Skip to main content
SpringerLink
Log in

Bar Coding Platforms for Nucleic Acid and Protein Detection

  • Chapter
Microarrays

Part of the book series: Integrated Analytical Systems ((ANASYS))

  • 1342 Accesses

Abstract

A variety of novel bar coding systems has been developed as multiplex testing platforms for applications in biological, chemical, and biomedical diagnostics. Instead of identifying a target through capture at a specific locus on an array, target analytes are captured by a bar coded tag, which then uniquely identifies the target, akin to putting a UPC bar code on a product. This requires an appropriate surface functionalization to ensure that the correct target is captured with high efficiency. Moreover the tag, or bar code, has to be readable with minimal error and at high speed, typically by flow analysis. For quantitative assays the target may be labeled separately, or the tag may also serve as the label. A great variety of materials and physicochemical principles has been exploited to generate this plethora of novel bar coding platforms. Their advantages compared to microarray-based assay platforms include in-solution binding kinetics, flexibility in assay design, compatibility with microplate-based assay automation, high sample throughput, and with some assay formats, increased sensitivity.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 89.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 119.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 169.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  1. Southern, E.M., 1975 Detection of specific sequences among DNA fragments separated by gel electrophoresis. J Mol Biol 98: 503–517.

    CAS  Google Scholar 

  2. Manns, R.L., 2003 Necessity is the mother of invention – The history of microplates. PharmaTech Series Business Briefing: Future Drug Discovery 2003, Business Briefing Ltd, pp. 108–112.

    Google Scholar 

  3. Mendoza, L.G., McQuary, P., Mongan, A., Gangadharan, R., Brignac, S., and Eggers, M., 1999 High-throughput microarray-based enzyme-linked immunosorbent assay (ELISA). Biotechniques 27: 778–780, 782–786, 788.

    CAS  Google Scholar 

  4. Taltech website, Introduction to Bar Coding, http://www.taltech.com/TALtech_web/resources/intro_to_bc/bcsymbol.htm

  5. Worth Data website, Bar Code Basics, http://www.barcodehq.com/primer.html

  6. Woodland, N.J. and Silver, B. 1952. U.S. Patent No. 2,612,994.

    Google Scholar 

  7. Ebach, M.C. and Holdrege, C., 2005 DNA barcoding is no substitute for taxonomy. Nature 434: 697.

    CAS  Google Scholar 

  8. Moritz, C. and Cicero, C., 2004 DNA barcoding: Promise and pitfalls. PLoS Biol 2: e354.

    Google Scholar 

  9. Schindel, D.E. and Miller, S.E., 2005 DNA barcoding a useful tool for taxonomists. Nature 435: 417.

    Google Scholar 

  10. Campbell, J., Francesconi, S., Boyd, J., Worth, L., and Moshier, T., 1999 Aug Environmental air sampling to detect biological warfare agents. Mil Med 164: 541–542.

    CAS  Google Scholar 

  11. Hajibabaei, M., Janzen, D.H., Burns, J.M., Hallwachs, W., and Hebert, P.D., 2006 DNA barcodes distinguish species of tropical Lepidoptera. Proc Natl Acad Sci U S A 103: 968–971.

    Google Scholar 

  12. Kress, W.J., Wurdack, K.J., Zimmer, E.A., Weigt, L.A., and Janzen, D.H., 2005 Use of DNA barcodes to identify flowering plants. Proc Natl Acad Sci U S A 102: 8369–8374.

    CAS  Google Scholar 

  13. Lorenz, J.G., Jackson, W.E., Beck, J.C., and Hanner, R., 2005 The problems and promise of DNA barcodes for species diagnosis of primate biomaterials. Philos Trans R Soc Lond B Biol Sci 360: 1869–1877.

    CAS  Google Scholar 

  14. Summerbell, R.C., Levesque, C.A., Seifert, K.A., Bovers, M., Fell, J.W., Diaz, M.R., Boekhout, T., de Hoog, G.S., Stalpers, J., and Crous, P.W., 2005 Microcoding: The second step in DNA barcoding. Philos Trans R Soc Lond B Biol Sci 360: 1897–1903.

