DNA-Directed Fluorescence Switching of Silver Clusters.

Silver clusters with ≲30 atoms are molecules with diverse electronic spectra and wide-ranging emission intensities. Specific cluster chromophores form within DNA strands, and we consider a DNA scaffold that transforms a pair of silver clusters. This ~20-nucleotide strand has two components, a cluster domain (S1) that stabilizes silver clusters and a recognition site (S2) that hybridizes with complementary oligonucleotides (S2C). The single-stranded S1-S2 exclusively develops clusters with violet absorption and low emission. This conjugate hybridizes with S2C to form S1-S2:S2C, and the violet chromophore transforms to a fluorescent counterpart with ≈ 490 nm/ ≈ 550 nm and with ~100-fold stronger emission. Our studies focus on both the S1 sequence and structure that direct this violet → blue-green cluster transformation. From the sequence perspective, CX sequences with X = adenine, thymine, and/or guanine favor the blue-green cluster, and the specificity of the binding site depends on three factors: the number of CX repeats, the identity of the X nucleobase, and the number of contiguous cytosines. A systematic series of oligonucleotides identified the optimal S1 sequence CACT and discerned distinct roles for the adenine, thymine, and cytosines. From the structure perspective, two factors guide the conformation of the CACT sequence: hybridization with the S2C complement and coordination by the cluster adduct. Spectroscopic and chromatographic studies show that the single-stranded CACT is folded by its blue-green cluster adduct. We propose a structural model in which the two CX motifs within CACT are cross-linked by the encapsulated cluster. These studies suggest that the structures of the DNA host and the cluster adduct are interdependent.