has been demonstrated by the implementation of a comprehensive set of crystallog. procedures for phasing, d. modification and refinement. User-friendly task-oriented input files are available for nearly all aspects of macromol. structure detn. by x-ray crystallog. and soln. NMR.
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    Wells, D. B.; Belkin, M.; Comer, J.; Aksimentiev, A. Assessing Graphene Nanopores for Sequencing DNA Nano Lett. 2012, 12, 4117– 4123 DOI: 10.1021/nl301655d
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    Assessing Graphene Nanopores for Sequencing DNA
    Wells, David B.; Belkin, Maxim; Comer, Jeffrey; Aksimentiev, Aleksei
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    Identification of single nucleotides in MoS2 nanopores
    Feng, Jiandong; Liu, Ke; Bulushev, Roman D.; Khlybov, Sergey; Dumcenco, Dumitru; Kis, Andras; Radenovic, Aleksandra
    Nature Nanotechnology (2015), 10 (12), 1070-1076CODEN: NNAABX; ISSN:1748-3387. (Nature Publishing Group)
    The size of the sensing region in solid-state nanopores is detd. by the size of the pore and the thickness of the pore membrane, so ultrathin membranes such as graphene and single-layer molybdenum disulfide could potentially offer the necessary spatial resoln. for nanopore DNA sequencing. However, the fast translocation speeds (3,000-50,000 nt ms-1) of DNA mols. moving across such membranes limit their usability. Here, we show that a viscosity gradient system based on room-temp. ionic liqs. can be used to control the dynamics of DNA translocation through MoS2 nanopores. The approach can be used to statistically detect all four types of nucleotide, which are identified according to current signatures recorded during their transient residence in the narrow orifice of the atomically thin MoS2 nanopore. Our technique, which exploits the high viscosity of room-temp. ionic liqs., provides optimal single nucleotide translocation speeds for DNA sequencing, while maintaining a signal-to-noise ratio higher than 10.
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  • Abstract

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    Figure 1

    Figure 1. (a) Simulation box consisting of a single-layer DNA origami (depicted in red), graphene sheet, water, ions, and translocating ssDNA (depicted in blue). (b) Bare graphene nanopore. (c) Single-layer DNA origami nanopore on top of a graphene nanopore.

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    Figure 2

    Figure 2. Characteristics of the hybrid nanopores under external biases. (a) I–V curves for the four types of nanopores. Lines are linear fits with the corresponding color for the symbols. (b) Conductance of different pores and their comparison with theoretical predictions. (c) Center-to-center distance of the DNA origami pore to the graphene pore in the x–y plane. Interaction between the DNA origami and the external positive bias does not disarrange the alignment of the hybrid nanopore.

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    Figure 3

    Figure 3. (a) Electrostatic potential map of the single-layer DNA origami hybrid nanopore under an external applied bias of 2 V. Ions and other point charges are approximated by Gaussian spheres with an inverse width of β = 0.25 Å–1. (b) The resulting mean bias across the pore along the z direction, averaged over x and y directions. The cyan and yellow regions approximately show, respectively, the area where the graphene nanopore and the DNA origami nanopore occupy along the z direction during the simulation time. The potential is primarily changing across the graphene nanopore.

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    Figure 4

    Figure 4. (a) Simulation system of DNA translocating through a bare graphene nanopore. The all-atom model contains a graphene nanopore, ssDNA (depicted in blue), water, and ions. (b) Simulation system of DNA translocating through a single-layer DNA origami hybrid nanopore. The all-atom model contains a single-layer DNA origami (depicted in red)–graphene nanopore, ssDNA (depicted in blue), water, and ions. (c) Simulation system of DNA translocating through a double-layer DNA origami hybrid nanopore. The all-atom model contains a double-layer DNA origami (depicted in red)–graphene nanopore, ssDNA (depicted in blue), water, and ions. (d) Translocation history of ssDNA in pristine graphene and single-layer DNA origami hybrid nanopores. (e) Translocation history of ssDNA in double-layer DNA origami hybrid nanopore. (f) Statistical distribution of the dwell times for different base types translocating through single-layer DNA origami hybrid nanopore under an external bias of 2 V. (g) Average residence time of base in single-layer DNA origami hybrid and bare graphene nanopores.

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    Figure 5

    Figure 5. (a) Snapshot of hydrogen bonds between poly(dA) and DNA origami (the black dashed lines represent HBs). (b) Snapshot of hydrogen bonds between poly(dT) and DNA origami (the black dashed lines represent HBs). (c) Average number of HBs between ssDNA and DNA origami nanoplates. (d) Time-dependent interaction energy between poly(dA) and DNA origami nanoplate (black). Translocation plot of poly(dA) through hybrid nanopore (red).

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    Figure 6

    Figure 6. (a) Schematic of the ionic current simulation system showing the interaction of the complementary bases (A–T). (b) Ionic currents for different bases computed from the translocation of poly ssDNAs through the single-layer DNA origami hybrid nanopore. (c) Density of different bases of the DNA origami nanoplate in the vicinity of the pore vs simulation time for translocation of poly(dA) through the single-layer DNA origami hybrid nanopore. (d) Average density of different bases of the DNA origami nanoplate in the vicinity of the pore during poly ssDNAs translocations through the single-layer DNA origami hybrid nanopore.

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    Figure 7

    Figure 7. Comparison of poly(dA) translocation rate through the single-layer DNA origami hybrid nanopore and the bare graphene nanopore.

