Please use this identifier to cite or link to this item: http://scholarbank.nus.edu.sg/handle/10635/119457
Title: MICROMECHANICS OF DNA UNDER SHARP BENDING
Authors: CONG PEIWEN
Keywords: Nucleic acids, DNA bending, DNA defects, molecular dynamics, stress strain responses, DNA elasticity
Issue Date: 14-Oct-2014
Citation: CONG PEIWEN (2014-10-14). MICROMECHANICS OF DNA UNDER SHARP BENDING. ScholarBank@NUS Repository.
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.
URI: http://scholarbank.nus.edu.sg/handle/10635/119457
Appears in Collections:Ph.D Theses (Open)

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