UC Irvine

Nucleic acids, despite being among the most important macromolecules involved in biological life, remain poorly understood in terms of atomistic resolution dynamics at biologically relevant timescales. Due to recent advances in computational power and high resolution structure elucidation we are able to investigate the dynamics of four important nucleic acid structures, namely 5'-CGAT₆GGC-3', 5'-CGCGAT₄GGC-3', 5' -GCATCGAT₂GGC- 3' (referred to as A₆, A₄, and A₂ DNA respectively) and the TAR HIV-1 RNA molecule on the nanosecond and microsecond timescales. The trajectories are numerically characterized by the NMR relaxation parameter S² which provides an established measure of motion comparable to experiment, from nanosecond based ensembles in the case of A₆, A₄, and A₂DNA, and microsecond based ensembles for A_{6DNA and TAR RNA. Specifically, this comparison suggests that while DNA exhibits saturated motions at the nanosecond-microsecond timescale, HIV-1 TAR RNA exhibits motions seemingly correlated across timescales suggesting it has not yet fully saturated motion at the microsecond timescale. Effects of internally correlated, temporally correlated, and diffusively continual motions for nucleic acids are discussed. Finally, the potential of mean force (PMF) of one such smooth transition, the A / B transition, is reported in the presence of a Single Walled Carbon Nanotube (SWNT) for DNA of GC and AT rich sequences.}