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      Schneider, Gregory F.; Kowalczyk, Stefan W.; Calado, Victor E.; Pandraud, Gregory; Zandbergen, Henny W.; Vandersypen, Lieven M. K.; Dekker, Cees
      Nano Letters (2010), 10 (8), 3163-3167CODEN: NALEFD; ISSN:1530-6984. (American Chemical Society)
      Nanopores - nanosized holes that can transport ions and mols. - are very promising devices for genomic screening, in particular DNA sequencing. Solid-state nanopores currently suffer from the drawback, however, that the channel constituting the pore is long, ∼100 times the distance between two bases in a DNA mol. (0.5 nm for single-stranded DNA). This paper provides proof of concept that it is possible to realize and use ultrathin nanopores fabricated in graphene monolayers for single-mol. DNA translocation. The pores are obtained by placing a graphene flake over a microsize hole in a silicon nitride membrane and drilling a nanosize hole in the graphene using an electron beam. As individual DNA mols. translocate through the pore, characteristic temporary conductance changes are obsd. in the ionic current through the nanopore, setting the stage for future single-mol. genomic screening devices.
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    11. 11
      Traversi, F.; Raillon, C.; Benameur, S. M.; Liu, K.; Khlybov, S.; Tosun, M.; Krasnozhon, D.; Kis, A.; Radenovic, A. Detecting the Translocation of DNA through a Nanopore Using Graphene Nanoribbons Nat. Nanotechnol. 2013, 8, 939– 945 DOI: 10.1038/nnano.2013.240
      11
      Detecting the translocation of DNA through a nanopore using graphene nanoribbons
      Traversi, F.; Raillon, C.; Benameur, S. M.; Liu, K.; Khlybov, S.; Tosun, M.; Krasnozhon, D.; Kis, A.; Radenovic, A.
      Nature Nanotechnology (2013), 8 (12), 939-945CODEN: NNAABX; ISSN:1748-3387. (Nature Publishing Group)
      Solid-state nanopores can act as single-mol. sensors and could potentially be used to rapidly sequence DNA mols. However, nanopores are typically fabricated in insulating membranes that are as thick as 15 bases, which makes it difficult for the devices to read individual bases. Graphene is only 0.335 nm thick (equiv. to the spacing between two bases in a DNA chain) and could therefore provide a suitable membrane for sequencing applications. Here, we show that a solid-state nanopore can be integrated with a graphene nanoribbon transistor to create a sensor for DNA translocation. As DNA mols. move through the pore, the device can simultaneously measure drops in ionic current and changes in local voltage in the transistor, which can both be used to detect the mols. We examine the correlation between these two signals and use the ionic current measurements as a real-time control of the graphene-based sensing device.
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    12. 12
      Saha, K. K.; Drndic, M.; Nikolic, B. K. DNA Base-Specific Modulation of Microampere Transverse Edge Currents through a Metallic Graphene Nanoribbon with a Nanopore Nano Lett. 2012, 12, 50– 55 DOI: 10.1021/nl202870y
      12
      DNA base-specific modulation of microampere transverse edge currents through a metallic graphene nanoribbon with a nanopore
      Saha, Kamal K.; Drndic, Marija; Nikolic, Branislav K.
      Nano Letters (2012), 12 (1), 50-55CODEN: NALEFD; ISSN:1530-6984. (American Chemical Society)
      We study two-terminal devices for DNA sequencing that consist of a metallic graphene nanoribbon with zigzag edges (ZGNR) and a nanopore in its interior through which the DNA mol. is translocated. Using the nonequil. Green functions combined with d. functional theory, we demonstrate that each of the four DNA nucleobases inserted into the nanopore, whose edge carbon atoms are passivated by either hydrogen or nitrogen, will lead to a unique change in the device conductance. Unlike other recent biosensors based on transverse electronic transport through translocated DNA, which utilize small (of the order of pA) tunneling current across a nanogap or a nanopore yielding a poor signal-to-noise ratio, our device concept relies on the fact that in ZGNRs local c.d. is peaked around the edges so that drilling a nanopore away from the edges will not diminish the conductance. Inserting a nucleobase into the nanopore affects the charge d. in the surrounding area, thereby modulating edge conduction currents whose magnitude is of the order of microampere at bias voltage 0.1 V. The proposed biosensors are not limited to ZGNRs and they could be realized with other nanowires supporting transverse edge currents, such as chiral GNRs or wires made of two-dimensional topol. insulators.
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      https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3MXhsFOht7%252FM&md5=fc4603eff1cd59aebff62f509202360b
    13. 13
      Merchant, C. A.; Healy, K.; Wanunu, M.; Ray, V.; Peterman, N.; Bartel, J.; Fischbein, M. D.; Venta, K.; Luo, Z. T.; Johnson, A. T. C.; Drndic, M. DNA Translocation through Graphene Nanopores Nano Lett. 2010, 10, 2915– 2921 DOI: 10.1021/nl101046t
      13
      DNA Translocation through Graphene Nanopores
      Merchant, Christopher A.; Healy, Ken; Wanunu, Meni; Ray, Vishva; Peterman, Neil; Bartel, John; Fischbein, Michael D.; Venta, Kimberly; Luo, Zhengtang; Johnson, A. T. Charlie; Drndic, Marija
      Nano Letters (2010), 10 (8), 2915-2921CODEN: NALEFD; ISSN:1530-6984. (American Chemical Society)
      The authors report on DNA translocations through nanopores created in graphene membranes. Devices consist of 1-5 nm thick graphene membranes with electron-beam sculpted nanopores from 5 to 10 nm in diam. Due to the thin nature of the graphene membranes, the authors observe larger blocked currents than for traditional solid-state nanopores. However, ionic current noise levels are several orders of magnitude larger than those for silicon nitride nanopores. These fluctuations are reduced with the at.-layer deposition of 5 nm of titanium dioxide over the device. Unlike traditional solid-state nanopore materials that are insulating, graphene is an excellent elec. conductor. Use of graphene as a membrane material opens the door to a new class of nanopore devices in which electronic sensing and control are performed directly at the pore.
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    14. 14
      Merchant, C. A.; Drndic, M. Graphene Nanopore Devices for DNA Sensing Methods Mol. Biol. (N. Y., NY, U. S.) 2012, 870, 211– 226 DOI: 10.1007/978-1-61779-773-6_12
      There is no corresponding record for this reference.
    15. 15
      Heerema, S. J.; Dekker, C. Graphene Nanodevices for DNA Sequencing Nat. Nanotechnol. 2016, 11, 127– 136 DOI: 10.1038/nnano.2015.307
      15
      Graphene nanodevices for DNA sequencing
      Heerema, Stephanie J.; Dekker, Cees
      Nature Nanotechnology (2016), 11 (2), 127-136CODEN: NNAABX; ISSN:1748-3387. (Nature Publishing Group)
      A review. Fast, cheap, and reliable DNA sequencing could be one of the most disruptive innovations of this decade, as it will pave the way for personalized medicine. In pursuit of such technol., a variety of nanotechnol.-based approaches have been explored and established, including sequencing with nanopores. Owing to its unique structure and properties, graphene provides interesting opportunities for the development of a new sequencing technol. In recent years, a wide range of creative ideas for graphene sequencers have been theor. proposed and the first exptl. demonstrations have begun to appear. Here, we review the different approaches to using graphene nanodevices for DNA sequencing, which involve DNA passing through graphene nanopores, nanogaps, and nanoribbons, and the physisorption of DNA on graphene nanostructures. We discuss the advantages and problems of each of these key techniques, and provide a perspective on the use of graphene in future DNA sequencing technol.
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    16. 16
      Garaj, S.; Liu, S.; Golovchenko, J. A.; Branton, D. Molecule-Hugging Graphene Nanopores Proc. Natl. Acad. Sci. U. S. A. 2013, 110, 12192– 12196 DOI: 10.1073/pnas.1220012110
      16
      Molecule-hugging graphene nanopores
      Garaj, Slaven; Liu, Song; Golovchenko, Jene A.; Branton, Daniel
      Proceedings of the National Academy of Sciences of the United States of America (2013), 110 (30), 12192-12196,S12192/1-S12192/3CODEN: PNASA6; ISSN:0027-8424. (National Academy of Sciences)
      It has recently been recognized that solid-state nanopores in single-at.-layer graphene membranes can be used to electronically detect and characterize single long charged polymer mols. We have now fabricated nanopores in single-layer graphene that are closely matched to the diam. of a double-stranded DNA mol. Ionic current signals during electrophoretically driven translocation of DNA through these nanopores were exptl. explored and theor. modeled. Our expts. show that these nanopores have unusually high sensitivity (0.65 nA/Å) to extremely small changes in the translocating mol.'s outer diam. Such atomically short graphene nanopores can also resolve nanoscale-spaced mol. structures along the length of a polymer, but do so with greatest sensitivity only when the pore and mol. diams. are closely matched. Modeling confirms that our most closely matched pores have an inherent resoln. of ≤0.6 nm along the length of the mol.
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    17. 17
      Fologea, D.; Uplinger, J.; Thomas, B.; McNabb, D. S.; Li, J. L. Slowing DNA Translocation in a Solid-State Nanopore Nano Lett. 2005, 5, 1734– 1737 DOI: 10.1021/nl051063o
      17
      Slowing DNA Translocation in a Solid-State Nanopore
      Fologea, Daniel; Uplinger, James; Thomas, Brian; McNabb, David S.; Li, Jiali
      Nano Letters (2005), 5 (9), 1734-1737CODEN: NALEFD; ISSN:1530-6984. (American Chemical Society)
      Reducing a DNA mol.'s translocation speed in a solid-state nanopore is a key step toward rapid single mol. identification. Here we demonstrate that DNA translocation speeds can be reduced by an order of magnitude over previous results. By controlling the electrolyte temp., salt concn., viscosity, and the elec. bias voltage across the nanopore, we obtain a 3 base/μs translocation speed for 3 kbp double-stranded DNA in a 4-8 nm diam. silicon nitride pore. Our results also indicate that the ionic cond. inside such a nanopore is smaller than it is in bulk.
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    18. 18
      Kowalczyk, S. W.; Wells, D. B.; Aksimentiev, A.; Dekker, C. Slowing Down DNA Translocation through a Nanopore in Lithium Chloride Nano Lett. 2012, 12, 1038– 1044 DOI: 10.1021/nl204273h
      18
      Slowing down DNA Translocation through a Nanopore in Lithium Chloride
      Kowalczyk, Stefan W.; Wells, David B.; Aksimentiev, Aleksei; Dekker, Cees
      Nano Letters (2012), 12 (2), 1038-1044CODEN: NALEFD; ISSN:1530-6984. (American Chemical Society)
      The charge of a DNA mol. is a crucial parameter in many DNA detection and manipulation schemes such as gel electrophoresis and lab-on-a-chip applications. Here, we study the partial redn. of the DNA charge due to counterion binding by means of nanopore translocation expts. and all-atom mol. dynamics (MD) simulations. Surprisingly, we find that the translocation time of a DNA mol. through a solid-state nanopore strongly increases as the counterions decrease in size from K+ to Na+ to Li+, both for double-stranded DNA (dsDNA) and single-stranded DNA (ssDNA). MD simulations elucidate the microscopic origin of this effect: Li+ and Na+ bind DNA stronger than K+. These fundamental insights into the counterion binding to DNA also provide a practical method for achieving at least 10-fold enhanced resoln. in nanopore applications.
