Ten-Atom Silver Cluster Signaling and Tempering DNA Hybridization

Abstract

Silver clusters with ∼10 atoms are molecules, and specific species develop within DNA strands. These molecular metals have sparsely organized electronic states with distinctive visible and near-infrared spectra that vary with cluster size, oxidation, and shape. These small molecules also act as DNA adducts and coordinate with their DNA hosts. We investigated these characteristics using a specific cluster-DNA conjugate with the goal of developing a sensitive and selective biosensor. The silver cluster has a single violet absorption band (λ(max) = 400 nm), and its single-stranded DNA host has two domains that stabilize this cluster and hybridize with target oligonucleotides. These target analytes transform the weakly emissive violet cluster to a new chromophore with blue-green absorption (λ(max) = 490 nm) and strong green emission (λ(max) = 550 nm). Our studies consider the synthesis, cluster size, and DNA structure of the precursor violet cluster-DNA complex. This species preferentially forms with relatively low amounts of Ag(+), high concentrations of the oxidizing agent O2, and DNA strands with ≳20 nucleotides. The resulting aqueous and gaseous forms of this chromophore have 10 silvers that coalesce into a single cluster. This molecule is not only a chromophore but also an adduct that coordinates multiple nucleobases. Large-scale DNA conformational changes are manifested in a 20% smaller hydrodynamic radius and disrupted nucleobase stacking. Multidentate coordination also stabilizes the single-stranded DNA and thereby inhibits hybridization with target complements. These observations suggest that the silver cluster-DNA conjugate acts like a molecular beacon but is distinguished because the cluster chromophore not only sensitively signals target analytes but also stringently discriminates against analogous competing analytes.

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

“…25 The violet cluster develops in a 20-nucleotide DNA strand with concentrations ≲ 10 Ag + :DNA and high oxygen pressures. We chose these conditions because they eliminate competing species and favored the violet cluster (Figure S1).…”

“…The single-stranded DNA host hybridizes with a complementary strand, and the violet precursor switches to a fluorescent cluster with ≳ 100-fold stronger emission. 25,34 The fluorescence spectrum is encoded by the DNA sequence. Furthermore, the violet precursor is regenerated when the duplex denatures.…”

Research Update: Density functional theory investigation of the interactions of silver nanoclusters with guanine

“…This position was also observed in previous work on individual silver cations interacting with guanine. 41 Since the silver-DNA complexes are experimentally known to be positively charged, 33,59,60 this suggests that the most favorable interaction for these clusters with guanine bases may occur through nitrogen 7 and the neighboring carbonyl group. For the cation and dication systems, nearly all silver clusters in position B appeared to interact with the oxygen atom as well as the nitrogen.…”

Fluorescent DNA-Protected Silver Nanoclusters for Ligand–HIV RNA Interaction Assay

“…It is well known that there are 2 types of quenching processes: static and dynamic quenching. 34 The value of K q (~1.4×10 12 L s -1 mol -1 ) was far greater than the maximum diffusion collision quenching rate constant of various quenchers with biopolymers (2.0×10 10 L s -1 mol -1 ), 37 indicating the fluorescence quenching of AgNCs caused by MTX occurs as a static quenching process.…”

“…Cu 2+ and Hg 2+ ) and some biomacromolecules. [28][29][30][31][32][33][34] However, to our knowledge, DNAAgNCs have not been applied to the study of ligand-RNA interactions. Fluorescent AgNCs biosensors for ligand-RNA interactions should be relatively simple, low-cost and sensitive compared with other reported approaches.…”