    CAS  Google Scholar 

  15. Blaxter, M., Mann, J., Chapman, T., Thomas, F., Whitton, C., Floyd, R., and Abebe, E., 2005 Defining operational taxonomic units using DNA barcode data. Philos Trans R Soc Lond B Biol Sci 360: 1935–1943.

    CAS  Google Scholar 

  16. DeSalle, R., Egan, M.G., and Siddall, M., 2005 The unholy trinity: Taxonomy, species delimitation and DNA barcoding. Philos Trans R Soc Lond B Biol Sci 360: 1905–1916.

    CAS  Google Scholar 

  17. Savolainen, V., Cowan, R.S., Vogler, A.P., Roderick, G.K., and Lane, R., 2005 Towards writing the encyclopedia of life: An introduction to DNA barcoding. Philos Trans R Soc Lond B Biol Sci 360: 1805–1811.

    CAS  Google Scholar 

  18. Leclair, B. and Scholl, T., 2005 Application of automation and information systems to forensic genetic specimen processing. Expert Rev Mol Diagn 5: 241–250.

    CAS  Google Scholar 

  19. Saji, F., 1993 Application of DNA fingerprinting to obstetrics and gynecology. Nippon Sanka Fujinka Gakkai Zasshi 45: 815–821.

    CAS  Google Scholar 

  20. Sullivan, K.M., Hopgood, R., and Gill, P., 1992 Identification of human remains by amplification and automated sequencing of mitochondrial DNA. Int J Legal Med 105: 83–86.

    CAS  Google Scholar 

  21. Caspersson, T., Farber, S., Foley, G.E., Kudynowski, J., Modest, E.J., Simonsson, E., Wagh, U., and Zech, L., 1968 Chemical differentiation along metaphase chromosomes. Exp Cell Res 49: 219–222.

    CAS  Google Scholar 

  22. Chaudhuri, J.P., Vogel, W., Voiculescu, I., and Wolf, U., 1971 A simplified method of demonstrating Giemsa-band pattern in human chromosomes. Humangenetik 14: 83–84.

    CAS  Google Scholar 

  23. Florijn, R.J., Bonden, L.A., Vrolijk, H., Wiegant, J., Vaandrager, J.W., Baas, F., den Dunnen, J.T., Tanke, H.J., van Ommen, G.J., and Raap, A.K., 1995 High-resolution DNA Fiber-FISH for genomic DNA mapping and colour bar-coding of large genes. Hum Mol Genet 4: 831–836.

    CAS  Google Scholar 

  24. Lengauer, C., Speicher, M.R., Popp, S., Jauch, A., Taniwaki, M., Nagaraja, R., Riethman, H.C., Donis-Keller, H., D'Urso, M., Schlessinger, D., and et al.., 1993 Chromosomal bar codes produced by multicolor fluorescence in situ hybridization with multiple YAC clones and whole chromosome painting probes. Hum Mol Genet 2: 505–512.

    CAS  Google Scholar 

  25. Muller, S., Eder, V., and Wienberg, J., 2004 A nonredundant multicolor bar code as a screening tool for rearrangements in neoplasia. Genes Chromosomes Cancer 39: 59–70.

    Google Scholar 

  26. Muller, S. and Wienberg, J., 2001 “Bar-coding” primate chromosomes: Molecular cytogenetic screening for the ancestral hominoid karyotype. Hum Genet 109: 85–94.

    CAS  Google Scholar 

  27. Cox, J.P., 2001 Bar coding objects with DNA. Analyst 126: 545–547.

    CAS  Google Scholar 

  28. Qiu, F., Guo, L., Wen, T.J., Liu, F., Ashlock, D.A., and Schnable, P. S., 2003 DNA sequence-based “bar codes” for tracking the origins of expressed sequence tags from a maize cDNA library constructed using multiple mRNA sources. Plant Physiol 133: 475–481.

    CAS  Google Scholar 

  29. Velculescu, V.E., Zhang, L., Vogelstein, B., and Kinzler, K.W., 1995 Serial analysis of gene expression. Science 270: 484–487.

    CAS  Google Scholar 

  30. Cai, H., White, P.S., Torney, D., Deshpande, A., Wang, Z., Keller, R.A., Marrone, B., and Nolan, J.P., 2000 Flow cytometry-based minisequencing: A new platform for high-throughput single-nucleotide polymorphism scoring. Genomics 66: 135–143.

