UC San Diego

Although surface-enhanced Raman spectroscopy (SERS) has been a valuable tool for chemical detection, the understanding of the contributions of the chemical enhancement effect in nucleic acid-silver composites remains limited. Nucleic acid-silver composites have unique optical properties such as fluorescence and enhanced

Raman generation, and thus need to be further analyzed and characterized.

In this dissertation, the static polarizability chemical effect is used to determine the preferential binding sites of nucleic acids to silver nanoparticles. The binding configuration dictates the optical properties, so it is imperative to determine which atoms are binding to the silver structures. Time-dependent density functional theory simulations are used to calculate the Raman frequencies of several systems and are then quantitatively compared to experimental measurements. The approximate composition of the binding sites for each nucleic acid to silver films is determined using the simulated Raman correlation spectroscopy process.

In the second part of the dissertation, the charge-transfer effect in nucleic acid-silver composites is harnessed in order to selectively enhance or reduce the SERS signals via wavelength selection. Depending on the molecular properties of the nucleic acids, the optimal excitation wavelength shifts from visible to near-infrared. The properties can be taken advantage of to better control the systems under study. The charge-transfer effect is further understood by utilizing a thin film of aluminum oxide to prevent electron transfer from occurring, and thus enabling the calculation of the order of magnitude of the charge-transfer effect.

The characterization of nucleic acid-silver composites is imperative to fully understanding the unique and exciting properties that these systems provide. While SERS has been limited in terms of DNA detection or sequencing, the restrictions have been caused by insufficient information. This dissertation offers additional information on the systems and explains the discrepancies seen in previous measurements of nucleic acid-silver composites.