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A Segregated, Partially Oxidized, and Compact Ag10 Cluster within an Encapsulating DNA Host

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† Department of Chemistry, Furman University, Greenville, South Carolina 29613, United States
‡ Department of Chemistry, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada
*[email protected]
Cite this: J. Am. Chem. Soc. 2016, 138, 10, 3469–3477
Publication Date (Web):February 28, 2016
https://doi.org/10.1021/jacs.5b13124
Copyright © 2016 American Chemical Society
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    Abstract

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    Silver clusters develop within DNA strands and become optical chromophores with diverse electronic spectra and wide-ranging emission intensities. These studies consider a specific cluster that absorbs at 400 nm, has low emission, and exclusively develops with single-stranded oligonucleotides. It is also a chameleon-like chromophore that can be transformed into different highly emissive fluorophores. We describe four characteristics of this species and conclude that it is highly oxidized yet also metallic. One, the cluster size was determined via electrospray ionization mass spectrometry. A common silver mass is measured with different oligonucleotides and thereby supports a Ag10 cluster. Two, the cluster charge was determined by mass spectrometry and Ag L3-edge X-ray absorption near-edge structure spectroscopy. Respectively, the conjugate mass and the integrated white-line intensity support a partially oxidized cluster with a +6 and +6.5 charge, respectively. Three, the cluster chirality was gauged by circular dichroism spectroscopy. This chirality changes with the length and sequence of its DNA hosts, and these studies identified a dispersed binding site with ∼20 nucleobases. Four, the structure of this complex was investigated via Ag K-edge extended X-ray absorption fine structure spectroscopy. A multishell fitting analysis identified three unique scattering environments with corresponding bond lengths, coordination numbers, and Debye–Waller factors for each. Collectively, these findings support the following conclusion: a Ag10+6 cluster develops within a 20-nucleobase DNA binding site, and this complex segregates into a compact, metal-like silver core that weakly links to an encapsulating silver–DNA shell. We consider different models that account for silver–silver coordination within the core.

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    The Supporting Information is available free of charge on the ACS Publications website at DOI: 10.1021/jacs.5b13124.

    • Figures describing size exclusion chromatograms of the native and cluster-bearing DNA strands, mass and mass:charge spectra of a longer oligonucleotide with the violet cluster, absorption spectra of violet clusters with the DNA templates from Table 1, mass:charge spectra of the native 20-nucleotide DNA in its −6 charge state, isotope model for the −6 charge state, mass:charge spectra of the −4 to −12 charge states for the violet cluster/DNA complexes, mass:charge spectrum of the 20-nucleotide DNA with the violet cluster in ammonium acetate, mass:charge spectra of the −4 to −11 charge states for the violet cluster/DNA complexes in a ammonium acetate buffer, mass:charge spectra of the −5, −7, −8, −9, −10, and −11 charge states for the Na+ complexes, mass spectra of Ag+-DNA complexes, circular dichroism spectra of the violet cluster with the 20 nucleotide strand at different temperatures, and the EXAFS oscillations are shown in k-space (PDF)

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