In this dissertation we focus on better understanding the interactions of silver with DNA, a topic with far reaching implications that range from the realization of more robust DNA nanotechnology, to silver clusters templated by DNA (AgN-DNA) that can serve as fluorophores and molecular sensors, to better understanding of biological interactions that could lead to development of new approaches to the treatment of diseases that exploit silver-nucleic acid interactions. One important aspect of the interaction of Ag+ with DNA is that Ag+ can specifically bind to DNA bases as opposed to the negatively charged phosphate backbone allowing for precise control on where the Ag+ binds. For DNA nanotechnology this is ideal since DNA nanostructures require intricate designs with DNA strands self-assembling in a precise manner. Current DNA nanotechnology has harnessed the decades of research in canonical base pairing to realize 3D nanostructures, ranging from simple molecular machines to more complex and functional assemblies. Unfortunately, DNA nanotechnology is somewhat limited by DNA nanostructure stability as they are held together by weak hydrogen bonds and pi-stacking interactions. This is an issue which incorporation of strong Ag+-mediated pairings could help resolve. But in order to effectively use Ag+ in DNA nanotechnology, many more details must be known about the interactions of Ag+ with DNA.

DNA nanostructures are typically formed by combining many different single-stranded DNA strands which can then self-assemble into spatially arranged duplexes by canonical base pairing. As such, we begin by removing the canonical duplex constraints and first explore interactions of Ag+ with single-stranded DNA. We test every combination of homobase strands of the four canonical bases adenine, cytosine, guanine and thymine with Ag+ using electro-spray ionization mass spectrometry (ESI-MS). Homobase Ag+-paired strands of guanine and cytosine bases were detected. The emergence of C-Ag+-C and G-Ag+-G base pairs was evidenced both by the binding ratio of Ag+ to DNA bases and the stability of Ag+-mediated base pairs from theoretical calculations. These Ag+-paired guanine and cytosine homobase strands were found to have exceptional thermal stability even at short, 6 base lengths. We also find these Ag+-paired cytosine and guanine homobase strands form monodisperse products in certain solution conditions and have good stabilities in typical conditions used to form DNA nanostructures. Even heterobase strands which contain both cytosine and guanine bases can form Ag+-paired strands, with increased Ag+ incorporation associated with heterobase composition. These Ag+-paired cytosine and guanine homobase pairs appear to have properties which would allow incorporation into DNA nanostructures with canonical base pairings.

We explore strand orientation in Ag+-paired guanine and cytosine strands by using dye labelled strands and Förster resonance energy transfer (FRET) techniques. We find that both Ag+-paired cytosine and guanine strands prefer a parallel strand orientation, which is a pivotal piece of knowledge to effectively incorporate Ag+-mediated bases into DNA nanotechnology. We explore the shape of Ag+-paired guanine and cytosine homobase strands of various lengths by ion-mobility spectrometry ESI-MS. In ion-mobility spectroscopy the gas-phase structures retain a memory of their solution phase structure, which can be a useful structural analysis tool. The Ag+-paired guanine homobase strands appear to be elongated and linear in the akin to a canonically paired duplex, while the Ag+-paired cytosine strands have a compact and extended form in the which depends on charge state.

AgN-DNA are an aspect of DNA nanotechnology which are particularly promising as emerging fluorophores. AgN-DNA have optical properties that differ depending on the sequence of the DNA template strand. Certain sequences template AgN-DNA with quantum yields which approach unity. AgN-DNA have also been discovered with wavelengths of emission ranging from the visible to near-infrared. We explore the structure of these AgN-DNA using high performance liquid chromatography (HPLC) to purify them and analyze them with circular dichroism (CD) spectroscopy. We find that agreement between experimental CD spectra and theoretical calculations of a slightly twisted silver wire suggest a chiral, rod-like shape for the cluster in the AgN-DNA. We additionally find that the CD signal of AgN-DNA suggest that Ag+-mediated base pairs form an important foundation in the DNA secondary structure for the formation of AgN-DNA.

Fluorescent silver clusters with unique rod-like geometries are stabilized by DNA. The sizes and colors of these clusters, or Ag_N-DNA, are selected by DNA base sequence, which can tune peak emission from blue-green into the near-infrared. Combined with DNA nanostructures, Ag_N-DNA promise exciting applications in nanophotonics and sensing. Until recently, however, a lack of understanding of the mechanisms controlling Ag_N-DNA fluorescence has challenged such applications. This dissertation discusses progress toward understanding the role of DNA as a "genome" for silver clusters and toward using DNA to achieve atomic-scale precision of silver cluster size and nanometer-scale precision of silver cluster position on a DNA breadboard. We also investigate sensitivity of Ag_N-DNA to local solvent environment, with an eye toward applications in chemical and biochemical sensing.

Using robotic techniques to generate large data sets, we show that fluorescent silver clusters are templated by certain DNA base motifs that select "magic-sized" cluster cores of enhanced stabilities. The linear arrangement of bases on the phosphate backbone imposes a unique rod-like geometry on the clusters. Harnessing machine learning and bioinformatics techniques, we also demonstrate that sequences of DNA templates can be selected to stabilize silver clusters with desired optical properties, including high fluorescence intensity and specific fluorescence wavelengths, with much higher rates of success as compared to current strategies.

The discovered base motifs can be also used to design modular DNA host strands that enable individual silver clusters with atomically precise sizes to bind at specific programmed locations on a DNA nanostructure. We show that DNA-mediated nanoscale arrangement enables near-field coupling of distinct clusters, demonstrated by dual-color cluster assemblies exhibiting resonant energy transfer. These results demonstrate a new degree of control over the optical properties and relative positions of nanoparticles, selected almost solely by the sequence of DNA.

Ag_N-DNA are promising chemical and biochemical sensors due to the sensitivity of their fluorescence to local environment. However, the mechanisms behind many sensing schemes are not understood, and the nature of the excited state of the silver cluster itself remains unknown. To probe the fluorescence mechanisms of Ag_N-DNA, we investigate the behavior of purified solutions of these clusters in various solvents. We find that standard models for fluorophore solvatochromism, including the Lippert-Mataga model, do not describe Ag_N-DNA fluorescence because such models neglect specific interactions between the cluster and surrounding solvent molecules. Fluorescence colors are well-modeled by Mie-Gans theory, suggesting that the local dielectric environment of the cluster does play a role in fluorescence, although additional specific solvent interactions and cluster shape changes may also determine fluorescence color and intensity. These results suggest that Ag_N-DNA may be sensitive to changes in local dielectric environment on nanometer length scales and may also act as sensors for small molecules with affinity for DNA.