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      https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC38XlsVCktg%253D%253D&md5=31be87d5508361ac5aba5a7120e51979
    19. 19
      Wanunu, M.; Sutin, J.; McNally, B.; Chow, A.; Meller, A. DNA Translocation Governed by Interactions with Solid-State Nanopores Biophys. J. 2008, 95, 4716– 4725 DOI: 10.1529/biophysj.108.140475
      19
      DNA translocation governed by interactions with solid-state nanopores
      Wanunu, Meni; Sutin, Jason; McNally, Ben; Chow, Andrew; Meller, Amit
      Biophysical Journal (2008), 95 (10), 4716-4725CODEN: BIOJAU; ISSN:0006-3495. (Biophysical Society)
      We investigate the voltage-driven translocation dynamics of individual DNA mols. through solid-state nanopores in the diam. range 2.7-5 nm. Our studies reveal an order of magnitude increase in the translocation times when the pore diam. is decreased from 5 to 2.7 nm, and steep temp. dependence, nearly threefold larger than would be expected if the dynamics were governed by viscous drag. As previously predicted for an interaction-dominated translocation process, we observe exponential voltage dependence on translocation times. Mean translocation times scale with DNA length by two power laws: for short DNA mols., in the range 150-3500 bp, we find an exponent of 1.40, whereas for longer mols., an exponent of 2.28 dominates. Surprisingly, we find a transition in the fraction of ion current blocked by DNA, from a length-independent regime for short DNA mols. to a regime where the longer the DNA, the more current is blocked. Temp. dependence studies reveal that for increasing DNA lengths, addnl. interactions are responsible for the slower DNA dynamics. Our results can be rationalized by considering DNA/pore interactions as the predominant factor detg. DNA translocation dynamics in small pores. These interactions markedly slow down the translocation rate, enabling higher temporal resoln. than obsd. with larger pores. These findings shed light on the transport properties of DNA in small pores, relevant for future nanopore applications, such as DNA sequencing and genotyping.
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    20. 20
      Farimani, A. B.; Heiranian, M.; Aluru, N. R. Electromechanical Signatures for DNA Sequencing through a Mechanosensitive Nanopore J. Phys. Chem. Lett. 2015, 6, 650– 657 DOI: 10.1021/jz5025417
      20
      Electromechanical signatures for DNA sequencing through a mechanosensitive nanopore
      Farimani, A. Barati; Heiranian, M.; Aluru, N. R.
      Journal of Physical Chemistry Letters (2015), 6 (4), 650-657CODEN: JPCLCD; ISSN:1948-7185. (American Chemical Society)
      Biol. nanopores have been extensively used for DNA base detection since these pores are widely available and tunable through mutations. Distinguishing bases of nucleic acids by passing them through nanopores has so far primarily relied on elec. signals-specifically, ionic currents through the nanopores. However, the low signal-to-noise ratio makes detection of ionic currents difficult. In this study, we show that the initially closed mechanosensitive channel of large conductance (MscL) protein pore opens for single-stranded DNA (ssDNA) translocation under an applied elec. field. As each nucleotide translocates through the pore, a unique mech. signal is obsd.-specifically, the tension in the membrane contg. the MscL pore is different for each nucleotide. In addn. to the membrane tension, we found that the ionic current is also different for the four nucleotide types. The initially closed MscL adapts its opening for nucleotide translocation due to the flexibility of the pore. This unique operation of MscL provides single nucleotide resoln. in both elec. and mech. signals. Finally, we also show that the speed of DNA translocation is roughly 1 order of magnitude slower in MscL compared to Mycobacterium smegmatis porin A (MspA), suggesting MscL to be an attractive protein pore for DNA sequencing.
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      https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2MXhsF2ntrk%253D&md5=94ec4a16716eb2fbcb85b026f067ebbf
    21. 21
      Luan, B. Q.; Stolovitzky, G.; Martyna, G. Slowing and Controlling the Translocation of DNA in a Solid-State Nanopore Nanoscale 2012, 4, 1068– 1077 DOI: 10.1039/C1NR11201E
      21
      Slowing and controlling the translocation of DNA in a solid-state nanopore
      Luan, Binquan; Stolovitzky, Gustavo; Martyna, Glenn
      Nanoscale (2012), 4 (4), 1068-1077CODEN: NANOHL; ISSN:2040-3372. (Royal Society of Chemistry)
      A review. DNA sequencing methods based on nanopores could potentially represent a low-cost and high-throughput pathway to practical genomics, by replacing current sequencing methods based on synthesis that are limited in speed and cost. The success of nanopore sequencing techniques requires the soln. to two fundamental problems: (1) sensing each nucleotide of a DNA strand, in sequence, as it passes through a nanopore; (2) delivering each nucleotide in a DNA strand, in turn, to a sensing site within the nanopore in a controlled manner. It has been demonstrated that a DNA nucleotide can be sensed using elec. signals, such as ionic current changes caused by nucleotide blockage at a constriction region in a protein pore or a tunneling current through the nucleotide-bridged gap of two nanoelectrodes built near a solid-state nanopore. However, it is not yet clear how each nucleotide in a DNA strand can be delivered in turn to a sensing site and held there for a sufficient time to ensure high fidelity sensing. This latter problem has been addressed by modifying macroscopic properties, such as a solvent viscosity, ion concn. or temp. Also, the DNA transistor, a solid state nanopore dressed with a series of metal-dielec. layers has been proposed as a soln. Mol. dynamics simulations provide the means to study and to understand DNA transport in nanopores microscopically. In this article, we review computational studies on how to slow down and control the DNA translocation through a solid-state nanopore.
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      https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC38Xhslarsrk%253D&md5=419f2aeb63d3338246d02095572a54d0
    22. 22
      Butler, T. Z.; Pavlenok, M.; Derrington, I. M.; Niederweis, M.; Gundlach, J. H. Single-Molecule DNA Detection with an Engineered Mspa Protein Nanopore Proc. Natl. Acad. Sci. U. S. A. 2008, 105, 20647– 20652 DOI: 10.1073/pnas.0807514106
      22
      Single-molecule DNA detection with an engineered MspA protein nanopore
      Butler, Tom Z.; Pavlenok, Mikhail; Derrington, Ian M.; Niederweis, Michael; Gundlach, Jens H.
      Proceedings of the National Academy of Sciences of the United States of America (2008), 105 (52), 20647-20652CODEN: PNASA6; ISSN:0027-8424. (National Academy of Sciences)
      Nanopores hold great promise as single-mol. anal. devices and biophys. model systems because the ionic current blockades they produce contain information about the identity, concn., structure, and dynamics of target mols. The porin MspA of Mycobacterium smegmatis has remarkable stability against environmental stresses and can be rationally modified based on its crystal structure. Further, MspA has a short and narrow channel constriction that is promising for DNA sequencing because it may enable improved characterization of short segments of a ssDNA mol. that is threaded through the pore. By eliminating the neg. charge in the channel constriction, we designed and constructed an MspA mutant capable of electronically detecting and characterizing single mols. of ssDNA as they are electrophoretically driven through the pore. A second mutant with addnl. exchanges of neg.-charged residues for pos.-charged residues in the vestibule region exhibited a factor of ≈ 20 higher interaction rates, required only half as much voltage to observe interaction, and allowed ssDNA to reside in the vestibule ≈ 100 times longer than the first mutant. Our results introduce MspA as a nanopore for nucleic acid anal. and highlight its potential as an engineerable platform for single-mol. detection and characterization applications.
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    23. 23
      Sint, K.; Wang, B.; Kral, P. Selective Ion Passage through Functionalized Graphene Nanopores J. Am. Chem. Soc. 2008, 130, 16448– 16449 DOI: 10.1021/ja804409f
      23
      Selective Ion Passage through Functionalized Graphene Nanopores
      Sint, Kyaw; Wang, Boyang; Kral, Petr
      Journal of the American Chemical Society (2008), 130 (49), 16448-16449CODEN: JACSAT; ISSN:0002-7863. (American Chemical Society)
      We design functionalized nanopores in graphene monolayers and show by mol. dynamics simulations that they provide highly selective passage of hydrated ions. Only ions that can be partly stripped of their hydration shells can pass through these ultrasmall pores with diams. of ∼5 Å. For example, a fluorine-nitrogen-terminated pore allows the passage of Li+, Na+, and K+ cations with the ratio 9:14:33, but it blocks the passage of anions. The hydrogen-terminated pore allows the passage of F-, Cl-, and Br- anions with the ratio 0:17:33, but it blocks the passage of cations. These nanopores could have potential applications in mol. sepn., desalination, and energy storage systems.
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    24. 24
      Wei, R. S.; Martin, T. G.; Rant, U.; Dietz, H. DNA Origami Gatekeepers for Solid-State Nanopores Angew. Chem., Int. Ed. 2012, 51, 4864– 4867 DOI: 10.1002/anie.201200688
      24
      DNA origami gatekeepers for solid-state nanopores
      Wei, Ruoshan; Martin, Thomas G.; Rant, Ulrich; Dietz, Hendrik
      Angewandte Chemie, International Edition (2012), 51 (20), 4864-4867, S4864/1-S4864/31CODEN: ACIEF5; ISSN:1433-7851. (Wiley-VCH Verlag GmbH & Co. KGaA)
      The authors have presented DNA nanoplates that function with solid-state nanopores, which can be fabricated through std. electron beam lithog. The nanoplates are permeable to small ions, but the passage of macromols. can be controlled by including custom apertures. The chem. addressability of the DNA nanoplates enables bait-prey single-mol. sensing expts., as highlighted here by the sequence-specific detection of DNA snippets and genomic phage DNA. Applications in biomol. interaction screens and for detecting DNA sequences by hybridization are readily conceivable. High-resoln. sensing applications, such as elec. DNA sequencing will require reducing both the leakage current and current fluctuations.
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    25. 25
      Yusko, E. C.; Johnson, J. M.; Majd, S.; Prangkio, P.; Rollings, R. C.; Li, J. L.; Yang, J.; Mayer, M. Controlling Protein Translocation through Nanopores with Bio-Inspired Fluid Walls Nat. Nanotechnol. 2011, 6, 253– 260 DOI: 10.1038/nnano.2011.12
      25
      Controlling protein translocation through nanopores with bio-inspired fluid walls
      Yusko, Erik C.; Johnson, Jay M.; Majd, Sheereen; Prangkio, Panchika; Rollings, Ryan C.; Li, Jiali; Yang, Jerry; Mayer, Michael
      Nature Nanotechnology (2011), 6 (4), 253-260CODEN: NNAABX; ISSN:1748-3387. (Nature Publishing Group)