    CAS  Google Scholar 

  31. Fan, J.B., Chen, X., Halushka, M.K., Berno, A., Huang, X., Ryder, T., Lipshutz, R.J., Lockhart, D.J., and Chakravarti, A., 2000 Parallel genotyping of human SNPs using generic high-density oligonucleotide tag arrays. Genome Res 10: 853–860.

    CAS  Google Scholar 

  32. Haff, L.A. and Smirnov, I.P., 1997 Multiplex genotyping of PCR products with MassTag-labeled primers. Nucleic Acids Res 25: 3749–3750.

    CAS  Google Scholar 

  33. Yan, H., LaBean, T.H., Feng, L., and Reif, J.H., 2003 Directed nucleation assembly of DNA tile complexes for barcode-patterned lattices. Proc Natl Acad Sci U S A 100: 8103–8108.

    CAS  Google Scholar 

  34. Li, Y., Cu, Y.T.H., and Luo, D., 2005. Multiplexed detection of pathogen DNA with DNA-based fluorescence nanobarcodes. Nat. Biotechnol 23: 885–889.

    CAS  Google Scholar 

  35. Müller, U.R. 1998. U.S. Patent No. 5,824,478.

    Google Scholar 

  36. Cruickshank, K.A., Olvera, J., and Müller, U.R., 1998 Simultaneous multiple analyte detection using fluorescent peptides and capillary isoelectric focusing. J Chromatogr A 817: 41–47.

    CAS  Google Scholar 

  37. Hofmann, O., Che, D., Cruickshank, K.A., and Müller, U.R., 1999 Adaptation of capillary isoelectric focusing to microchannels on a glass chip. Anal Chem 71: 678–686.

    CAS  Google Scholar 

  38. Horan, P.K. and Wheeless, L.L., Jr, 1977 Quantitative single cell analysis and sorting. Science 198: 149–157.

    CAS  Google Scholar 

  39. McHugh, T.M., Miner, R.C., Logan, L.H., and Stites, D.P., 1988 Simultaneous detection of antibodies to cytomegalovirus and herpes simplex virus by using flow cytometry and a microsphere-based fluorescence immunoassay. J Clin Microbiol 26: 1957–1961.

    CAS  Google Scholar 

  40. Baetens, D.G. and Van Renterghem, L.M., 2001 Coupled particle light scattering: a new technique for serodiagnosis of Epstein-Barr virus infection. J Med Virol 64: 519–525.

    CAS  Google Scholar 

  41. Benecky, M.J., Post, D.R., Schmitt, S.M., and Kochar, M.S., 1997 Detection of hepatitis B surface antigen in whole blood by coupled particle light scattering (Copalis). Clin Chem 43: 1764–1770.

    CAS  Google Scholar 

  42. Benecky, M.J., McKinney, K.L., Peterson, K.M., and Kamerud, J.Q., 1998 Simultaneous detection of multiple analytes using Copalis technology: A reduction to practice. Clin Chem 44: 2052–2054.

    CAS  Google Scholar 

  43. Pris, A.D. and Porter, M.D., 2004 Nanoparticle coding: Size-based assays using atomic force microscopy. Langmuir 20: 6969–6973.

    CAS  Google Scholar 

  44. Link, S. and El-Sayed, M.A., 2003 Optical properties and ultrafast dynamics of metallic nanocrystals. Annu Rev Phys Chem 54: 331–366.

    CAS  Google Scholar 

  45. Yguerabide, J. and Yguerabide, E.E., 1998a Light-scattering submicroscopic particles as highly fluorescent analogs and their use as tracer labels in clinical and biological applications. II. Experimental Characterization. Anal Biochem 262: 157–176.

    CAS  Google Scholar 

  46. Yguerabide, J. and Yguerabide, E.E., 1998b Light-scattering submicroscopic particles as highly fluorescent analogs and their use as tracer labels in clinical and biological applications. I. Theory. Anal Biochem 262: 137–156.

    CAS  Google Scholar 

  47. Yguerabide, J. and Yguerabide, E.E., 2001 Resonance light scattering particles as ultrasensitive labels for detection of analytes in a wide range of applications. J Cell Biochem Suppl 37: 71–81.

