MODEL BUILDING & SIMULATION OF DNA & RNA AT MULTIPLE LENGTH SCALES

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This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. This resource project is targeted at development and testing of reduced models for DNA and RNA. We have been exploring electrostatic interactions in nucleic acids, specifically by considering the application of continuum solvent models (where all the degrees of freedom of the solvent and mobile counterions are removed) to conformational problems in nucleic acids. We have shown, for the first time, that these effective solvation models provide a convincing account of structures and relative energies of DNA and RNA helices and loops. Key goals for the coming project period will be to further explore divalent metal-ion binding and to incorporate realistic low-resolution models for RNA and DNA into the CHARMM and Amber programs.