Characterizing the Conformational Fluctuations of DNA Under Physiological and Salt-Stabilized Conditions

Abstract

The Marcus Group conducts studies on the dynamics of macromolecules in biological environments. In our experiments, we used a variety of techniques to analyze the structure of DNA with the overall goal of better understanding the conformations it can take. Our studies were focused in two areas: (1) understanding the mechanisms of DNA breathing, and (2) conducting experiments on the stabilizing and destabilizing properties of salt solutions on DNA. Techniques included circular and linear dichroism, UV-Vis spectroscopy, and Förster Resonance Energy Transfer (FRET). Determining the structure of DNA is crucial to understanding biochemical and molecular events essential for gene expression and DNA replication. For these processes to occur, various proteins must access ssDNA coding templates which are otherwise inaccessible due to complementary base pairing in dsDNA. Proteins rely on thermal fluctuations in the DNA double-stranded region at physiological temperatures known as DNA ‘breathing’. Studies are ongoing, but thus far have led us to a better understanding of the energetic favorability of various conformations of DNA.