DNA-Directed Fluorescence Switching of Silver Clusters

Abstract

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 λex ≈ 490 nm/λem ≈ 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, C4X 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 C4X repeats, the identity of the X nucleobase, and the number of contiguous cytosines. A systematic series of oligonucleotides identified the optimal S1 sequence C4AC4T and discerned distinct roles for the adenine, thymine, and cytosines. From the structure perspective, two factors guide the conformation of the C4AC4T sequence: hybridization with the S2C complement and coordination by the cluster adduct. Spectroscopic and chromatographic studies show that the single-stranded C4AC4T is folded by its blue-green cluster adduct. We propose a structural model in which the two C4X motifs within C4AC4T are cross-linked by the encapsulated cluster. These studies suggest that the structures of the DNA host and the cluster adduct are interdependent.

Chiral Noble Metal Nanoparticles and Nanostructures

“…These assemblies have potential applications in photonics and as optical polarizers, sensors, catalysts, etc . During the interaction of noble metal NPs with biomolecules, formation of two types of nanostructures are possible: i) metal clusters are nested on the outside of the biomolecule that are arranged in external helical chains around these peptide or DNA molecules, producing plasmonic helical metal NP assemblies ( Figure ), and ii) clusters consisting of a few to tens of metals atoms that are located inside the DNA molecule, between two polynucleotide strands …”

“…Different DNA sequences can lead to different clusters, potentially with different shapes. Compact silver clusters encapsulated within DNA were obtained and described by Petty and co‐workers . The cluster size was determined by mass spectroscopy to be Ag 10 .…”

“…[9,[77][78][79] During the interaction of noble metal NPs with biomolecules, formation of two types of nanostructures are possible: i) metal clusters are nested on the outside of the biomolecule that are arranged in external helical chains around these peptide or DNA molecules, producing plasmonic helical metal NP assemblies (Figure 24), [9,[79][80][81] and ii) clusters consisting of a few to tens of metals atoms that are located inside the DNA molecule, between two polynucleotide strands. [82][83][84][85][86][87][88][89][90][91][92][93][94][95] The second type of noble metal-biomolecule clusters (denoted as M:DNA, where M = Au or Ag), where metals atoms are located inside the DNA molecule, is a very interesting class. In particular, Ag:DNA nanoclusters have an extremely wide range of emission colors.…”

“…Compact silver clusters encapsulated within DNA were obtained and described by Petty and co-workers. [85,86] The cluster size was determined by mass spectroscopy to be Ag 10 . [85] The total charge (+6) and the structure of the complex were obtained by mass spectrometry and Ag L 3 -edge X-ray absorption near-edge structure spectroscopy.…”

DNA-stabilized Ag–Au bimetallic clusters: the effects of alloying and embedding on optical properties

“…Several experimental studies have indicated that silver clusters can be stabilized by the interaction with cytosine-based oligomers, [80][81][82][83] or even be encircled by a DNA hairpin loop. 42,44,56,57 For small gold clusters, on the other hand, preferential binding to purine bases has been predicted theoretically. 84 In order to rationalize these observations and to provide further insights into possible mechanisms of binding, a reliable identification of the ground-state structures of the cluster-organic aggregates and a careful analysis of the chemical nature of the bonds formed would be particularly useful.…”