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Investigation of the Sequence-Dependent dsDNA Mechanical Behavior using Clustered Atomistic-Continuum Method

C-A Yuan, C-N Han and K-N Chiang
National Tsing Hua University, TW

Keywords:
meso-mechanics, double-strand DNA, clustered atomistic-continuum method, transient finite element method

Abstract:
A novel clustered atomistic-continuum method (CACM) based on the transient finite element theory is proposed herein to simulate the dynamic structural transitions of the double strand DNA (dsDNA) under external loading. Moreover, the meso-mechanics of dsDNA molecules is then studied via the CACM model, including the base-stacking interaction between DNA adjacent nucleotide base pairs, the Hydrogen bond of complementary base-pairs and electrostatic interactions along DNA backbones. Due to that sequence information is embedded in the dsDNA model, the mechanical uniqueness of the distinct genome could be then clarified. Although the CACM models have reduced the degree-of-freedom (DOF) of nicked dsDNA, good agreement is achieved between the numerical simulation and experimental result. Moreover, the both-strand-fixed dsDNA model evolved from the validated dsDNA model could accurately represent the mechanical characteristics obtained by the single molecular manipulation experiment. Furthermore, based on the robust model validated by the experimental results, one would further study the sequence-depended mechanical response of dsDNA, and the multiple single strand break (SSB) of dsDNA.

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