Ten-Atom Silver Cluster Signaling and Tempering DNA Hybridization Jeffrey T. Petty,* ,† Orlin O. Sergev, Andrew G. Kantor, Ian J. Rankine, Mainak Ganguly, Frederic D. David, Sandra K. Wheeler, and John F. Wheeler Department of Chemistry, Furman University, Greenville, South Carolina 29613, United States * S Supporting Information ABSTRACT: Silver clusters with ∼10 atoms are molecules, and specific species develop within DNA strands. These molecular metals have sparsely organized electronic states with distinctive visible and near- infrared spectra that vary with cluster size, oxidation, and shape. These small molecules also act as DNA adducts and coordinate with their DNA hosts. We investigated these characteristics using a specific cluster-DNA conjugate with the goal of developing a sensitive and selective biosensor. The silver cluster has a single violet absorption band (λ max = 400 nm), and its single-stranded DNA host has two domains that stabilize this cluster and hybridize with target oligonucleotides. These target analytes transform the weakly emissive violet cluster to a new chromophore with blue-green absorption (λ max = 490 nm) and strong green emission (λ max = 550 nm). Our studies consider the synthesis, cluster size, and DNA structure of the precursor violet cluster-DNA complex. This species preferentially forms with relatively low amounts of Ag + , high concentrations of the oxidizing agent O 2 , and DNA strands with ≳20 nucleotides. The resulting aqueous and gaseous forms of this chromophore have 10 silvers that coalesce into a single cluster. This molecule is not only a chromophore but also an adduct that coordinates multiple nucleobases. Large-scale DNA conformational changes are manifested in a 20% smaller hydrodynamic radius and disrupted nucleobase stacking. Multidentate coordination also stabilizes the single-stranded DNA and thereby inhibits hybridization with target complements. These observations suggest that the silver cluster-DNA conjugate acts like a molecular beacon but is distinguished because the cluster chromophore not only sensitively signals target analytes but also stringently discriminates against analogous competing analytes. B iosensors identify chemical signatures that characterize food safety, air and water quality, and human diseases. 1,2 Their wide-ranging capabilities emanate from two fundamental functions, recognizing and identifying specific target analytes. 3,4 Our studies focus on recognition using DNA-based sensors and identification using silver cluster labels. Nucleic acids provide a synthetic platform to develop sensors for a broad range of analytes, and the targets are recognized through strong and specific biomolecular interactions. 5,6 For example, DNA hairpins bind oligonucleotide analytes via their single-stranded loops. They balance the stabilities of their intermolecular loop- analyte vs intramolecular stem duplexes and thereby discern oligonucleotides with single nucleotide differences. 7,8 Nucleic acid aptamers expand the scope of analytes because their distinctive tertiary structures define unique substrate binding sites. 9 Systematic evolution has yielded aptamers that discriminate species ranging from metal ions to cells and that distinguish closely related analytes such as theophylline and its methylated analogue caffeine. 10 Analytes not only associate with but can also structurally alter biosensors, and DNA conformational changes underlie highly sensitive detection strategies. For example, DNA hairpins hybridize with their complementary target and unfold from compact hairpins to open duplexes. 11−14 Such distinct conformations are tracked by exogenous labels such as organic dyes, semiconductor and noble metal nanoparticles, and conjugated polymers. 3,6 High- contrast signals develop through different mechanisms, such as when analytes alter the coupling between covalently bound labels or generate new chromophore binding sites. 6 We are particularly interested in optical signals because they offer high sensitivity over a large concentration range and the potential for remote, in vivo detection. 3,15 We consider the advantages of chromophore labels based on silver clusters. Silver clusters with ∼10 atoms are molecules with discrete electronic states and their optical spectra vary with the number of silver atoms, net oxidation state, and cluster shape. 16−18 Such small clusters agglomerate without ligands, and DNA strands yield functional chromophores in two respects. First, oligonucleotides stabilize specific clusters. The electron-rich nucleobases coordinate silver atoms and restrain cluster growth, and the primary sequence and secondary structure of DNA strands define specific cluster binding sites. 19,20 A resulting suite of chromophores is spectrally diverse and optically bright. They absorb and emit throughout the visible to near-infrared region from 400−900 nm and have extinction coefficients of ∼10 5 M −1 cm −1 , fluorescence quantum yields of ∼40%, and fluorescence lifetimes of ∼1 ns. 19,21 Second, longer DNA strands both coordinate silver clusters and bind target analytes such as metal ions, peptides, and oligonucleotides. 5,22−27 Such analytes bind with the DNA strand and transform the cluster Received: February 3, 2015 Accepted: April 29, 2015 Article pubs.acs.org/ac © XXXX American Chemical Society A DOI: 10.1021/acs.analchem.5b01265 Anal. Chem. XXXX, XXX, XXX−XXX