Repeated and Folded DNA Sequences and Their Modular Ag106+ Cluster

Abstract

Molecular silver clusters are optical chromophores, and species with distinct spectra form with DNA strands. One such hybrid chromophore is a violet cluster bound to repeated C2X sequences where X ≠ C. We varied the number of C2X repeats and the X nucleobase and consider three observations. First, different lengths of (C2A)y and (C2T)y strands with y = 3–12 identify a minimal (C2X)6 scaffold that forms a specific Ag10 adduct. This cluster has a +6 oxidation state, absorbs between 400–450 nm, and folds its DNA host. Second, different X nucleobases alter the (C2X)6 binding site. The natural nucleobases preferentially form the Ag106+ cluster and yield strong circular dichroism. These ligands coordinate via their heteroatoms, and the N3 of thymine was identified via cluster fluorescence that varies with pH. In contrast, abasic sites and imidazole substitutions suppress circular dichroism and diminish the number of silver adducts. These observations suggest that a (C2X)6 coordinates Ag106+ via multiple nucleobases. Third, beyond the minimal (C2X)6 binding site, longer strands still form Ag106+ but can also coordinate additional Ag+ adducts. The added Ag+ do not perturb the Ag0 and their spectra and thus may partition to open C2X subunits outside the core (C2X)6–Ag106+ complex. Thus, these modular complexes distinguish oxidized and reduced silvers. Collectively, these three observations suggest that the DNA and silver cluster play complementary roles: a repeated C2X sequence stabilizes the Ag106+ cluster, while the cluster folds its host. We specifically suggest that the Ag+ within Ag106+ cross-links remote C2X subunits and the Ag0 coordinate with mismatch sites in a hairpin-like secondary structure. Distinct roles for Ag+ and Ag0 within a cluster are considered in light of the X-ray spectra of related complexes.