    Google Scholar 

  48. Elghanian, R., Storhoff, J.J., Mucic, R.C., Letsinger, R.L., and Mirkin, C.A., 1997 Selective colorimetric detection of polynucleotides based on the distance-dependent optical properties of gold nanoparticles. Science 277: 1078–1081.

    CAS  Google Scholar 

  49. Storhoff, J.J., Lucas, A.D., Garimella, V., Bao, Y.P., and Müller, U.R., 2004a Homogeneous detection of unamplified genomic DNA sequences based on colorimetric scatter of gold nano-particle probes. Nat Biotechnol 22: 883–887.

    CAS  Google Scholar 

  50. Evans, M., Sewter, C., and Hill, E., 2003 An encoded particle array tool for multiplex bio-assays. Assay Drug Dev Technol 1: 199–207.

    CAS  Google Scholar 

  51. Smartbead Technologies website, UltraPlexTM Barcodes Molecules. http://www.smartbead.com

  52. Finkel, N.H., Lou, X., Wang, C., and He, L., 2004 Barcoding the microworld. Anal Chem 76: 352A–359A.

    CAS  Google Scholar 

  53. Penn, S.G., He, L., and Natan, M.J., 2003 Nanoparticles for bioanalysis. Curr Opin Chem Biol 7: 609–615.

    CAS  Google Scholar 

  54. Zhou, H., Roy, S., Schulman, H., and Natan, M.J., 2001 Solution and chip arrays in protein profiling. Trends Biotechnol 19: S34–39.

    CAS  Google Scholar 

  55. Nicewarner-Pena, S.R., Freeman, R.G., Reiss, B.D., He, L., Pena, D.J., Walton, I.D., Cromer, R., Keating, C.D., and Natan, M.J., 2001 Submicrometer metallic barcodes. Science 294: 137–141.

    CAS  Google Scholar 

  56. Walton, I.D., Norton, S.M., Balasingham, A., He, L., Oviso, D.F., Jr, Gupta, D., Raju, P.A., Natan, M.J., and Freeman, R.G., 2002 Particles for multiplexed analysis in solution: detection and identification of striped metallic particles using optical microscopy. Anal Chem 74: 2240–2247.

    CAS  Google Scholar 

  57. Freeman, R.G., Raju, P.A., Norton, S.M., Walton, I.D., Smith, P.C., He, L., Natan, M.J., Sha, M.Y., and Penn, S.G., 2005 Use of nanobarcodes particles in bioassays. Methods Mol Biol 303: 73–83.

    CAS  Google Scholar 

  58. Galitonov, G.S., Birtwell, S.W., and Zheludev, N.I., 2006 High capacity tagging using nanos-tructured diffraction barcodes. Optics Express 14: 1382–1387.

    CAS  Google Scholar 

  59. Speicher, M.R., Gwyn Ballard, S., and Ward, D.C., 1996 Apr Karyotyping human chromosomes by combinatorial multi-fluor FISH. Nat Genet 12: 368–375.

    CAS  Google Scholar 

  60. Morrison, L.E. and Legator, M.S., 1997 Two-color ratio-coding of chromosome targets in fluorescence in situ hybridization: Quantitative analysis and reproducibility. Cytometry 27: 314–326.

    CAS  Google Scholar 

  61. Fulton, R.J., McDade, R.L., Smith, P.L., Kienker, L.J., and Kettman, J.R., Jr, 1997 Advanced multiplexed analysis with the FlowMetrix system. Clin Chem 43: 1749–1756.

    CAS  Google Scholar 

  62. Dias, D., Va n Doren, J., Schlottmann, S., Kelly, S., Puchalski, D., Ruiz, W., Boerckel, P., Kessler, J., Antonello, J.M., Green, T., Brown, M., Smith, J., Chirmule, N., Barr, E., Jansen, K.U., and Esser, M.T., 2005 Optimization and validation of a multiplexed luminex assay to quantify antibodies to neutralizing epitopes on human papillomaviruses 6, 11, 16, and 18. Clin Diagn Lab Immunol 12: 959–969.

