Here we investigate the correlations between optical and physical properties of few-atom fluorescent silver nanoclusters, stabilized by DNA. Specifically, we examine how fluorescence colors depend on the stabilizing strand's base and sugar type, on the number of silver atoms in the cluster and on cluster shape. We study the fluorescence properties of silver clusters stabilized by DNA and RNA homopolymers under a wide range of synthesis conditions and discover that both DNA and RNA display the same striking base dependence, establishing a C,G vs A, T(U) dichotomy. Despite demonstrating the same general base dependence, DNA and RNA homopolymer analogs display unique optical properties, suggesting that the composition of the backbone additionally plays a role in controlling cluster properties.

To examine the physical properties of the cluster, we develop a high performance liquid chromatography- mass spectrometry (HPLC-MS) method with in-line absorbance and fluorescence spectroscopy, which directly correlates optical properties with the mass and charge of the complex. We find that emission colors trend to longer wavelengths as the number of silver atoms (NAg) in the cluster increases. We additionally find a direct correlation between cluster charge and NAg, which together with absorbance spectral features and polarization dependencies reveals that DNA-stabilized silver clusters have rod-like structures, whose emission colors are dictated by the length of their free electron systems. Our findings have motivated two new applications for oligonucleotide-stabilized silver clusters. We first exploit the sequence dependence of Ag:RNAs and their bias against formation on dsRNA to track the assembly of an RNA nanostructure.

This new method is highly advantageous over current laborious methods to verify the complete assembly of RNA (or DNA) structures. Lastly, we broach the long-term goal of incorporating fluorescent silver nanoclusters into DNA assemblies with the aim of constructing highly ordered optical arrays on the nanoscale. We demonstrate a proof-of-principle for such a structure by developing a method to bring two distinct silver clusters together, producing a dual-color assembly. We verify the nanoscale proximity of the two clusters by observing inter-cluster FRET, an optical readout occurring only when a donor and acceptor fluorophore are within nm proximity.