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Albany 2015:Book of Abstracts

Albany 2015
Conversation 19
June 9-13 2015
©Adenine Press (2012)

The Distribution of Water and Ions around Nucleic Acids

Biomolecules always perturb the solutions into which they are placed. The distribtuions of water and ions around them can be monintored by a variety of tools, including dialysis, measurements of partial molar volumes, and X-ray scattering. Computational methods include explicit solvent simulations and integral equation theories (here, the 3D-RISM model). I will describe our recent efforts to simulate the distribution of water and ions around DNA and RNA, including single-strands, duplexes and quadruplexes. An emphasis will be on the use of such models to interpret X-ray scattering, to small- and wide-angle scattering in solution, and to scattering from disordered solvent in biomolecular crystals. Estimates of excess ion and hydration numbers (in solution) and total solvent content (in crystals) can be compared to experiment as a test of the theory. In turn, a microscopic description of the molecular environment can yield novel insights into the conformational behavior of nucleic acids.

References
    Janowski, P.A., Cerutti, D.S., Holton, J. & Case, D.A. (2013) Peptide crystal simulations reveal hidden dynamics. J. Am. Chem. Soc. 135, 7938-7948

    G.M. Giambasu, Luchko, T., Herschlag, D., York, D.M. & Case, D.A (2014) Ion counting from explicit solvent simulations and 3D-RISM. Biophys. J. 104, 883-894.

    Nguyen, H., Pabitt, S.A., Meisburger, S., Pollack, L. & Case, D.A. (2014) Accurate small and wide angle X-ray scattering profiles from atomic models of proteins and nucleic acids. J. Chem. Phys. 114, 22D508.

    Liu, C., Janowski, P.A. & Case, D.A. (2015) All-atom crystal simulations of DNA and RNA duplexes. Biochim. Biophys. Acta 1850, 1059-1071.


David A. Case

Department of Chemistry and Chemical Biology
Rutgers University
Piscataway, NJ 08854

Ph: (848)-445-5885
case@biomaps.rutgers.edu