    CAS  Google Scholar 

  63. Dunbar, S.A., 2006 Applications of Luminex xMAP technology for rapid, high-throughput multiplexed nucleic acid detection. Clin Chim Acta 363: 71–82.

    CAS  Google Scholar 

  64. Hansson, O., Zetterberg, H., Buchhave, P., Londos, E., Blennow, K., and Minthon, L., 2006 Association between CSF biomarkers and incipient Alzheimer's disease in patients with mild cognitive impairment: A follow-up study. Lancet Neurol 5: 228–234.

    CAS  Google Scholar 

  65. Lash, G.E., Scaife, P.J., Innes, B.A., Otun, H.A., Robson, S.C., Searle, R.F., and Bulmer, J.N., 2006 Comparison of three multiplex cytokine analysis systems: Luminex, SearchLight and FAST. Quant J Immunol Meth 309: 205–208.

    CAS  Google Scholar 

  66. Chen, R., Lowe, L., Wilson, J.D., Crowther, E., Tzeggai, K., Bishop, J.E., and Varro, R., 1999 Simultaneous quantification of six human cytokines in a single sample using microparticle-based flow cytometric technology. Clin Chem 45: 1693–1694.

    Google Scholar 

  67. Morgan, E., Varro, R., Sepulveda, H., Ember, J.A., Apgar, J., Wilson, J., Lowe, L., Chen, R., Shivraj, L., Agadir, A., Campos, R., Ernst, D., and Gaur, A., 2004 Cytometric bead array: A multiplexed assay platform with applications in various areas of biology. Clin Immunol 110: 252–266.

    CAS  Google Scholar 

  68. Tarnok, A., Hambsch, J., Chen, R., and Varro, R., 2003 Cytometric bead array to measure six cytokines in twenty-five microliters of serum. Clin Chem 49: 1000–1002.

    CAS  Google Scholar 

  69. Goix, P, 2006. Single molecule “flow immunoassay” detection: Repurposing existing marker for clinical validation. CHI Clinical Biomarker Summit Presentation, San Diego.

    Google Scholar 

  70. Krutzig, P.O. and Nolan, G.P., 2006 Fluorescent cell barcoding in flow cytometry allows high-throughput drug screening and signal profiling. Nature Meth 3: 361–368.

    Google Scholar 

  71. Chan, W.C., Maxwell, D.J., Gao, X., Bailey, R.E., Han, M., and Nie, S., 2002 Luminescent quantum dots for multiplexed biological detection and imaging. Curr Opin Biotechnol 13: 40–46.

    CAS  Google Scholar 

  72. Gao, X., Chan, W.C., and Nie, S., 2002 Quantum-dot nanocrystals for ultrasensitive biological labeling and multicolor optical encoding. J Biomed Opt 7: 532–537.

    CAS  Google Scholar 

  73. Gao, X. and Nie, S., 2005 Quantum dot-encoded beads. Methods Mol Biol 303: 61–71.

    CAS  Google Scholar 

  74. Han, M., Gao, X., Su, J.Z., and Nie, S., 2001 Quantum-dot-tagged microbeads for multiplexed optical coding of biomolecules. Nat Biotechnol 19: 631–635.

    CAS  Google Scholar 

  75. Bhalgat, M.K., Haugland, R.P., Pollack, J.S., Swan, S., and Haugland, R.P., 1998 Green- and red-fluorescent nanospheres for the detection of cell surface receptors by flow cytometry. J Immunol Methods 219: 57–68.

    CAS  Google Scholar 

  76. Wang, L. and Tan, W., 2006 Multicolor FRET silica nanoparticles by single wavelength excitation. Nano Lett 6: 84–88.

    CAS  Google Scholar 

  77. Lian, W., Litherland, S.A., Badrane, H., Tan, W., Wu, D., Baker, H.V., Gulig, P.A., Lim, D.V., and Jin, S., 2004 Ultrasensitive detection of biomolecules with fluorescent dye-doped nano-particles. Anal Biochem 334: 135–144.

    CAS  Google Scholar 

  78. Mattheakis, L.C., Dias, J.M., Choi, Y.J., Gong, J., Bruchez, M.P., Liu, J., and Wang, E., 2004 Optical coding of mammalian cells using semiconductor quantum dots. Anal Biochem 327: 200–208.

