Large-scale investigation of the effects of nucleobase sequence on fluorescence excitation and Stokes shifts of DNA-stabilized silver clusters

Abstract

DNA-stabilized silver clusters (Ag_N-DNAs) exhibit diverse sequence-programmed fluorescence, making these tunable nanoclusters promising sensors and bioimaging probes. Recent advances in the understanding of Ag_N-DNA structures and optical properties have largely relied on detailed characterization of single species isolated by chromatography. Because most Ag_N-DNAs are unstable under chromatography, such studies do not fully capture the diversity of these clusters. As an alternative method, we use high-throughput synthesis and spectroscopy to measure steady state Stokes shifts of hundreds of Ag_N-DNAs. Steady state Stokes shift is of interest because its magnitude is determined by energy relaxation processes which may be sensitive to specific cluster geometry, attachment to the DNA template, and structural engagement of solvent molecules. We identify 305 Ag_N-DNA samples with single-peaked emission and excitation spectra, a characteristic of pure solutions and single emitters, which thus likely contain a dominant emissive Ag_N-DNA species. Steady state Stokes shifts of these samples vary widely, are in agreement with values reported for purified clusters, and are several times larger than for typical organic dyes. We then examine how DNA sequence selects Ag_N-DNA excitation energies and Stokes shifts, comment on possible mechanisms for energy relaxation processes in Ag_N-DNAs, and discuss how differences in Ag_N-DNA structure and DNA conformation may result in the wide distribution of optical properties observed here. These results may aid computational studies seeking to understand the fluorescence process in Ag_N-DNAs and the relations of this process to Ag_N-DNA structure.