MICROMECHANICS OF DNA UNDER SHARP BENDING

Abstract

Several recent experiments suggested that sharply bent short DNA deviates from the worm-like chain predictions, but the cause is poorly understood. We performed full-atom molecular dynamics simulations on 20 basepair DNA fragment with bending controlled by external compressing forces, which is analogous to some experiments. We show that sharp bending could excite flexible defects that consists of 1-3 disrupted basepairs at the center of DNA with an effective persistence length around 15 nm. Consequently, it leads to the formation of large local bends at defects and reduces DNA overall bending energy. For a DNA containing a pre-existing nick that mimics some experiments, it bends like normal B-DNA under weak constraints; but nick promotes defect excitations at nicked site under strong bending in temperature dependent manner. Overall, our results provide direct insights to those experiments, and reveal the micromechanics of sharply bent DNA at atomic level.