Spatiotemporal Characterization of DNA Hydration Water and Development of Method for Analyzing Liquid Sample in Terahertz Spectroscopy

Abstract

Water around DNA called DNA hydration water is well-known to be important for both DNAs structure and function. Without DNA hydration water, double helical structure of DNA and functional complex formation with protein is impossible. Conventional techniques such as X-ray crystallography, NMR and MD simulations have revealed that tightly bound extends about 4 Å from DNA surface with nanosecond-timescale reorientational time. Recently, as experimental technique is developed, DNA hydration water with picosecond-timescale reorientational time is suggested by time-resolved fluorescence spectroscopy and MD simulations. However, spatial and temporal information of picosecond-time scale DNA hydration water are unclear, yet. For other hydration water around protein and lipid, a-few-nanometer-thick hydration water with picosecond timescale is revealed by Terahertz (THz) spectroscopy. In this thesis, spatiotemporal characteristics of DNA hydration water is investigated by means of THz spectroscopy. Also, to probe subtle changes in hydration water, a new method to analyze liquid sample is developed. To probe slight changes in hydration water, experimental set-up with high SNR or more rigorous data analysis method is required. In the aspect of data processing, imprecise sample thickness hampers accuracy of optical constant. This thesis developed a novel algorithm for determining liquid sample thickness using Kramers-Kronig relations. For tens of micrometers thick water samples, the accuracy of sample thickness is improved by an order of magnitude (up to submicrometer) using the algorithm leading to obtain precise optical parameters of water. The broad applicability of the method is demonstrated for measuring various materials. Using THz spectroscopy, reorintational relaxation of water around mode DNA is studied. By controlling the DNA concentration, the relaxation time for water reorientation and the width of the DNA hydration layer are determined. A 7.6 Å-thick-layer of weakly bound hydration water, with a relaxation time of 11.6 ps is revealed by applying Double-Debye relaxation model and Bruggeman effective medium approximation to the acquired data from THz spectroscopy. This result demonstrates that a shell of hydration water, with reorientation time on the order of tens of picoseconds, exists beyond the structurally integrated water usually observed around DNA.