Two-dimensional infrared spectroscopy of nucleic acids : application to tautomerism and DNA aptamer unfolding dynamics

Thesis: Ph. D., Massachusetts Institute of Technology, Department of Chemistry, 2014.Cataloged from PDF version of thesis. Vita.Includes bibliographical references.The structural dynamics of nucleic acids are intimately related to their biological functions; however, our ability to study these molecular dynamics has been largely impeded by the lack of techniques that possess both high time resolution and structural sensitivity. The motivation for the work in this thesis was to develop and apply two-dimensional infrared spectroscopy (2D IR) as a new experimental tool to investigate nucleic acid dynamics. Infrared spectroscopy is sensitive to structural changes of nucleic acids and 2D IR offers sub-picosecond time resolution. 2D IR spectroscopy is advantageous over the linear infrared absorption spectroscopy because the vibrational spectrum is spread onto two frequency axes, giving rise to the structurally sensitive cross-peaks. These cross-peaks allow the determination of vibrational couplings, which encode chemical bond connectivity, distance and orientation. However, 2D IR spectroscopy of nucleic acids is underdeveloped due to the difficulties in modeling highly delocalized and coupled vibrations of nucleobases. This thesis initiated the efforts to develop 2D IR spectroscopy of nucleic acids by first characterizing the 2D IR spectra and vibrational eigenstates of nucleobases, using a model of multiple anharmonically coupled oscillators. With pronounced cross-peaks existing between all the vibrations for a give nucleobase, 2D IR spectroscopy was shown to be capable of distinguishing between different tautomers, using pyridone as a model system. Coupled with a laser-induced temperature-jump (T-jump), 2D IR was used to monitor rapidly exchanging tautomers in real time under physiological conditions on the nanosecond timescale. Systematically characterizing the tautomer exchange rates as a function of various experimental variables lead to a two-state concerted mechanism involving bridging water wires for the lactam-lactim tautomerization of 6-chloro-2-pyridone. This method was then applied to study the tautomerism of a deoxycytidine analog, KP1212, which is an anti-HIV drug. Multiple tautomers, including the normally rare enol tautomers, were found under physiological conditions. This observation supports the rare tautomer hypothesis, which states that each tautomer displays a distinct base-pairing preference, eventually leading to mutations and population collapse of the HIV viruses. Beyond studies on the single nucleotide level, 2D IR was used to characterize the structural dynamics of thrombin-binding aptamer (TBA), which is a 15mer DNA folded into a guanine-quadruplex (G-quadruplex). The 2D IR spectral signatures of G-quadruplex were established, and T-jump transient 2D IR was employed to investigate the unfolding dynamics of TBA. A mechanism of the early unfolding of TBA was proposed: A ~100 nanosecond response was attributed to the local deformation of the G-quadruplex, and a few-microsecond response was ascribed to be the fraying of the 3'-tail of TBA. This observation was consistent with a mechanism suggested by molecular dynamics simulations. Finally, the dissociation of double-stranded DNA formed by TBA and its complementary strand was found to be on the timescale of tens to hundreds of microseconds. The experiments in this thesis demonstrate the capability of 2D IR to investigate nucleic acid dynamics spanning a wide range of timescales.by Chunte Sam Peng.Ph. D