Stacy M. Copp

Magic Numbers in DNA-Stabilized Fluorescent Silver Clusters Lead to Magic Colors

DNA-stabilized silver clusters are remarkable for the selection of fluorescence color by the sequence of the stabilizing DNA oligomer. Yet despite a growing number of applications that exploit this property, no large-scale studies have probed origins of cluster color or whether certain colors occur more frequently than others. Here we employ a set of 684 randomly chosen 10-base oligomers to address these questions. Rather than a flat distribution, we find that specific color bands dominate. Cluster size data indicate that these “magic colors” originate from the existence of magic numbers for DNA-stabilized silver clusters, which differ from those of spheroidal gold clusters stabilized by small-molecule ligands. Elongated cluster structures, enforced by multiple base ligands along the DNA, can account for both magic number sizes and color variation around peak wavelength populations.

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.

DNA-Protected Silver Clusters for Nanophotonics

DNA-protected silver clusters (AgN-DNA) possess unique fluorescence properties that depend on the specific DNA template that stabilizes the cluster. They exhibit peak emission wavelengths that range across the visible and near-IR spectrum. This wide color palette, combined with low toxicity, high fluorescence quantum yields of some clusters, low synthesis costs, small cluster sizes and compatibility with DNA are enabling many applications that employ AgN-DNA. Here we review what is known about the underlying composition and structure of AgN-DNA, and how these relate to the optical properties of these fascinating, hybrid biomolecule-metal cluster nanomaterials. We place AgN-DNA in the general context of ligand-stabilized metal clusters and compare their properties to those of other noble metal clusters stabilized by small molecule ligands. The methods used to isolate pure AgN-DNA for analysis of composition and for studies of solution and single-emitter optical properties are discussed. We give a brief overview of structurally sensitive chiroptical studies, both theoretical and experimental, and review experiments on bringing silver clusters of distinct size and color into nanoscale DNA assemblies. Progress towards using DNA scaffolds to assemble multi-cluster arrays is also reviewed.

Dual-color nanoscale assemblies of structurally stable, few-atom silver clusters, as reported by fluorescence resonance energy transfer.

We develop approaches to hold fluorescent silver clusters composed of only 10-20 atoms in nanoscale proximity, while retaining the individual structure of each cluster. This is accomplished using DNA clamp assemblies that incorporate a 10 atom silver cluster and a 15 or 16 atom silver cluster. Thermally modulated fluorescence resonance energy transfer (FRET) verifies assembly formation. Comparison to Förster theory, using measured spectral overlaps, indicates that the DNA clamps hold clusters within roughly 5 to 6 nm separations, in the range of the finest resolutions achievable on DNA scaffolds. The absence of spectral shifts in dual-cluster FRET pairs, relative to the individual clusters, shows that select few-atom silver clusters of different sizes are sufficiently stable to retain structural integrity within a single nanoscale DNA construct. The spectral stability of the cluster persists in a FRET pair with an organic dye molecule, in contrast to the blue-shifted emission of the dye.

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, AgN-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 AgN-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 AgN-DNA may have potential for fluorescence-reported changes in dielectric environment at length scales of ∼1 nm.

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 (AgN-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 AgN-DNAs are selected, the exact mechanisms responsible for fluorescence remain unknown. To explore these mechanisms, we study four distinct purified AgN-DNAs in ethanol-water and methanol-water mixtures and find that the solvatochromic behavior of AgN-DNAs varies widely among different cluster species and differs markedly from prior results on impure material. Placing AgN-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 AgN-DNAs. Instead, alcohol-induced solvatochromism of AgN-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.

Base Motif Recognition and Design of DNA Templates for Fluorescent Silver Clusters by Machine Learning.

Discriminative base motifs within DNA templates for fluorescent silver clusters are identified using methods that combine large experimental data sets with machine learning tools for pattern recognition. Combining the discovery of certain multibase motifs important for determining fluorescence brightness with a generative algorithm, the probability of selecting DNA templates that stabilize fluorescent silver clusters is increased by a factor of >3.

Unusually large Stokes shift for a near-infrared emitting DNA-stabilized silver nanocluster

In this paper we present a new near-IR emitting silver nanocluster (NIR-DNA-AgNC) with an unusually large Stokes shift between absorption and emission maximum (211 nm or 5600 cm-1). We studied the effect of viscosity and temperature on the steady state and time-resolved emission. The time-resolved results on NIR-DNA-AgNC show that the relaxation dynamics slow down significantly with increasing viscosity of the solvent. In high viscosity solution, the spectral relaxation stretches well into the nanosecond scale. As a result of this slow spectral relaxation in high viscosity solutions, a multi-exponential fluorescence decay time behavior is observed, in contrast to the more mono-exponential decay in low viscosity solution.