Tug-of-War between DNA Chelation and Silver Agglomeration in DNA-Silver Cluster Chromophores.

Supramolecular chromophores form when a DNA traps silvers that then coalesce into clusters with discrete, molecular electronic states. However, DNA strands are polymeric ligands that disperse silvers and thus curb agglomeration. We study this competition using two chromophores that share three common components: a dimeric DNA scaffold, Ag-nucleobase base pairs, and Ag chromophores. The DNA host C-A-CT mimics structural elements in a DNA-cluster crystal structure using a phosphodiester backbone with combined 5' → 3' and 3' → 5' (indicated by "") directions. The backbone directions must alternate to form the two silver clusters, and this interdependence supports a silver-linked structure. This template creates two chromophores with distinct sizes, charges, and hence spectra: (C-A-CT)/Ag with λ/λ = 430/520 nm and (C-A-CT)/Ag with λ/λ = 510/630 nm. The Ag and Ag constituents in these partially oxidized clusters are linked with structural elements in C-A-CT. Ag alone binds sparsely but strongly to form C-A-CT/3-4 Ag and (C-A-CT)/7-8 Ag complexes, and these stoichiometries suggest that Ag cross-links pairs of cytosines to form a hairpin with a metallo-C/C duplex and an adenine loop. The Ag are chemically orthogonal because they can be oxidatively etched without disrupting the underlying Ag-DNA matrix, and their reactivity is attributed to their valence electrons and weaker chelation by the adenines. These studies suggest that Ag disperses with the cytosines to create an adenine binding pocket for the Ag cluster chromophores.