    CAS  Google Scholar 

  79. Xu, H., Sha, M.Y., Wong, E.Y., Uphoff, J., Xu, Y., Treadway, J.A., Truong, A., O'Brien, E., Asquith, S., Stubbins, M., Spurr, N.K., Lai, E.H., and Mahoney, W., 2003 Multiplexed SNP genotyping using the Qbead system: A quantum dot-encoded microsphere-based assay. Nucleic Acids Res 31: e43.

    Google Scholar 

  80. Eastman, P.S., Ruan, W., Doctolero, M., Nuttall, R., de Feo, G., Park, J.S., Chu, J.S.F., Cooke, P., Gray, J.W., Li, S., and Chen, F.F., 2006 Qdot nanobarcodes for multiplexed gene expression analysis. Nano Lett 6: 1059–1064.

    CAS  Google Scholar 

  81. Gunderson, K.L., Kruglyak, S., Graige, M.S., Garcia, F., Kermani, B. G., Zhao, C., Che, D., Dickinson, T., Wickham, E., Bierle, J., Doucet, D., Milewski, M., Yang, R., Siegmund, C., Haas, J., Zhou, L., Oliphant, A., Fan, J.B., Barnard, S., and Chee, M.S., 2004 Decoding randomly ordered DNA arrays. Genome Res 14: 870–877.

    CAS  Google Scholar 

  82. Dejneka, M.J., Streltsov, A., Pal, S., Frutos, A.G., Powell, C.L., Yost, K., Yuen, P.K., Müller, U., and Lahiri, J., 2003 Rare earth-doped glass microbarcodes. Proc Natl Acad Sci U S A 100: 389–393.

    CAS  Google Scholar 

  83. Garcia-Vidal, F.J. and Pendry, J.B., 1996 Collective theory for surface enhanced Raman scattering. Phys Rev Lett 77: 1163–6.

    CAS  Google Scholar 

  84. Helmenstine, A., Uziel, M., and Vo-Dinh, T., 1993 Measurement of DNA adducts using surface-enhanced Raman spectroscopy. J Toxicol Environ Health 40: 195–202.

    CAS  Google Scholar 

  85. Nie, S. and Emory, S.R., 1997 Probing single molecules and single nanoparticles by surface-enhanced Raman scattering. Science 275: 1102–1106.

    CAS  Google Scholar 

  86. Isola, N.R., Stokes, D.L., and Vo-Dinh, T., 1998 Surface-enhanced Raman gene probe for HIV detection. Anal Chem 70: 1352–1356.

    CAS  Google Scholar 

  87. Cao, Y.C., Jin, R., and Mirkin, C.A., 2002 Nanoparticles with Raman spectroscopic fingerprints for DNA and RNA detection. Science 297: 1536–1540.

    CAS  Google Scholar 

  88. Cao, Y.C., Jin, R., Nam, J.M., Thaxton, C.S., and Mirkin, C.A., 2003 Raman dye-labeled nanoparticle probes for proteins. J Am Chem Soc 125: 14676–14677.

    CAS  Google Scholar 

  89. Doering, W.E. and Nie, S., 2003 Spectroscopic tags using dye-embedded nanoparticles and surface-enhanced Raman scattering. Anal Chem 75: 6171–6176.

    CAS  Google Scholar 

  90. Faulds, K., Smith, W.E., and Graham, D., 2004 Jan 15 Evaluation of surface-enhanced resonance Raman scattering for quantitative DNA analysis. Anal Chem 76: 412–417.

    CAS  Google Scholar 

  91. Graham, D., Mallinder, B.J., Whitcombe, D., Watson, N.D., and Smith, W.E., 2002 Simple multiplex genotyping by surface-enhanced resonance Raman scattering. Anal Chem 74: 1069–1074.

    CAS  Google Scholar 

  92. Lu, Y., Liu, G.L., Kim, J., Mejia, Y.X., and Lee, L.P., 2005 Nanophotonic crescent moon structures with sharp edge for ultrasensitive biomolecular detection by local electromagnetic field enhancement effect. Nano Lett 5: 119–124.

