(743b) Intermediate-Resolution Model for Simulating DNA Structure and Hybridization

Simplified DNA models can provide insight into molecular-level properties of DNA systems that is not easily accessible through current experimental techniques. In this contribution, a DNA model of resolution intermediate between that of atomistic and continuous models is designed for use with discontinuous molecular dynamics (DMD) simulations. The model was developed using a multiscale modeling approach in which the geometric and energetic parameters are obtained by collecting data from atomistic simulations of single- and double-stranded DNA molecules with explicit solvent and counterions. The sugar, phosphate, and base in the model are each represented by single spheres connected via bonds with appropriate lengths and angles. Hydrogen bonding is modeled using an angle-dependent square-well scheme and base stacking is modeled using explicit intra-strand interactions between nearest neighbor bases. DMD simulations were performed on model single- and double-stranded DNA molecules. The model was applied to study the temperature-dependent melting behavior of double-stranded DNA and the hybridization process from initially single-stranded molecules into a dynamic double helical structure. Structural properties such as relevant helical parameters, characteristic length, and their dependence on sequence and temperature are studied and compared with predicted ideal values and available experimental data.