Single Molecule Spectroscopy for Studying Conformational Dynamics of Short Oligonucleotides

Understanding biology at the molecular level has been driving technological advances in biological and medical science for many years. Methods for probing molecular systems are often dependent on sampling the concerted actions of large assemblies of molecules rather than for studying individual molecules operating in isolation. Most methods used in experimental biology are largely insensitive to the activity of a single molecule. Over the past twenty five years, advances in a variety of disciplines have been employed which allow researchers to use single molecule approaches to for examining biomolecules, a development which has had remarkable implications for advancing the understanding of cellular processes. Single molecule techniques have been used to resolve questions about everything from replication, recombination, transcription and translation and protein folding, among other subjects.The structure-function relationship in biology is central to the understanding of cellular processes, and has provided one of the most significant intellectual frameworks for understanding molecular pathways. Its success is validated by numerous studies using X-ray crystallography that now routinely allow researchers to make rational predictions explaining why and how biomolecules interact. The famous "lock and key" model for enzymatic function perhaps best exemplifies this framework. Despite their predictive power, structure-functional relationships often gloss over a basic fact of biological systems--both structure and function may in fact possess a remarkable degree of dynamism. This dissertation summarizes my efforts to develop and refine methods for interrogating the dynamical properties of single molecules, with a particular emphasis on studying structural properties of DNA and examining protein-DNA interactions. I provide an overview of fluorescence, FRET and fluorescence lifetime spectroscopy in Chapter 1, and discuss the methods I developed using fluorescence lifetime to examine conformational fluctuations of sub-persistence length segments of DNA. In Chapter 2, I describe a microfluidic-based platform developed in the Shimon Weiss Lab for conducting single molecule FRET assays, which was used to exploit persistence length changes in DNA upon hybridization to screen context-dependent RNA polymerase transcription. Finally, in Chapter 3, I describe a new detector with improved red spectrum sensitivity, which provides a foundation for further work applying fluorescence lifetime analysis to studying structural perturbations in DNA on nanosecond timescales