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

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.

Automated summary

DNA-stabilized silver clusters exhibit diverse fluorescence properties based on DNA sequence, with differences in excitation energies and Stokes shifts possibly stemming from variations in cluster structure and DNA conformation. Steady state Stokes shifts of Ag-N-DNAs may provide valuable insights into the optical diversity of these nanoclusters.