      Synthetic nanopores have been used to study individual biomols. in high throughput, but their performance as sensors does not match that of biol. ion channels. Challenges include control of nanopore diams. and surface chem., modification of the translocation times of single-mol. analytes through nanopores, and prevention of nonspecific interactions with pore walls. Here, inspired by the olfactory sensilla of insect antennae, the authors show that coating nanopores with a fluid lipid bilayer tailors their surface chem. and allows fine-tuning and dynamic variation of pore diams. in subnanometer increments. Incorporation of mobile ligands in the lipid bilayer conferred specificity and slowed the translocation of targeted proteins sufficiently to time-resolve translocation events of individual proteins. Lipid coatings also prevented pores from clogging, eliminated nonspecific binding and enabled the translocation of amyloid-beta (Aβ) oligomers and fibrils. Through combined anal. of their translocation time, vol., charge, shape and ligand affinity, different proteins were identified.
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    26. 26
      Martin, C. R.; Siwy, Z. S. Learning Nature’s Way: Biosensing with Synthetic Nanopores Science 2007, 317, 331– 332 DOI: 10.1126/science.1146126
      26
      Learning Nature's Way: Biosensing with Synthetic Nanopores
      Martin, Charles R.; Siwy, Zuzanna S.
      Science (Washington, DC, United States) (2007), 317 (5836), 331-332CODEN: SCIEAS; ISSN:0036-8075. (American Association for the Advancement of Science)
      A review. Synthetic sensors use mol. recognition events in nanometer-scale pores for selective detection of proteins, nucleotides, and drugs.
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    27. 27
      Iqbal, S. M.; Akin, D.; Bashir, R. Solid-State Nanopore Channels with DNA Selectivity Nat. Nanotechnol. 2007, 2, 243– 248 DOI: 10.1038/nnano.2007.78
      27
      Solid-state nanopore channels with DNA selectivity
      Iqbal, Samir M.; Akin, Demir; Bashir, Rashid
      Nature Nanotechnology (2007), 2 (4), 243-248CODEN: NNAABX; ISSN:1748-3387. (Nature Publishing Group)
      Solid-state nanopores have emerged as possible candidates for next-generation DNA sequencing devices. In such a device, the DNA sequence would be detd. by measuring how the forces on the DNA mols., and also the ion currents through the nanopore, change as the mols. pass through the nanopore. Unlike their biol. counterparts, solid-state nanopores have the advantage that they can withstand a wide range of analyte solns. and environments. Here we report solid-state nanopore channels that are selective towards single-stranded DNA (ssDNA). Nanopores functionalized with a 'probe' of hair-pin loop DNA can, under an applied elec. field, selectively transport short lengths of 'target' ssDNA that are complementary to the probe. Even a single base mismatch between the probe and the target results in longer translocation pulses and a significantly reduced no. of translocation events. Our single-mol. measurements allow us to measure sep. the mol. flux and the pulse duration, providing a tool to gain fundamental insight into the channel-mol. interactions. The results can be explained in the conceptual framework of diffusive mol. transport with particle-channel interactions.
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    28. 28
      Rothemund, P. W. K. Folding DNA to Create Nanoscale Shapes and Patterns Nature 2006, 440, 297– 302 DOI: 10.1038/nature04586
      28
      Folding DNA to create nanoscale shapes and patterns
      Rothemund, Paul W. K.
      Nature (London, United Kingdom) (2006), 440 (7082), 297-302CODEN: NATUAS; ISSN:0028-0836. (Nature Publishing Group)
      'Bottom-up fabrication', which exploits the intrinsic properties of atoms and mols. to direct their self-organization, is widely used to make relatively simple nanostructures. A key goal for this approach is to create nanostructures of high complexity, matching that routinely achieved by 'top-down' methods. The self-assembly of DNA mols. provides an attractive route towards this goal. Here the author describe a simple method for folding long, single-stranded DNA mols. into arbitrary two-dimensional shapes. The design for a desired shape is made by raster-filling the shape with a 7-kilobase single-stranded scaffold and by choosing over 200 short oligonucleotide 'staple strands' to hold the scaffold in place. Once synthesized and mixed, the staple and scaffold strands self-assemble in a single step. The resulting DNA structures are roughly 100 nm in diam. and approx. desired shapes such as squares, disks and five-pointed stars with a spatial resoln. of 6 nm. Because each oligonucleotide can serve as a 6-nm pixel, the structures can be programmed to bear complex patterns such as words and images on their surfaces. Finally, individual DNA structures can be programmed to form larger assemblies, including extended periodic lattices and a hexamer of triangles (which constitutes a 30-megadalton mol. complex).
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      https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD28XitlKgu7g%253D&md5=583caefdda9b1deb5d3f2ef78d9e6ecb
    29. 29
      Andersen, E. S.; Dong, M.; Nielsen, M. M.; Jahn, K.; Subramani, R.; Mamdouh, W.; Golas, M. M.; Sander, B.; Stark, H.; Oliveira, C. L. P.; Pedersen, J. S.; Birkedal, V.; Besenbacher, F.; Gothelf, K. V.; Kjems, J. Self-Assembly of a Nanoscale DNA Box with a Controllable Lid Nature 2009, 459, 73– 75 DOI: 10.1038/nature07971
      29
      Self-assembly of a nanoscale DNA box with a controllable lid
      Andersen, Ebbe S.; Dong, Mingdong; Nielsen, Morten M.; Jahn, Kasper; Subramani, Ramesh; Mamdouh, Wael; Golas, Monika M.; Sander, Bjoern; Stark, Holger; Oliveira, Cristiano L. P.; Pedersen, Jan Skov; Birkedal, Victoria; Besenbacher, Flemming; Gothelf, Kurt V.; Kjems, Jorgen
      Nature (London, United Kingdom) (2009), 459 (7243), 73-76CODEN: NATUAS; ISSN:0028-0836. (Nature Publishing Group)
      The unique structural motifs and self-recognition properties of DNA can be exploited to generate self-assembling DNA nanostructures of specific shapes using a 'bottom-up' approach. Several assembly strategies have been developed for building complex three-dimensional (3D) DNA nanostructures. Recently, the DNA 'origami' method was used to build two-dimensional addressable DNA structures of arbitrary shape that can be used as platforms to arrange nanomaterials with high precision and specificity. A long-term goal of this field has been to construct fully addressable 3D DNA nanostructures. Here we extend the DNA origami method into three dimensions by creating an addressable DNA box 42 × 36 × 36 nm3 in size that can be opened in the presence of externally supplied DNA 'keys'. We thoroughly characterize the structure of this DNA box using cryogenic transmission electron microscopy, small-angle X-ray scattering and at. force microscopy, and use fluorescence resonance energy transfer to optically monitor the opening of the lid. Controlled access to the interior compartment of this DNA nanocontainer could yield several interesting applications, for example as a logic sensor for multiple-sequence signals or for the controlled release of nanocargos.
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      https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD1MXlsF2ltrs%253D&md5=eff8881786f7bd1a8c06ae3d26cf47cd
    30. 30
      Sobczak, J. P. J.; Martin, T. G.; Gerling, T.; Dietz, H. Rapid Folding of DNA into Nanoscale Shapes at Constant Temperature Science 2012, 338, 1458– 1461 DOI: 10.1126/science.1229919
      30
      Rapid Folding of DNA into Nanoscale Shapes at Constant Temperature
      Sobczak, Jean-Philippe J.; Martin, Thomas G.; Gerling, Thomas; Dietz, Hendrik
      Science (Washington, DC, United States) (2012), 338 (6113), 1458-1461CODEN: SCIEAS; ISSN:0036-8075. (American Association for the Advancement of Science)
      At const. temp., hundreds of DNA strands can cooperatively fold a long template DNA strand within minutes into complex nanoscale objects. Folding occurred out of equil. along nucleation-driven pathways at temps. that could be influenced by the choice of sequences, strand lengths, and chain topol. Unfolding occurred in apparent equil. at higher temps. than those for folding. Folding at optimized const. temps. enabled the rapid prodn. of three-dimensional DNA objects with yields that approached 100%. The results point to similarities with protein folding in spite of chem. and structural differences. The possibility for rapid and high-yield assembly will enable DNA nanotechnol. for practical applications.
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    31. 31
      Falconi, M.; Oteri, F.; Chillemi, G.; Andersen, F. F.; Tordrup, D.; Oliveira, C. L. P.; Pedersen, J. S.; Knudsen, B. R.; Desideri, A. Deciphering the Structural Properties That Confer Stability to a DNA Nanocage ACS Nano 2009, 3, 1813– 1822 DOI: 10.1021/nn900468y
      There is no corresponding record for this reference.
    32. 32
      Zadegan, R. M.; Jepsen, M. D. E.; Thomsen, K. E.; Okholm, A. H.; Schaffert, D. H.; Andersen, E. S.; Birkedal, V.; Kjems, J. Construction of a 4 Zeptoliters Switchable 3d DNA Box Origami ACS Nano 2012, 6, 10050– 10053 DOI: 10.1021/nn303767b
      32
      Construction of a 4 Zeptoliters Switchable 3D DNA Box Origami
      Zadegan, Reza M.; Jepsen, Mette D. E.; Thomsen, Karen E.; Okholm, Anders H.; Schaffert, David H.; Andersen, Ebbe S.; Birkedal, Victoria; Kjems, Joergen
      ACS Nano (2012), 6 (11), 10050-10053CODEN: ANCAC3; ISSN:1936-0851. (American Chemical Society)
      The DNA origami technique is a recently developed self-assembly method that allows construction of 3D objects at the nanoscale for various applications. In the current study we report the prodn. of a 18 × 18 × 24 nm3 hollow DNA box origami structure with a switchable lid. The structure was efficiently produced and characterized by at. force microscopy, transmission electron microscopy, and Foerster resonance energy transfer spectroscopy. The DNA box has a unique reclosing mechanism, which enables it to repeatedly open and close in response to a unique set of DNA keys. This DNA device can potentially be used for a broad range of applications such as controlling the function of single mols., controlled drug delivery, and mol. computing.
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    33. 33
      Langecker, M.; Arnaut, V.; Martin, T. G.; List, J.; Renner, S.; Mayer, M.; Dietz, H.; Simmel, F. C. Synthetic Lipid Membrane Channels Formed by Designed DNA Nanostructures Science 2012, 338, 932– 936 DOI: 10.1126/science.1225624
      33
      Synthetic Lipid Membrane Channels Formed by Designed DNA Nanostructures
      Langecker, Martin; Arnaut, Vera; Martin, Thomas G.; List, Jonathan; Renner, Stephan; Mayer, Michael; Dietz, Hendrik; Simmel, Friedrich C.
      Science (Washington, DC, United States) (2012), 338 (6109), 932-936CODEN: SCIEAS; ISSN:0036-8075. (American Association for the Advancement of Science)
      We created nanometer-scale transmembrane channels in lipid bilayers by means of self-assembled DNA-based nanostructures. Scaffolded DNA origami was used to create a stem that penetrated and spanned a lipid membrane, as well as a barrel-shaped cap that adhered to the membrane, in part via 26 cholesterol moieties. In single-channel electrophysiol. measurements, we found similarities to the response of natural ion channels, such as conductances on the order of 1 nanosiemens and channel gating. More pronounced gating was seen for mutations in which a single DNA strand of the stem protruded into the channel. Single-mol. translocation expts. show that the synthetic channels can be used to discriminate single DNA mols.
