Silver clusters develop within DNA strands and become optical chromophores with diverse electronic spectra and wide-ranging emission intensities. These studies consider a specific cluster that absorbs at 400 nm, has low emission, and exclusively develops with single-stranded oligonucleotides. It is also a chameleon-like chromophore that can be transformed into different highly emissive fluorophores. We describe four characteristics of this species and conclude that it is highly oxidized yet also metallic. One, the cluster size was determined via electrospray ionization mass spectrometry. A common silver mass is measured with different oligonucleotides and thereby supports a Ag10 cluster. Two, the cluster charge was determined by mass spectrometry and Ag L3-edge X-ray absorption near-edge structure spectroscopy. Respectively, the conjugate mass and the integrated white-line intensity support a partially oxidized cluster with a +6 and +6.5 charge, respectively. Three, the cluster chirality was gauged by circular dichroism spectroscopy. This chirality changes with the length and sequence of its DNA hosts, and these studies identified a dispersed binding site with ~20 nucleobases. Four, the structure of this complex was investigated via Ag K-edge extended X-ray absorption fine structure spectroscopy. A multishell fitting analysis identified three unique scattering environments with corresponding bond lengths, coordination numbers, and Debye–Waller factors for each. Collectively, these findings support the following conclusion: a Ag10+6 cluster develops within a 20-nucleobase DNA binding site, and this complex segregates into a compact, metal-like silver core that weakly links to an encapsulating silver–DNA shell. We consider different models that account for silver–silver coordination within the core.

Molecular silver clusters conjugated with DNA act as analyte sensors. Our studies evaluate a type of cluster-laden DNA strand whose structure and silver stoichiometry changes with hybridization. The sensor strand integrates two functions: the 3′ region binds target DNA strands through base recognition while the 5′ sequence C3AC3AC3TC3A favors formation of a near infrared absorbing and emitting cluster. This precursor form exclusively harbors an ~11 silver atom cluster that absorbs at 400 nm and that condenses its single-stranded host. The 3′ recognition site associates with a complementary target strand, thereby effecting a 330 nm red-shift in cluster absorption and a background-limited recovery of cluster emission at 790 nm. One factor underlying these changes is sensor unfolding and aggregation. Variations in salt and oligonucleotide concentrations control cluster development by influencing DNA association. Structural studies using fluorescence anisotropy, fluorescence correlation spectroscopy, and size exclusion chromatography show that the sensor-cluster conjugate opens and subsequently dimerizes with hybridization. A second factor contributing to the spectral and photophysical changes is cluster transformation. Empirical silver stoichiometries are preserved through hybridization, so hybridized, dimeric near infrared conjugates host twice the amount of silver in relation to their violet absorbing predecessors. These DNA structure and net silver stoichiometry alterations provide insight into how DNA-silver conjugates recognize analytes.

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.

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.

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.