Sequence-specific cleavage of DNA under ultrasound is due to intra-molecular dynamics. 1. Sugar Ring Dynamics within the Dickerson–Drew dodecamer

We present results from MD simulations of the Drew-Dickerson dodecamer d(CGCGAATTCGCG)2 (DDD) on 2 μs trajectories in six force fields: AMBER (parm99, bsc0, bsc1, OL15) and CHARMM (Ch27 and Ch36). The aim of this work was to reveal the context-dependent dynamics of β-D-deoxyribose in nucleotides at different DDD positions. Trajectory analysis revealed that the lifetime of the N- and S-states of furanose rings and the frequency of their S↔N interconversions depend on the type of the nucleotide and its context. We use several metrics to analyze the conformational dynamics of β-D-deoxyribose. Specifically: phase angle distribution and percentage of N-type conformers at each DDD position; relative lifetime of the N-state simultaneously in both 5′-terminal nucleotides of complementary double-stranded dinucleotides and relative lifetime of the N-state simultaneously in neighboring nucleotides along the strand; frequency of S→N transition to the deep N region (to a conformation with a phase angle less than 60 degrees) and maximum lifetime of the subsequent deep N state; the population of nucleotides with an acute angle between the C3‘-O3’ bond and the helix axis in each DDD position. As well, we analyzed the percentage of BII-conformers at each DDD position. We compared our simulation results with the statistical data on sequence-specific ultrasonic cleavage of double-stranded DNA.