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    34. 34
      Seifert, A.; Gopfrich, K.; Burns, J. R.; Fertig, N.; Keyser, U. F.; Howorka, S. Bilayer-Spanning DNA Nanopores with Voltage-Switching between Open and Closed State ACS Nano 2015, 9, 1117– 1126 DOI: 10.1021/nn5039433
      34
      Bilayer-Spanning DNA Nanopores with Voltage-Switching between Open and Closed State
      Seifert, Astrid; Goepfrich, Kerstin; Burns, Jonathan R.; Fertig, Niels; Keyser, Ulrich F.; Howorka, Stefan
      ACS Nano (2015), 9 (2), 1117-1126CODEN: ANCAC3; ISSN:1936-0851. (American Chemical Society)
      Membrane-spanning nanopores from folded DNA are a recent example of biomimetic man-made nanostructures that can open up applications in biosensing, drug delivery, and nanofluidics. The authors generate a DNA nanopore based on the archetypal six-helix-bundle architecture and systematically characterize it via single-channel current recordings to address several fundamental scientific questions in this emerging field. The DNA pores exhibit two voltage-dependent conductance states. Low transmembrane voltages favor a stable high-conductance level, which corresponds to an unobstructed DNA pore. The expected inner width of the open channel is confirmed by measuring the conductance change as a function of poly(ethylene glycol) (PEG) size, whereby smaller PEGs are assumed to enter the pore. PEG sizing also clarifies that the main ion-conducting path runs through the membrane-spanning channel lumen as opposed to any proposed gap between the outer pore wall and the lipid bilayer. At higher voltages, the channel shows a main low-conductance state probably caused by elec.-field-induced changes of the DNA pore in its conformation or orientation. This voltage-dependent switching between the open and closed states is obsd. with planar lipid bilayers as well as bilayers mounted on glass nanopipettes. These findings settle a discrepancy between two previously published conductances. By systematically exploring a large space of parameters and answering key questions, the authors' report supports the development of DNA nanopores for nanobiotechnol.
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    35. 35
      Hernandez-Ainsa, S.; Bell, N. A. W.; Thacker, V. V.; Gopfrich, K.; Misiunas, K.; Fuentes-Perez, M. E.; Moreno-Herrero, F.; Keyser, U. F. DNA Origami Nanopores for Controlling DNA Translocation ACS Nano 2013, 7, 6024– 6030 DOI: 10.1021/nn401759r
      35
      DNA Origami Nanopores for Controlling DNA Translocation
      Hernandez-Ainsa, Silvia; Bell, Nicholas A. W.; Thacker, Vivek V.; Gopfrich, Kerstin; Misiunas, Karolis; Fuentes-Perez, Maria Eugenia; Moreno-Herrero, Fernando; Keyser, Ulrich F.
      ACS Nano (2013), 7 (7), 6024-6030CODEN: ANCAC3; ISSN:1936-0851. (American Chemical Society)
      The authors combine DNA origami structures with glass nanocapillaries to reversibly form hybrid DNA origami nanopores. Trapping of the DNA origami onto the nanocapillary is proven by imaging fluorescently labeled DNA origami structures and simultaneous ionic current measurements of the trapping events. The authors then show two applications highlighting the versatility of these DNA origami nanopores. First, by tuning the pore size the authors can control the folding of dsDNA mols. ("phys. control"). Second, the specific introduction of binding sites in the DNA origami nanopore allows selective detection of ssDNA as a function of the DNA sequence ("chem. control").
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      https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3sXovFWgtro%253D&md5=7b647421b919ef722499829cca81fa2f
    36. 36
      Wei, R. S.; Gatterdam, V.; Wieneke, R.; Tampe, R.; Rant, U. Stochastic Sensing of Proteins with Receptor-Modified Solid-State Nanopores Nat. Nanotechnol. 2012, 7, 257– 263 DOI: 10.1038/nnano.2012.24
      36
      Stochastic sensing of proteins with receptor-modified solid-state nanopores
      Wei, Ruoshan; Gatterdam, Volker; Wieneke, Ralph; Tampe, Robert; Rant, Ulrich
      Nature Nanotechnology (2012), 7 (4), 257-263CODEN: NNAABX; ISSN:1748-3387. (Nature Publishing Group)
      Solid-state nanopores are capable of the label-free anal. of single mols. It is possible to add biochem. selectivity by anchoring a mol. receptor inside the nanopore, but it is difficult to maintain single-mol. sensitivity in these modified nanopores. Here, we show that metalized silicon nitride nanopores chem. modified with nitrilotriacetic acid (NTA) receptors can be used for the stochastic sensing of proteins. The reversible binding and unbinding of the proteins to the receptors is obsd. in real time, and the interaction parameters are statistically analyzed from single-mol. binding events. To demonstrate the versatile nature of this approach, we detect His-tagged proteins and discriminate between the subclasses of rodent IgG antibodies.
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    37. 37
      Yoo, J.; Aksimentiev, A. In Situ Structure and Dynamics of DNA Origami Determined through Molecular Dynamics Simulations Proc. Natl. Acad. Sci. U. S. A. 2013, 110, 20099– 20104 DOI: 10.1073/pnas.1316521110
      37
      In situ structure and dynamics of DNA origami determined through molecular dynamics simulations
      Yoo, Jejoong; Aksimentiev, Aleksei
      Proceedings of the National Academy of Sciences of the United States of America (2013), 110 (50), 20099-20104,S20099/1-S20099/24CODEN: PNASA6; ISSN:0027-8424. (National Academy of Sciences)
      The DNA origami method permits folding of long single-stranded DNA into complex 3-dimensional structures with subnanometer precision. Transmission electron microscopy (TEM), at. force microscopy ATM), and recently cryo-electron microscopic tomog. have been used to characterize the properties of such DNA origami objects; however, their microscopic structures and dynamics have remained unknown. Here, the authors report the results of all-atom mol. dynamics (MD) simulations that characterized the structural and mech. properties of DNA origami objects in unprecedented microscopic detail. When simulated in an aq. environment, the structures of DNA origami objects departed from their idealized targets as a result of steric, electrostatic, and solvent-mediated forces. Whereas the global structural features of such relaxed conformations conformed to the target designs, local deformations were abundant and varied in magnitude along the structures. In contrast to their free-soln. conformation, the Holliday junctions in the DNA origami structures adopted a left-handed antiparallel conformation. The authors found that the DNA origami structures underwent considerable temporal fluctuations on both local and global scales. Anal. of such structural fluctuations revealed the local mech. properties of the DNA origami objects. The lattice type of the structures considerably affected global mech. properties such as bending rigidity. This study demonstrated the potential of all-atom MD simulations to play a considerable role in future development of the DNA origami field by providing accurate, quant. assessment of local and global structural and mech. properties of DNA origami objects.
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    38. 38
      Li, C. Y.; Hemmig, E. A.; Kong, J. L.; Yoo, J.; Hernandez-Ainsa, S.; Keyser, U. F.; Aksimentiev, A. Ionic Conductivity, Structural Deformation, and Programmable Anisotropy of DNA Origami in Electric Field ACS Nano 2015, 9, 1420– 1433 DOI: 10.1021/nn505825z
      38
      Ionic Conductivity, Structural Deformation, and Programmable Anisotropy of DNA Origami in Electric Field
      Li, Chen-Yu; Hemmig, Elisa A.; Kong, Jinglin; Yoo, Jejoong; Hernandez-Ainsa, Silvia; Keyser, Ulrich F.; Aksimentiev, Aleksei
      ACS Nano (2015), 9 (2), 1420-1433CODEN: ANCAC3; ISSN:1936-0851. (American Chemical Society)
      The DNA origami technique can enable functionalization of inorg. structures for single-mol. elec. current recordings. Several layers of DNA mols., a DNA origami plate, placed on top of a solid-state nanopore is permeable to ions. Here, the authors report a comprehensive characterization of the ionic cond. of DNA origami plates by all-atom mol. dynamics (MD) simulations and nanocapillary elec. current recordings. Using the MD method, the authors characterize the ionic cond. of several origami constructs, revealing the local distribution of ions, the distribution of the electrostatic potential and contribution of different mol. species to the current. The simulations det. the dependence of the ionic cond. on the applied voltage, the no. of DNA layers, the nucleotide content and the lattice type of the plates. Increasing the concn. of Mg2+ ions makes the origami plates more compact, reducing their cond. The conductance of a DNA origami plate on top of a solid-state nanopore is detd. by the two competing effects: bending of the DNA origami plate that reduces the current and sepn. of the DNA origami layers that increases the current. The latter is produced by the electroosmotic flow and is reversible at the time scale of a hundred nanoseconds. The conductance of a DNA origami object depends on its orientation, reaching max. when the elec. field aligns with the direction of the DNA helixes. The authors' work demonstrates feasibility of programming the elec. properties of a self-assembled nanoscale object using DNA.
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    39. 39
      Gao, B.; Sarveswaran, K.; Bernstein, G. H.; Lieberman, M. Guided Deposition of Individual DNA Nanostructures on Silicon Substrates Langmuir 2010, 26, 12680– 12683 DOI: 10.1021/la101343k
      39
      Guided Deposition of Individual DNA Nanostructures on Silicon Substrates
      Gao, Bo; Sarveswaran, Koshala; Bernstein, Gary H.; Lieberman, Marya
      Langmuir (2010), 26 (15), 12680-12683CODEN: LANGD5; ISSN:0743-7463. (American Chemical Society)
      The authors demonstrate immobilization of DNA nanostructures (37 nm × 8 nm) on silicon by a combination of top-down fabrication and bottom-up self-assembly. Anchor lines and pads were defined using electron beam lithog. and a cationic mol. monolayer. Individual DNA nanostructures bind in 85% yield onto the anchor pads and can be washed and imaged in air. The strength of the binding interaction between a DNA nanostructure and its anchor pad is at least -43 kJ/mol.
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      https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3cXot1als70%253D&md5=e1ca119f9cf892d7717196ac66949573
    40. 40
      Teshome, B.; Facsko, S.; Keller, A. Topography-Controlled Alignment of DNA Origami Nanotubes on Nanopatterned Surfaces Nanoscale 2014, 6, 1790– 1796 DOI: 10.1039/C3NR04627C
      There is no corresponding record for this reference.
    41. 41
      Pearson, A. C.; Pound, E.; Woolley, A. T.; Linford, M. R.; Harb, J. N.; Davis, R. C. Chemical Alignment of DNA Origami to Block Copolymer Patterned Arrays of 5 Nm Gold Nanoparticles Nano Lett. 2011, 11, 1981– 1987 DOI: 10.1021/nl200306w
      There is no corresponding record for this reference.
    42. 42
      Gu, H. Z.; Chao, J.; Xiao, S. J.; Seeman, N. C. Dynamic Patterning Programmed by DNA Tiles Captured on a DNA Origami Substrate Nat. Nanotechnol. 2009, 4, 245– 248 DOI: 10.1038/nnano.2009.5
