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Research Abstracts Online
January 2008 - March 2009

St. Olaf College
Department of Chemistry

PI: Jeff Schwinefus

Urea Preferential Interactions With Double-stranded DNA Helices

Cellular biochemical reactions involving nucleic acids occur in aqueous solutions of salts, cosolutes, and biopolymers, such as proteins. These cosolutes, small organic solutes such as amino acids, nucleic acid precursors, simple sugars, and metabolites, can have dramatic influences on the structure and stability of nucleic acids. The long-term objective of this project is to elucidate the mechanism of cosolute modulation of folded nucleic acid stability, so as to better understand cosolute interaction with biopolymers and how these interactions influence biopolymer structural change and biochemical reactions. To this end, the project: 1) uses molecular dynamics (MD) simulations to quantify the preferential interaction of urea with double-stranded DNA helices to determine what roles solvent accessible chemical functional groups and sequence-mediated hydration play in urea accumulation or exclusion at the duplex surface, and 2) uses MD simulations to quantify urea preferential interaction coefficients using a statistical mechanical model. These experiments will provide a foundation for an improved understanding of nucleic acid structural stability in cellular environments and a broader understanding of biopolymer folding and unfolding processes, leading to insights into biopolymer function and biopolymer folding diseases.