The Role of Hydrogen Bonds in the Stabilization of Silver-Mediated Cytosine Tetramers

Peer reviewe

Silver (I) as DNA glue: Ag(+)-mediated guanine pairing revealed by removing Watson-Crick constraints.

Metal ion interactions with DNA have far-reaching implications in biochemistry and DNA nanotechnology. Ag(+) is uniquely interesting because it binds exclusively to the bases rather than the backbone of DNA, without the toxicity of Hg(2+). In contrast to prior studies of Ag(+) incorporation into double-stranded DNA, we remove the constraints of Watson-Crick pairing by focusing on homo-base DNA oligomers of the canonical bases. High resolution electro-spray ionization mass spectrometry reveals an unanticipated Ag(+)-mediated pairing of guanine homo-base strands, with higher stability than canonical guanine-cytosine pairing. By exploring unrestricted binding geometries, quantum chemical calculations find that Ag(+) bridges between non-canonical sites on guanine bases. Circular dichroism spectroscopy shows that the Ag(+)-mediated structuring of guanine homobase strands persists to at least 90 °C under conditions for which canonical guanine-cytosine duplexes melt below 20 °C. These findings are promising for DNA nanotechnology and metal-ion based biomedical science

Atomically Precise Arrays of Fluorescent Silver Clusters: A Modular Approach for Metal Cluster Photonics on DNA Nanostructures

The remarkable precision that DNA scaffolds provide for arraying nanoscale optical elements enables optical phenomena that arise from interactions of metal nanoparticles, dye molecules, and quantum dots placed at nanoscale separations. However, control of ensemble optical properties has been limited by the difficulty of achieving uniform particle sizes and shapes. Ligand-stabilized metal clusters offer a route to atomically precise arrays that combine desirable attributes of both metals and molecules. Exploiting the unique advantages of the cluster regime requires techniques to realize controlled nanoscale placement of select cluster structures. Here we show that atomically monodisperse arrays of fluorescent, DNA-stabilized silver clusters can be realized on a prototypical scaffold, a DNA nanotube, with attachment sites separated by <10 nm. Cluster attachment is mediated by designed DNA linkers that enable isolation of specific clusters prior to assembly on nanotubes and preserve cluster structure and spectral purity after assembly. The modularity of this approach generalizes to silver clusters of diverse sizes and DNA scaffolds of many types. Thus, these silver cluster nano-optical elements, which themselves have colors selected by their particular DNA templating oligomer, bring unique dimensions of control and flexibility to the rapidly expanding field of nano-optics

Heterogeneous Solvatochromism of Fluorescent DNA-Stabilized Silver Clusters Precludes Use of Simple Onsager-Based Stokes Shift Models

The diverse optical and chemical properties of DNA-stabilized silver clusters (Ag_<i>N</i>-DNAs) have challenged the development of a common model for these sequence-tunable fluorophores. Although correlations between cluster geometry and fluorescence color have begun to shed light on how the optical properties of Ag_<i>N</i>-DNAs are selected, the exact mechanisms responsible for fluorescence remain unknown. To explore these mechanisms, we study four distinct purified Ag_<i>N</i>-DNAs in ethanol–water and methanol–water mixtures and find that the solvatochromic behavior of Ag_<i>N</i>-DNAs varies widely among different cluster species and differs markedly from prior results on impure material. Placing Ag_<i>N</i>-DNAs within the context of standard Lippert–Mataga solvatochromism models based on the Onsager reaction field, we show that such nonspecific solvent models are not universally applicable to Ag_<i>N</i>-DNAs. Instead, alcohol-induced solvatochromism of Ag_<i>N</i>-DNAs may be governed by changes in hydration of the DNA template, with spectral shifts resulting from cluster shape changes and/or dielectric changes in the local vicinity of the cluster

Cluster Plasmonics: Dielectric and Shape Effects on DNA-Stabilized Silver Clusters

This work investigates the effects of dielectric environment and cluster shape on electronic excitations of fluorescent DNA-stabilized silver clusters, Ag_N–DNA. We first establish that the longitudinal plasmon wavelengths predicted by classical Mie-Gans (MG) theory agree with previous quantum calculations for excitation wavelengths of linear silver atom chains, even for clusters of just a few atoms. Application of MG theory to Ag_N–DNA with 400–850 nm cluster excitation wavelengths indicates that these clusters are characterized by a collective excitation process and suggests effective cluster thicknesses of ∼2 silver atoms and aspect ratios of 1.5 to 5. To investigate sensitivity to the surrounding medium, we measure the wavelength shifts produced by addition of glycerol. These are smaller than reported for much larger gold nanoparticles but easily detectable due to narrower line widths, suggesting that Ag_N–DNA may have potential for fluorescence-reported changes in dielectric environment at length scales of ∼1 nm

Chiral Electronic Transitions in Fluorescent Silver Clusters Stabilized by DNA

Fluorescent, DNA-stabilized silver clusters are receiving much attention for sequence-selected colors and high quantum yields. However, limited knowledge of cluster structure is constraining further development of these “Ag_N-DNA” nanomaterials. We report the structurally sensitive, chiroptical activity of four pure Ag_N-DNA with wide ranging colors. Ubiquitous features in circular dichroism (CD) spectra include a positive dichroic peak overlying the lowest energy absorbance peak and highly anisotropic, negative dichroic peaks at energies well below DNA transitions. Quantum chemical calculations for bare chains of silver atoms with nonplanar curvature also exhibit these striking features, indicating electron flow along a chiral, filamentary metallic path as the origin for low-energy Ag_N-DNA transitions. Relative to the bare DNA, marked UV changes in CD spectra of Ag_N-DNA and silver cation–DNA solutions indicate that ionic silver content constrains nucleobase conformation. Changes in solvent composition alone can reorganize cluster structure, reconfiguring chiroptical properties and fluorescence