      42
      Dynamic patterning programmed by DNA tiles captured on a DNA origami substrate
      Gu, Hongzhou; Chao, Jie; Xiao, Shou-Jun; Seeman, Nadrian C.
      Nature Nanotechnology (2009), 4 (4), 245-248CODEN: NNAABX; ISSN:1748-3387. (Nature Publishing Group)
      The aim of nanotechnol. is to put specific at. and mol. species where we want them, when we want them there. Achieving such dynamic and functional control could lead to programmable chem. synthesis and nanoscale systems that are responsive to their environments. Structural DNA nanotechnol. offers a powerful route to this goal by combining stable branched DNA motifs with cohesive ends to produce programmed nanomech. devices and fixed or modified patterned lattices. Here, we demonstrate a dynamic form of patterning in which a pattern component is captured between two independently programmed DNA devices. A simple and robust error-correction protocol has been developed that yields programmed targets in all cases. This capture system can lead to dynamic control either on patterns or on programmed elements; this capability enables computation or a change of structural state as a function of information in the surroundings of the system.
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    43. 43
      Kershner, R. J.; Bozano, L. D.; Micheel, C. M.; Hung, A. M.; Fornof, A. R.; Cha, J. N.; Rettner, C. T.; Bersani, M.; Frommer, J.; Rothemund, P. W. K.; Wallraff, G. M. Placement and Orientation of Individual DNA Shapes on Lithographically Patterned Surfaces Nat. Nanotechnol. 2009, 4, 557– 561 DOI: 10.1038/nnano.2009.220
      43
      Placement and orientation of individual DNA shapes on lithographically patterned surfaces
      Kershner, Ryan J.; Bozano, Luisa D.; Micheel, Christine M.; Hung, Albert M.; Fornof, Ann R.; Cha, Jennifer N.; Rettner, Charles T.; Bersani, Marco; Frommer, Jane; Rothemund, Paul W. K.; Wallraff, Gregory M.
      Nature Nanotechnology (2009), 4 (9), 557-561CODEN: NNAABX; ISSN:1748-3387. (Nature Publishing Group)
      Artificial DNA nanostructures show promise for the organization of functional materials to create nanoelectronic or nano-optical devices. DNA origami, in which a long single strand of DNA is folded into a shape using shorter staple strands', can display 6-nm-resoln. patterns of binding sites, in principle allowing complex arrangements of carbon nanotubes, silicon nanowires, or quantum dots. However, DNA origami are synthesized in soln. and uncontrolled deposition results in random arrangements; this makes it difficult to measure the properties of attached nanodevices or to integrate them with conventionally fabricated microcircuitry. Here the authors describe the use of electron-beam lithog. and dry oxidative etching to create DNA origami-shaped binding sites on technol. useful materials, such as SiO2 and diamond-like carbon. In buffer with ∼100 mM MgCl2, DNA origami bind with high selectivity and good orientation: 70-95% of sites have individual origami aligned with an angular dispersion ( ± 1 s d.) as low as ±10° (on diamond-like carbon) or ±20° (on SiO2).
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    44. 44
      Yun, J. M.; Kim, K. N.; Kim, J. Y.; Shin, D. O.; Lee, W. J.; Lee, S. H.; Lieberman, M.; Kim, S. O. DNA Origami Nanopatterning on Chemically Modified Graphene Angew. Chem., Int. Ed. 2012, 51, 912– 915 DOI: 10.1002/anie.201106198
      There is no corresponding record for this reference.
    45. 45
      Zhang, X. N.; Rahman, M.; Neff, D.; Norton, M. L. DNA Origami Deposition on Native and Passivated Molybdenum Disulfide Substrates Beilstein J. Nanotechnol. 2014, 5, 501– 506 DOI: 10.3762/bjnano.5.58
      45
      DNA origami deposition on native and passivated molybdenum disulfide substrates
      Zhang, Xiaoning; Rahman, Masudur; Neff, David; Norton, Michael L.
      Beilstein Journal of Nanotechnology (2014), 5 (), 501-506, 6 pp.CODEN: BJNEAH; ISSN:2190-4286. (Beilstein-Institut zur Foerderung der Chemischen Wissenschaften)
      Maintaining the structural fidelity of DNA origami structures on substrates is a prerequisite for the successful fabrication of hybrid DNA origami/semiconductor-based biomedical sensor devices. Molybdenum disulfide (MoS2) is an ideal substrate for such future sensors due to its exceptional elec., mech. and structural properties. In this work, we performed the first investigations into the interaction of DNA origami with the MoS2 surface. In contrast to the structure-preserving interaction of DNA origami with mica, another atomically flat surface, it was obsd. that DNA origami structures rapidly lose their structural integrity upon interaction with MoS2. In a further series of studies, pyrene and 1-pyrenemethylamine, were evaluated as surface modifications which might mitigate this effect. While both species were found to form adsorption layers on MoS2 via physisorption, 1-pyrenemethyamine serves as a better protective agent and preserves the structures for significantly longer times. These findings will be benefcial for the fabrication of future DNA origami/MoS2 hybrid electronic structures.
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    46. 46
      Bell, N. A. W.; Keyser, U. F. Nanopores Formed by DNA Origami: A Review FEBS Lett. 2014, 588, 3564– 3570 DOI: 10.1016/j.febslet.2014.06.013
      46
      Nanopores formed by DNA origami: A review
      Bell, Nicholas A. W.; Keyser, Ulrich F.
      FEBS Letters (2014), 588 (19), 3564-3570CODEN: FEBLAL; ISSN:0014-5793. (Elsevier B.V.)
      A review. Nanopores have emerged over the past two decades to become an important technique in single mol. exptl. physics and biomol. sensing. Recently DNA nanotechnol., in particular DNA origami, has been used for the formation of nanopores in insulating materials. DNA origami is a very attractive technique for the formation of nanopores since it enables the construction of 3D shapes with precise control over geometry and surface functionality. DNA origami has been applied to nanopore research by forming hybrid architectures with solid state nanopores and by direct insertion into lipid bilayers. This review discusses recent exptl. work in this area and provides an outlook for future avenues and challenges.
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    47. 47
      Kale, L.; Skeel, R.; Bhandarkar, M.; Brunner, R.; Gursoy, A.; Krawetz, N.; Phillips, J.; Shinozaki, A.; Varadarajan, K.; Schulten, K. Namd2: Greater Scalability for Parallel Molecular Dynamics J. Comput. Phys. 1999, 151, 283– 312 DOI: 10.1006/jcph.1999.6201
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      NAMD2: Greater Scalability for Parallel Molecular Dynamics
      Kale, Laxmikant; Skeel, Robert; Bhandarkar, Milind; Brunner, Robert; Gursoy, Attila; Krawetz, Neal; Phillips, James; Shinozaki, Aritomo; Varadarajan, Krishnan; Schulten, Klaus
      Journal of Computational Physics (1999), 151 (1), 283-312CODEN: JCTPAH; ISSN:0021-9991. (Academic Press)
      Mol. dynamics programs simulate the behavior of biomol. systems, leading to understanding of their functions. However, the computational complexity of such simulations is enormous. Parallel machines provide the potential to meet this computational challenge. To harness this potential, it is necessary to develop a scalable program. It is also necessary that the program be easily modified by application-domain programmers. The NAMD2 program presented in this paper seeks to provide these desirable features. It uses spatial decompn. combined with force decompn. to enhance scalability. It uses intelligent periodic load balancing, so as to maximally utilize the available compute power. It is modularly organized, and implemented using Charm++, a parallel C++ dialect, so as to enhance its modifiability. It uses a combination of numerical techniques and algorithms to ensure that energy drifts are minimized, ensuring accuracy in long running calcns. NAMD2 uses a portable run-time framework called Converse that also supports interoperability among multiple parallel paradigms. As a result, different components of applications can be written in the most appropriate parallel paradigms. NAMD2 runs on most parallel machines including workstation clusters and has yielded speedups in excess of 180 on 220 processors. This paper also describes the performance obtained on some benchmark applications. (c) 1999 Academic Press.
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    48. 48
      Humphrey, W.; Dalke, A.; Schulten, K. Vmd: Visual Molecular Dynamics J. Mol. Graphics 1996, 14, 33– 38 DOI: 10.1016/0263-7855(96)00018-5
      48
      VDM: visual molecular dynamics
      Humphrey, William; Dalke, Andrew; Schulten, Klaus
      Journal of Molecular Graphics (1996), 14 (1), 33-8, plates, 27-28CODEN: JMGRDV; ISSN:0263-7855. (Elsevier)
      VMD is a mol. graphics program designed for the display and anal. of mol. assemblies, in particular, biopolymers such as proteins and nucleic acids. VMD can simultaneously display any no. of structures using a wide variety of rendering styles and coloring methods. Mols. are displayed as one or more "representations," in which each representation embodies a particular rendering method and coloring scheme for a selected subset of atoms. The atoms displayed in each representation are chosen using an extensive atom selection syntax, which includes Boolean operators and regular expressions. VMD provides a complete graphical user interface for program control, as well as a text interface using the Tcl embeddable parser to allow for complex scripts with variable substitution, control loops, and function calls. Full session logging is supported, which produces a VMD command script for later playback. High-resoln. raster images of displayed mols. may be produced by generating input scripts for use by a no. of photorealistic image-rendering applications. VMD has also been expressly designed with the ability to animate mol. dynamics (MD) simulation trajectories, imported either from files or from a direct connection to a running MD simulation. VMD is the visualization component of MDScope, a set of tools for interactive problem solving in structural biol., which also includes the parallel MD program NAMD, and the MDCOMM software used to connect the visualization and simulation programs, VMD is written in C++, using an object-oriented design; the program, including source code and extensive documentation, is freely available via anonymous ftp and through the World Wide Web.
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    49. 49
      Douglas, S. M.; Marblestone, A. H.; Teerapittayanon, S.; Vazquez, A.; Church, G. M.; Shih, W. M. Rapid Prototyping of 3d DNA-Origami Shapes with Cadnano Nucleic Acids Res. 2009, 37, 5001– 5006 DOI: 10.1093/nar/gkp436
      49
      Rapid prototyping of 3D DNA-origami shapes with caDNAno
      Douglas, Shawn M.; Marblestone, Adam H.; Teerapittayanon, Surat; Vazquez, Alejandro; Church, George M.; Shih, William M.
      Nucleic Acids Research (2009), 37 (15), 5001-5006CODEN: NARHAD; ISSN:0305-1048. (Oxford University Press)