    CAS  Google Scholar 

  93. Kraemer, T., Antonenko, V.V., Mortezaei, R., Kulikov, N.V. 2002 Encoding technologies. In Handbook of Combinatorial Chemistry: Drugs, Catalysts, Materials, 170–189. Wiley-VCH, Weinheim.

    Google Scholar 

  94. Cain, J.T., Clark, W.W., Schaefer, L.A., Ulinski, D.J., Mickle, M.H., and Mandecki, W.M., 2001 Energy harvesting for DNA gene sifting and sorting. Int J Parallel Distrib Syst Netw 4: 140–149.

    Google Scholar 

  95. Mandecki, W, Pappas, M, Kogan, N, Wang, Z, Zamlynny, B. 2002 Light-powered micro-transponders for high multiple-level analyses of nucleic acids. ACS Symposium Series 815, 57–69.

    CAS  Google Scholar 

  96. Czarnik, A.W., 1997 Encoding strategies in combinatorial chemistry. Proc Natl Acad Sci U S A 94: 12738–12739.

    CAS  Google Scholar 

  97. Ohlmeyer, M.H., Swanson, R.N., Dillard, L.W., Reader, J.C., Asouline, G., Kobayashi, R., Wigler, M., and Still, W.C., 1993 Complex synthetic chemical libraries indexed with molecular tags. Proc Natl Acad Sci U S A 90: 10922–10926.

    CAS  Google Scholar 

  98. Chun, S., Xu, J., Cheng, J., Ding, L., Winograd, N., and Fenniri, H., 2006 Spectroscopically encoded resins for high throughput imaging time-of-flight secondary ion mass spectrometry. J Comb Chem 8: 18–25.

    CAS  Google Scholar 

  99. Fenniri, H., Chun, S., Ding, L., Zyrianov, Y., and Hallenga, K., 2003 Preparation, physical properties, on-bead binding assay and spectroscopic reliability of 25 barcoded polystyrene-poly (ethylene glycol) graft copolymers. J Am Chem Soc 125: 10546–10560.

    CAS  Google Scholar 

  100. Fenniri, H., Terreau, O., Chun, S., Oh, S.J., Finney, W.F., and Morris, M.D., 2006 Classification of spectroscopically encoded resins by Raman mapping and infrared hyper-spectral imaging. J Comb Chem 8: 192–198.

    CAS  Google Scholar 

  101. Su, X., Zhang, J., Sun, L., Koo, T.W., Chan, S., Sundararajan, N., Yamakawa, M., and Berlin, A.A., 2005 Composite organic-inorganic nanoparticles (COINs) with chemically encoded optical signatures. Nano Lett 5: 49–54.

    CAS  Google Scholar 

  102. Brenner, S. and Lerner, R.A., 1992 Encoded combinatorial chemistry. Proc Natl Acad Sci U S A 89: 5381–5383.

    CAS  Google Scholar 

  103. Nam, J.M., Park, S.J., and Mirkin, C.A., 2002 Bio-barcodes based on oligonucleotide-modified nanoparticles. J Am Chem Soc 124: 3820–3821.

    CAS  Google Scholar 

  104. Nam, J.M., Thaxton, C.S., and Mirkin, C.A., 2003 Nanoparticle-based bio-bar codes for the ultrasensitive detection of proteins. Science 301: 1884–1886.

    CAS  Google Scholar 

  105. Storhoff, J.J., Marla, S.S., Bao, P., Hagenow, S., Mehta, H., Lucas, A., Garimella, V., Patno, T.J., Buckingham, W., Cork, W.H., and Müller, U.R., 2004b Gold nanoparticle-based detection of genomic DNA targets on microarrays using a novel optical detection system. Biosens Bioelectron 19: 875–883.

    CAS  Google Scholar 

  106. Georganopoulou, D.G., Chang, L., Nam, J.M., Thaxton, C.S., Mufson, E.J., Klein, W.L., and Mirkin, C.A., 2005 Nanoparticle-based detection in cerebral spinal fluid of a soluble pathogenic biomarker for Alzheimer's disease. Proc Natl Acad Sci U S A 102: 2273–2276.

    CAS  Google Scholar 

  107. Nam, J.M., Stoeva, S.I., and Mirkin, C.A., 2004 Bio-bar-code-based DNA detection with PCR-like sensitivity, J Am Chem Soc 126: 5932–5933.

