(736a) A Coarse Grained Model for Short Double Stranded Ribonucleic Acid

The phenomenon of RNA interference has given birth to an explosion of research into a multitude of therapeutic applications. There is a fundamental need to understand the structure and stability of siRNA duplexes at the nanometer length scale, and ultimately how chemical modifications to the nucleic acid structure influence hybridization and binding. Moreover, a model that accounts for sequence specificity, as well as specific ionic effects may add insight into the design of possible delivery mechanisms.

A new coarse-grained (CG) potential is presented for dsRNA. Using simple functional forms, while preserving local electrostatic charge, force field parameters are optimized to account for base interactions, as well as base solvation. Intramolecular interactions are obtained from all-atom molecular dynamics at physiological salt conditions. Hybridization free energies are compared with experimentally obtained (relative) association energies for several short RNA sequences.