      DNA nanotechnol. exploits the programmable specificity afforded by base-pairing to produce self-assembling macromol. objects of custom shape. For building megadalton-scale DNA nanostructures, a long scaffold' strand can be employed to template the assembly of hundreds of oligonucleotide staple' strands into a planar antiparallel array of cross-linked helixes. The authors recently adapted this scaffolded DNA origami' method to producing 3-dimensional shapes formed as pleated layers of double helixes constrained to a honeycomb lattice. However, completing the required design steps can be cumbersome and time-consuming. Here the authors present caDNAno, an open-source software package with a graphical user interface that aids in the design of DNA sequences for folding 3-dimensional honeycomb-pleated shapes rectangular-block motifs were designed, assembled, and analyzed to identify a well-behaved motif that could serve as a building block for future studies. The use of caDNAno significantly reduces the effort required to design 3-dimensional DNA-origami structures. The software is available at http://cadnano.org/, along with example designs and video tutorials demonstrating their construction. The source code is released under the MIT license.
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    50. 50
      Ryckaert, J. P.; Ciccotti, G.; Berendsen, H. J. C. Numerical-Integration of Cartesian Equations of Motion of a System with Constraints - Molecular-Dynamics of N-Alkanes J. Comput. Phys. 1977, 23, 327– 341 DOI: 10.1016/0021-9991(77)90098-5
      50
      Numerical integration of the Cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes
      Ryckaert, Jean Paul; Ciccotti, Giovanni; Berendsen, Herman J. C.
      Journal of Computational Physics (1977), 23 (3), 327-41CODEN: JCTPAH; ISSN:0021-9991.
      A numerical algorithm integrating the 3N Cartesian equation of motion of a system of N points subject to holonomic constraints is applied to mol. dynamics simulation of a liq. of 64 butane mols.
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    51. 51
      MacKerell, A. D.; Banavali, N. K. All-Atom Empirical Force Field for Nucleic Acids: Ii. Application to Molecular Dynamics Simulations of DNA and Rna in Solution J. Comput. Chem. 2000, 21, 105– 120 DOI: 10.1002/(SICI)1096-987X(20000130)21:2<105::AID-JCC3>3.0.CO;2-P
      51
      All-atom empirical force field for nucleic acids: II. Application to molecular dynamics simulations of DNA and RNA in solution
      Mackerell, Alexander D.; Banavali, Nilesh K.
      Journal of Computational Chemistry (2000), 21 (2), 105-120CODEN: JCCHDD; ISSN:0192-8651. (John Wiley & Sons, Inc.)
      Mol. dynamics simulations based on empirical force fields can greatly enhance knowledge of DNA and RNA structure and dynamics in soln. Presented are results on simulations of three DNA sequences and one RNA sequence using the new all-atom CHARMM27 force field for nucleic acids presented in the accompanying manuscript (Foloppe, MacKerell, J Comput Chem, this issue). Data are reported on structural, dynamic, and hydration properties including dihedral angle, sugar puckering, and helicoidal parameter probability distributions. Also presented are calcns. of a DNA hexamer in 0 and 75% ethanol starting from both the canonical A and B forms. Anal. of RMS differences with respect to the canonical A and B forms of DNA show a highly anticorrelated behavior indicating that the force field samples the equil. between the A and B forms of DNA. Proper stabilization of B form DNA in aq. soln. and A form DNA in 75% ethanol show that this equil. can be perturbed by environmental contributions. Success of the force field in reproducing a variety of exptl. data for duplex DNA and RNA indicates that it is of general use for computational investigations of nucleic acids as well as nucleic acids in complexes with proteins and lipids.
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    52. 52
      Darden, T.; York, D.; Pedersen, L. Particle Mesh Ewald - an N.Log(N) Method for Ewald Sums in Large Systems J. Chem. Phys. 1993, 98, 10089– 10092 DOI: 10.1063/1.464397
      52
      Particle mesh Ewald: an N·log(N) method for Ewald sums in large systems
      Darden, Tom; York, Darrin; Pedersen, Lee
      Journal of Chemical Physics (1993), 98 (12), 10089-92CODEN: JCPSA6; ISSN:0021-9606.
      An N·log(N) method for evaluating electrostatic energies and forces of large periodic systems is presented. The method is based on interpolation of the reciprocal space Ewald sums and evaluation of the resulting convolution using fast Fourier transforms. Timings and accuracies are presented for three large cryst. ionic systems.
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    53. 53
      Nose, S. A Unified Formulation of the Constant Temperature Molecular-Dynamics Methods J. Chem. Phys. 1984, 81, 511– 519 DOI: 10.1063/1.447334
      53
      A unified formulation of the constant-temperature molecular-dynamics methods
      Nose, Shuichi
      Journal of Chemical Physics (1984), 81 (1), 511-19CODEN: JCPSA6; ISSN:0021-9606.
      Three recently proposed const. temp. mol. dynamics methods [N., (1984) (1); W. G. Hoover et al., (1982) (2); D. J. Evans and G. P. Morris, (1983) (2); and J. M. Haile and S. Gupta, 1983) (3)] are examd. anal. via calcg. the equil. distribution functions and comparing them with that of the canonical ensemble. Except for effects due to momentum and angular momentum conservation, method (1) yields the rigorous canonical distribution in both momentum and coordinate space. Method (2) can be made rigorous in coordinate space, and can be derived from method (1) by imposing a specific constraint. Method (3) is not rigorous and gives a deviation of order N-1/2 from the canonical distribution (N the no. of particles). The results for the const. temp.-const. pressure ensemble are similar to the canonical ensemble case.
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    54. 54
      Hoover, W. G. Canonical Dynamics - Equilibrium Phase-Space Distributions Phys. Rev. A: At., Mol., Opt. Phys. 1985, 31, 1695– 1697 DOI: 10.1103/PhysRevA.31.1695
      54
      Canonical dynamics: Equilibrium phase-space distributions
      Hoover
      Physical review. A, General physics (1985), 31 (3), 1695-1697 ISSN:0556-2791.
      There is no expanded citation for this reference.
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    55. 55
      Brunger, A. T.; Adams, P. D.; Clore, G. M.; DeLano, W. L.; Gros, P.; Grosse-Kunstleve, R. W.; Jiang, J. S.; Kuszewski, J.; Nilges, M.; Pannu, N. S.; Read, R. J.; Rice, L. M.; Simonson, T.; Warren, G. L. Crystallography & Nmr System: A New Software Suite for Macromolecular Structure Determination Acta Crystallogr., Sect. D: Biol. Crystallogr. 1998, 54, 905– 921 DOI: 10.1107/S0907444998003254
      55
      Crystallography & NMR System: a new software suite for macromolecular structure determination
      Brunger, Axel T.; Adams, Paul D.; Clore, G. Marius; DeLano, Warren L.; Gros, Piet; Grosse-Kunstleve, Ralf W.; Jiang, Jian-Sheng; Kuszewski, John; Nilges, Michael; Pannu, Navraj S.; Read, Randy J.; Rice, Luke M.; Simonson, Thomas; Warren, Gregory L.
      Acta Crystallographica, Section D: Biological Crystallography (1998), D54 (5), 905-921CODEN: ABCRE6; ISSN:0907-4449. (Munksgaard International Publishers Ltd.)
      A new software suite, called Crystallog. & NMR System (CNS), has been developed for macromol. structure detn. by x-ray crystallog. or soln. NMR (NMR) spectroscopy. In contrast to existing structure-detn. programs the architecture of CNS is highly flexible, allowing for extension to other structure-detn. methods, such as electron microscopy and solid-state NMR spectroscopy. CNS has a hierarchical structure: a high-level hypertext markup language (HTML) user interface, task-oriented user input files, module files, a symbolic structure-detn. language (CNS language), and low-level source code. Each layer is accessible to the user. The novice user may just use the HTML interface, while the more advanced user may use any of the other layers. The source code will be distributed, thus source-code modification is possible. The CNS language is sufficiently powerful and flexible that many new algorithms can be easily implemented in the CNS language without changes to the source code. The CNS language allows the user to perform operations on data structures, such as structure factors, electron-d. maps, and at. properties. The power of the CNS language has been demonstrated by the implementation of a comprehensive set of crystallog. procedures for phasing, d. modification and refinement. User-friendly task-oriented input files are available for nearly all aspects of macromol. structure detn. by x-ray crystallog. and soln. NMR.
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    56. 56
      Wells, D. B.; Belkin, M.; Comer, J.; Aksimentiev, A. Assessing Graphene Nanopores for Sequencing DNA Nano Lett. 2012, 12, 4117– 4123 DOI: 10.1021/nl301655d
      56
      Assessing Graphene Nanopores for Sequencing DNA
      Wells, David B.; Belkin, Maxim; Comer, Jeffrey; Aksimentiev, Aleksei
      Nano Letters (2012), 12 (8), 4117-4123CODEN: NALEFD; ISSN:1530-6984. (American Chemical Society)
      Using all-atom mol. dynamics and at.-resoln. Brownian dynamics, we simulate the translocation of single-stranded DNA through graphene nanopores and characterize the ionic current blockades produced by DNA nucleotides. We find that transport of single DNA strands through graphene nanopores may occur in single nucleotide steps. For certain pore geometries, hydrophobic interactions with the graphene membrane lead to a dramatic redn. in the conformational fluctuations of the nucleotides in the nanopores. Furthermore, we show that ionic current blockades produced by different DNA nucleotides are, in general, indicative of the nucleotide type, but very sensitive to the orientation of the nucleotides in the nanopore. Taken together, our simulations suggest that strand sequencing of DNA by measuring the ionic current blockades in graphene nanopores may be possible, given that the conformation of DNA nucleotides in the nanopore can be controlled through precise engineering of the nanopore surface.
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    57. 57
      Wanunu, M.; Dadosh, T.; Ray, V.; Jin, J. M.; McReynolds, L.; Drndic, M. Rapid Electronic Detection of Probe-Specific Micrornas Using Thin Nanopore Sensors Nat. Nanotechnol. 2010, 5, 807– 814 DOI: 10.1038/nnano.2010.202
      57
      Rapid electronic detection of probe-specific microRNAs using thin nanopore sensors
      Wanunu, Meni; Dadosh, Tali; Ray, Vishva; Jin, Jingmin; McReynolds, Larry; Drndic, Marija
      Nature Nanotechnology (2010), 5 (11), 807-814CODEN: NNAABX; ISSN:1748-3387. (Nature Publishing Group)
      Small RNA mols. have an important role in gene regulation and RNA silencing therapy, but it is challenging to detect these mols. without the use of time-consuming radioactive labeling assays or error-prone amplification methods. Here, we present a platform for the rapid electronic detection of probe-hybridized microRNAs from cellular RNA. In this platform, a target microRNA is first hybridized to a probe. This probe:microRNA duplex is then enriched through binding to the viral protein p19. Finally, the abundance of the duplex is quantified using a nanopore. Reducing the thickness of the membrane contg. the nanopore to 6 nm leads to increased signal amplitudes from biomols., and reducing the diam. of the nanopore to 3 nm allows the detection and discrimination of small nucleic acids based on differences in their phys. dimensions. We demonstrate the potential of this approach by detecting picogram levels of a liver-specific miRNA from rat liver RNA.
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    58. 58
      Kowalczyk, S. W.; Grosberg, A. Y.; Rabin, Y.; Dekker, C. Modeling the Conductance and DNA Blockade of Solid-State Nanopores. Nanotechnology 2011, 22. 315101 DOI: 10.1088/0957-4484/22/31/315101