    CAS  Google Scholar 

  108. Nam, J.-M., Wise, A.R., and Groves, J.T., 2005 Colorimetric bio-barcode amplification assay for cytokines. Anal Chem 77: 6985–6988.

    CAS  Google Scholar 

  109. Bao, Y.P., Wei, T.F., Lefebvre, P.A., An, H., He, L., Kunkel, G.T., and Müller, U.R., 2006 Detection of protein analytes via nanoparticle-based bio bar code technology. Anal Chem 78: 2055–2059.

    CAS  Google Scholar 

  110. Brongersma, M.L., 2003 Nanoscale photonics: Nanoshells: Gifts in a gold wrapper. Nat Mater 2: 296–297.

    CAS  Google Scholar 

  111. Gerhardt, W., Ljungdahl, L., Collinson, P.O., Lovis, C., Mach, F., Sylven, C., Rasmanis, G., Leinberger, R., Zerback, R., Muller-Bardorff, M., and Katus, H.A., 1997 An improved rapid troponin T test with a decreased detection limit: A multicentre study of the analytical and clinical performance in suspected myocardial damage. Scand J Clin Lab Invest 57: 549–557.

    CAS  Google Scholar 

  112. Siddiqui, J. and Remick, D.G., 2003 Improved sensitivity of colorimetric compared to chemi-luminescence ELISAs for cytokine assays. J Immunoassay Immunochem 24: 273–283.

    CAS  Google Scholar 

  113. Saviranta, P., Okon, R., Brinker, A., Warashina, M., Eppinger, J., and Geierstanger, B.H., 2004 Evaluating sandwich immunoassays in microarray format in terms of the ambient analyte regime. Clin Chem 50: 1907–1920.

    CAS  Google Scholar 

  114. Bao, P., Frutos, A.G., Greef, C., Lahiri, J., Müller, U., Peterson, T.C., Warden, L., and Xie, X., 2002 High-sensitivity detection of DNA hybridization on microarrays using resonance light scattering. Anal Chem 74: 1792–1797.

    CAS  Google Scholar 

  115. Wei, J., Mu, Y., Song, D., Fang, X., Liu, X., Bu, L., Zhang, H., Zhang, G., Ding, J., Wang, W., Jin, Q., and Luo, G., 2003 A novel sandwich immunosensing method for measuring cardiac troponin I in sera. Anal Biochem 321: 209–216.

    CAS  Google Scholar 

  116. Ihara, T., Tanaka, S., Chikaura, Y., and Jyo, A., 2004 Preparation of DNA-modified nanopar-ticles and preliminary study for colorimetric SNP analysis using their selective aggregations. Nucleic Acids Res 32: e105.

    Google Scholar 

  117. Storhoff, J.J., Lucas, A., Müller, U.R., Bao, Y.P., Senical, M., and Garimella, V., 2006 U.S. Patent Appl. No. 20050250094.

    Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Nanosphere, Inc., 4088 Commercial Avenue, Northbrook, IL, 60062, USA

    Uwe R. Müller

Authors
  1. Uwe R. Müller
    View author publications

    You can also search for this author in PubMed Google Scholar

Editor information

Editors and Affiliations

  1. CombiMatrix Corporation, Inc. 6500 Harbour Heights Parkway, Suite 301, Mukilteo, WA, 98275, USA

    Kilian Dill

  2. Osmetech Molecular Diagnostics, 757 S. Raymond Ave., Pasadena, CA, 91105, USA

    Robin Hui Liu

  3. National Institutes of Health National Cancer Institute, 31 Center Drive, Bethesda, MD, 20892, USA

    Piotr Grodzinski

Rights and permissions

Reprints and permissions

Copyright information

© 2009 Springer Science+Business Media, LLC

About this chapter

Cite this chapter

Müller, U.R. (2009). Bar Coding Platforms for Nucleic Acid and Protein Detection. In: Dill, K., Liu, R.H., Grodzinski, P. (eds) Microarrays. Integrated Analytical Systems. Springer, New York, NY. https://doi.org/10.1007/978-0-387-72719-6_16

Download citation

Publish with us

Policies and ethics

Search

Navigation