Silver Clusters as Both Chromophoric Reporters and DNA Ligands

Petty, Jeffrey T.; Giri, Banabihari; Miller, Ian; Nicholson, D A; Sergev, Orlin O.; Banks, Taylor M.; Story, Sandra P.

doi:10.1021/ac303531y

Cited by 51 publications

(130 citation statements)

References 74 publications

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“…20 74,75 Analogously, reduced silver clusters with near-infrared absorption and emission cross-link two cytosine-rich strands and form intermolecular dimers in dilute solutions with 500 nM oligonucleotide concentrations. 31,76,77 On the other hand, DNA strands mold their silver cluster adducts. The nucleobases anchor silver clusters, and cytosine forms the strongest complexes.…”

Section: ■ Discussionmentioning

confidence: 99%

Ten-Atom Silver Cluster Signaling and Tempering DNA Hybridization

et al. 2015

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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 O2, 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.

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Section: ■ Discussionmentioning

confidence: 99%

Ten-Atom Silver Cluster Signaling and Tempering DNA Hybridization

et al. 2015

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“…Size exclusion chromatography studies were conducted as described earlier. 27 We used a 300 × 7.8 mm i.d. column (BioSep, Phenomenex) on a HPLC system (Prominence, Shimadzu) using a 10 mM citrate buffer at pH = 7 with 300 mM NaClO 4 to minimize matrix adsorption.…”

Section: Methodsmentioning

confidence: 99%

“…39 After HPLC purification, the quantity of silver in the resulting DNA-conjugate was determined by inductively coupled plasma-atomic emission spectroscopy (Optima 7300 DV, Perkin Elmer). 27 Control samples containing oligonucleotide and Ag + were used to account for matrix effects. 14 …”

Section: Methodsmentioning

confidence: 99%

“…29,30 Our earlier studies considered an ~11 silver atom cluster with violet absorption and low emission. 27 This cluster forms within a single-stranded DNA that has a cytosine-rich cluster domain and a recognition site for complementary oligonucleotides. Complements hybridize with this recognition site, and cluster absorption shifts from violet to near-infrared and near-infrared emission develops.…”

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A Silver Cluster–DNA Equilibrium

et al. 2013

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DNA encapsulates silver clusters, and these hybrid nanomaterials form molecular sensors. We discuss a silver cluster-oligonucleotide sensor with four characteristics. First, a specific reporting cluster forms within a single-stranded DNA. This template uses the 5’ cluster domain CCCCAACTCCTT with different 3’ recognition sites for complementary oligonucleotides. The modular composite strand exclusively forms a cluster with λmax = 400 nm and with low emission. Conjugates were chromatographically purified, and their elemental analysis measured a cluster adduct with ~11 silver atoms. Second, hybridization transforms the cluster. Size exclusion chromatography shows that the 3’ recognition sites of the single-stranded conjugates hybridize with their complements. This secondary structural change both shifts cluster absorption from 400 to 490 nm and develops emission at 550 nm. Third, cluster size remains intact. Like their violet predecessors, purified blue-green clusters have ~11 silver atoms. Cluster integrity is further supported by extracting the complement from the blue-green conjugate and reversing the spectral changes. Fourth, the cluster transformation is an equilibrium. Complementary strands generate an isosbestic point and thus directly link single-stranded hosts for the violet cluster and their hybridized analogs for the blue-green cluster. This equilibrium shifts with temperature. A van’t Hoff analysis shows that longer and more stable duplexes favor the blue-green cluster. However, hybridized cluster hosts are less stable than their native DNA counterparts, and stability further degrades when short complements expose nucleobases within S1-S2. Duplex instability suggests that unpaired nucleobases coordinate the violet cluster and favor the single-stranded sensor. A balance between innate hybridization and exogenous folding highlights a distinct feature of silver clusters for sensing – they are both chromophoric reporters and ligands that modulate analyte-sensor interactions.

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“…28 Two variants, S2C a and dT 10 -S2C a , used the same complementary sequence for S2 a (Table 1). On the latter complement, the thymine appendage is chemically innocuous because it projects away from the S1 cluster domain and because neutral pH protonates and blocks the N3 cluster binding site on thymine.…”

Section: Resultsmentioning

confidence: 99%

Near-Infrared Silver Cluster Optically Signaling Oligonucleotide Hybridization and Assembling Two DNA Hosts

et al. 2014

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Silver clusters with ∼10 atoms form within DNA strands, and the conjugates are chemical sensors. The DNA host hybridizes with short oligonucleotides, and the cluster moieties optically respond to these analytes. Our studies focus on how the cluster adducts perturb the structure of their DNA hosts. Our sensor is comprised of an oligonucleotide with two components: a 5′-cluster domain that complexes silver clusters and a 3′-recognition site that hybridizes with a target oligonucleotide. The single-stranded sensor encapsulates an ∼11 silver atom cluster with violet absorption at 400 nm and with minimal emission. The recognition site hybridizes with complementary oligonucleotides, and the violet cluster converts to an emissive near-infrared cluster with absorption at 730 nm. Our key finding is that the near-infrared cluster coordinates two of its hybridized hosts. The resulting tertiary structure was investigated using intermolecular and intramolecular variants of the same dimer. The intermolecular dimer assembles in concentrated (∼5 μM) DNA solutions. Strand stoichiometries and orientations were chromatographically determined using thymine-modified complements that increase the overall conjugate size. The intramolecular dimer develops within a DNA scaffold that is founded on three linked duplexes. The high local cluster concentrations and relative strand arrangements again favor the antiparallel dimer for the near-infrared cluster. When the two monomeric DNA/violet cluster conjugates transform to one dimeric DNA/near-infrared conjugate, the DNA strands accumulate silver. We propose that these correlated changes in DNA structure and silver stoichiometry underlie the violet to near-infrared cluster transformation.

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Silver Clusters as Both Chromophoric Reporters and DNA Ligands

Cited by 51 publications

References 74 publications

Ten-Atom Silver Cluster Signaling and Tempering DNA Hybridization

Ten-Atom Silver Cluster Signaling and Tempering DNA Hybridization

A Silver Cluster–DNA Equilibrium

Near-Infrared Silver Cluster Optically Signaling Oligonucleotide Hybridization and Assembling Two DNA Hosts

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