      58
      Modeling the conductance and DNA blockade of solid-state nanopores
      Kowalczyk, Stefan W.; Grosberg, Alexander Y.; Rabin, Yitzhak; Dekker, Cees
      Nanotechnology (2011), 22 (31), 315101/1-315101/5, S315101/1-S315101/11CODEN: NNOTER; ISSN:1361-6528. (Institute of Physics Publishing)
      We present measurements and theor. modeling of the ionic conductance G of solid-state nanopores with 5-100 nm diams., with and without DNA inserted into the pore. First, we show that it is essential to include access resistance to describe the conductance, in particular for larger pore diams. We then present an exact soln. for G of an hourglass-shaped pore, which agrees very well with our measurements without any adjustable parameters, and which is an improvement over the cylindrical approxn. Subsequently we discuss the conductance blockade ΔG due to the insertion of a DNA mol. into the pore, which we study exptl. as a function of pore diam. We find that ΔG decreases with pore diam., contrary to the predictions of earlier models that forecasted a const. ΔG. We compare three models for ΔG, all of which provide good agreement with our exptl. data.
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    59. 59
      Plesa, C.; Ananth, A. N.; Linko, V.; Gulcher, C.; Katan, A. J.; Dietz, H.; Dekker, C. Ionic Permeability and Mechanical Properties of DNA Origami Nanoplates on Solid-State Nanopores ACS Nano 2014, 8, 35– 43 DOI: 10.1021/nn405045x
      59
      Ionic Permeability and Mechanical Properties of DNA Origami Nanoplates on Solid-State Nanopores
      Plesa, Calin; Ananth, Adithya N.; Linko, Veikko; Guelcher, Coen; Katan, Allard J.; Dietz, Hendrik; Dekker, Cees
      ACS Nano (2014), 8 (1), 35-43CODEN: ANCAC3; ISSN:1936-0851. (American Chemical Society)
      While DNA origami is a popular and versatile platform, its structural properties are still poorly understood. In this study we use solid-state nanopores to investigate the ionic permeability and mech. properties of DNA origami nanoplates. DNA origami nanoplates of various designs are docked onto solid-state nanopores where we subsequently measure their ionic conductance. The ionic permeability is found to be high for all origami nanoplates. We observe the conductance of docked nanoplates, relative to the bare nanopore conductance, to increase as a function of pore diam., as well as to increase upon lowering the ionic strength. The honeycomb lattice nanoplate is found to have slightly better overall performance over other plate designs. After docking, we often observe spontaneous discrete jumps in the current, a process which can be attributed to mech. buckling. All nanoplates show a nonlinear current-voltage dependence with a lower conductance at higher applied voltages, which we attribute to a phys. bending deformation of the nanoplates under the applied force. At sufficiently high voltage (force), the nanoplates are strongly deformed and can be pulled through the nanopore. These data show that DNA origami nanoplates are typically very permeable to ions and exhibit a no. of unexpected mech. properties, which are interesting in their own right, but also need to be considered in the future design of DNA origami nanostructures.
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    60. 60
      Hernandez-Ainsa, S.; Misiunas, K.; Thacker, V. V.; Hemmig, E. A.; Keyser, U. F. Voltage-Dependent Properties of DNA Origami Nanopores Nano Lett. 2014, 14, 1270– 1274 DOI: 10.1021/nl404183t
      There is no corresponding record for this reference.
    61. 61
      Aksimentiev, A.; Schulten, K. Imaging Alpha-Hemolysin with Molecular Dynamics: Ionic Conductance, Osmotic Permeability, and the Electrostatic Potential Map Biophys. J. 2005, 88, 3745– 3761 DOI: 10.1529/biophysj.104.058727
      61
      Imaging α-hemolysin with molecular dynamics: Ionic conductance, osmotic permeability, and the electrostatic potential map
      Aksimentiev, Aleksij; Schulten, Klaus
      Biophysical Journal (2005), 88 (6), 3745-3761CODEN: BIOJAU; ISSN:0006-3495. (Biophysical Society)
      α-Hemolysin of Staphylococcus aureus is a self-assembling toxin that forms a water-filled transmembrane channel upon oligomerization in a lipid membrane. Apart from being one of the best-studied toxins of bacterial origin, α-hemolysin is the principal component in several biotechnol. applications, including systems for controlled delivery of small solutes across lipid membranes, stochastic sensors for small solutes, and an alternative to conventional technol. for DNA sequencing. Through large-scale mol. dynamics simulations, we studied the permeability of the α-hemolysin/lipid bilayer complex for water and ions. The studied system, composed of ∼300,000 atoms, included one copy of the protein, a patch of a DPPC lipid bilayer, and a 1 M water soln. of KCl. Monitoring the fluctuations of the pore structure revealed an asym., on av., cross section of the α-hemolysin stem. Applying external electrostatic fields produced a transmembrane ionic current; repeating simulations at several voltage biases yielded a current/voltage curve of α-hemolysin and a set of electrostatic potential maps. The selectivity of α-hemolysin to Cl- was found to depend on the direction and the magnitude of the applied voltage bias. The results of our simulations are in excellent quant. agreement with available exptl. data. Analyzing trajectories of all water mol., we computed the α-hemolysin's osmotic permeability for water as well as its electroosmotic effect, and characterized the permeability of its seven side channels. The side channels were found to connect seven His-144 residues surrounding the stem of the protein to the bulk soln.; the protonation of these residues was obsd. to affect the ion conductance, suggesting the seven His-144 to comprise the pH sensor that gates conductance of the α-hemolysin channel.
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    62. 62
      Essmann, U.; Perera, L.; Berkowitz, M. L.; Darden, T.; Lee, H.; Pedersen, L. G. A Smooth Particle Mesh Ewald Method J. Chem. Phys. 1995, 103, 8577– 8593 DOI: 10.1063/1.470117
      62
      A smooth particle mesh Ewald method
      Essmann, Ulrich; Perera, Lalith; Berkowitz, Max L.; Darden, Tom; Lee, Hsing; Pedersen, Lee G.
      Journal of Chemical Physics (1995), 103 (19), 8577-93CODEN: JCPSA6; ISSN:0021-9606. (American Institute of Physics)
      The previously developed particle mesh Ewald method is reformulated in terms of efficient B-spline interpolation of the structure factors. This reformulation allows a natural extension of the method to potentials of the form 1/rp with p ≥ 1. Furthermore, efficient calcn. of the virial tensor follows. Use of B-splines in the place of Lagrange interpolation leads to analytic gradients as well as a significant improvement in the accuracy. The authors demonstrate that arbitrary accuracy can be achieved, independent of system size N, at a cost that scales as N log(N). For biomol. systems with many thousands of atoms and this method permits the use of Ewald summation at a computational cost comparable to that of a simple truncation method of 10 Å or less.
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    63. 63
      Meller, A.; Nivon, L.; Brandin, E.; Golovchenko, J.; Branton, D. Rapid Nanopore Discrimination between Single Polynucleotide Molecules Proc. Natl. Acad. Sci. U. S. A. 2000, 97, 1079– 1084 DOI: 10.1073/pnas.97.3.1079
      63
      Rapid nanopore discrimination between single polynucleotide molecules
      Meller, Amit; Nivon, Lucas; Brandin, Eric; Golovchenko, Jene; Branton, Daniel
      Proceedings of the National Academy of Sciences of the United States of America (2000), 97 (3), 1079-1084CODEN: PNASA6; ISSN:0027-8424. (National Academy of Sciences)
      A variety of different DNA polymers were electrophoretically driven through the nanopore of an α-hemolysin channel in a lipid bilayer. Single-channel recording of the translocation duration and current flow during traversal of individual polynucleotides yielded a unique pattern of events for each of the several polymers tested. Statistical data derived from this pattern of events demonstrate that in several cases a nanopore can distinguish between polynucleotides of similar length and compn. that differ only in sequence. Studies of temp. effects on the translocation process show that translocation duration scales as ∼T-2. A strong correlation exists between the temp. dependence of the event characteristics and the tendency of some polymers to form secondary structure. Because nanopores can rapidly discriminate and characterize unlabeled DNA mols. at low copy no., refinements of the exptl. approach demonstrated here could eventually provide a low-cost high-throughput method of analyzing DNA polynucleotides.
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    64. 64
      Krishnakumar, P.; Gyarfas, B.; Song, W. S.; Sen, S.; Zhang, P. M.; Krstic, P.; Lindsay, S. Slowing DNA Trans Location through a Nanopore Using a Functionalized Electrode ACS Nano 2013, 7, 10319– 10326 DOI: 10.1021/nn404743f
      There is no corresponding record for this reference.
    65. 65
      Feng, J. D.; Liu, K.; Bulushev, R. D.; Khlybov, S.; Dumcenco, D.; Kis, A.; Radenovic, A. Identification of Single Nucleotides in Mos2 Nanopores Nat. Nanotechnol. 2015, 10, 1070– 1076 DOI: 10.1038/nnano.2015.219
      65
      Identification of single nucleotides in MoS2 nanopores
      Feng, Jiandong; Liu, Ke; Bulushev, Roman D.; Khlybov, Sergey; Dumcenco, Dumitru; Kis, Andras; Radenovic, Aleksandra
      Nature Nanotechnology (2015), 10 (12), 1070-1076CODEN: NNAABX; ISSN:1748-3387. (Nature Publishing Group)
      The size of the sensing region in solid-state nanopores is detd. by the size of the pore and the thickness of the pore membrane, so ultrathin membranes such as graphene and single-layer molybdenum disulfide could potentially offer the necessary spatial resoln. for nanopore DNA sequencing. However, the fast translocation speeds (3,000-50,000 nt ms-1) of DNA mols. moving across such membranes limit their usability. Here, we show that a viscosity gradient system based on room-temp. ionic liqs. can be used to control the dynamics of DNA translocation through MoS2 nanopores. The approach can be used to statistically detect all four types of nucleotide, which are identified according to current signatures recorded during their transient residence in the narrow orifice of the atomically thin MoS2 nanopore. Our technique, which exploits the high viscosity of room-temp. ionic liqs., provides optimal single nucleotide translocation speeds for DNA sequencing, while maintaining a signal-to-noise ratio higher than 10.
      >> More from SciFinder ®
      https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2MXhsFaqtb7P&md5=777cbd29b760c158dd68bdc9b92c736a

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    The Supporting Information is available free of charge on the ACS Publications website at DOI: 10.1021/acsami.6b11001.

    • Calculation of resistivity and conductivity of different nanopore architectures, the design and structure of single-layer and double-layer DNA origami nanopore, density of bases around the pore mouth, motion of DNA origami on top of graphene under external biases, sandwiched DNA origami–graphene hybrid nanopore analysis and I–V curve of hybrid nanopore solvated in 1 M KCl aqueous solution. (PDF)


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