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The structure and dynamics of Ag complexes derived from single stranded DNA (ssDNA) is less understood than their double stranded (dsDNA) counterparts despite their great promise as fluorescent biological probes and sensors. In this work, we seek new insights into the structure of single stranded AgNDNA clusters using analytical ultracentrifugation (AUC), nuclear magnetic resonance spectroscopy, infrared spectroscopy and molecular dynamics simulations (MD) of an (AgNDNA)8+ nanocluster. The results show that the purified (AgNDNA)8+ nanocluster switches between multiple conformations, preferring two distinct long-lived states: one extended, the other more compact. Ag(I) interacts preferentially with the nucleobase rather than the phosphate backbone, affording a restructuring of the DNA strand relative to the bare DNA. Infrared spectroscopy and MD simulations of (AgNDNA)8+ and model nucleic acid homopolymers suggest that Ag(I) has a higher affinity for cytosine over guanine bases, little interaction with adenine, and virtually none with thymine. Ag(I) shows a tendency to interact with cytosine N3 and O2 and guanine N7 and O6, opening the possibility for a Ag(I)-base bifurcated bond to act as a nanocluster nucleation and strand stabilizing site.
nanocluster, AgDNA, analytical ultracentrifuge, nuclear magnetic resonance spectroscopy, infrared spectroscopy, molecular dynamics simulations