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 Ag0 chromophores. The DNA host C4-A2-iC4T mimics structural elements in a DNA-cluster crystal structure using a phosphodiester backbone with combined 5' → 3' and 3' → 5' (indicated by "i") 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: (C4-A2-iC4T)2/Ag117+ with λabs/λem = 430/520 nm and (C4-A2-iC4T)2/Ag148+ with λabs/λem = 510/630 nm. The Ag+ and Ag0 constituents in these partially oxidized clusters are linked with structural elements in C4-A2-iC4T. Ag+ alone binds sparsely but strongly to form C4-A2-iC4T/3-4 Ag+ and (C4-A2-iC4T)2/7-8 Ag+ complexes, and these stoichiometries suggest that Ag+ cross-links pairs of cytosines to form a hairpin with a metallo-C4/iC4 duplex and an adenine loop. The Ag0 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 Ag0 cluster chromophores.

Long-lived Ag10 6+ luminescence and a split DNA scaffold.

Molecular silver clusters emit across the visible to near-infrared, and specific chromophores can be formed using DNA strands. We study C4AC4TC3G that selectively coordinates and encapsulates Ag10 6+, and this chromophore has two distinct electronic transitions. The green emission is strong and prompt with ϕ = 18% and τ = 1.25 ns, and the near-infrared luminescence is weaker, slower with τ = 50 µs, and is partly quenched by oxygen, suggesting phosphorescence. This lifetime can be modulated by the DNA host, and we consider two derivatives of C4AC4TC3G with similar sequences but distinct structures. In one variant, thymine was excised to create an abasic gap in an otherwise intact strand. In the other, the covalent phosphate linkage was removed to split the DNA scaffold into two fragments. In relation to the contiguous strands, the broken template speeds the luminescence decay by twofold, and this difference may be due to greater DNA flexibility. These modifications suggest that a DNA can be structurally tuned to modulate metastable electronic states in its silver cluster adducts.

Improving NanoCluster Beacon performance by blocking the unlabeled NC probes.

While NanoCluster Beacon (NCB) is a versatile molecular probe, it suffers from a low target-specific signal issue due to impurities. Here we show that adding a "blocker" strand to the reaction can effectively block the nonfunctional probes and enhance the target-specific signal by 14 fold at a 0.1 target/probe ratio.