Investigation of dsDNA stretching meso-mechanics using finite element method

This paper proposes a novel transient finite element model with equivalent meso-mechanics theory for studying the entropic elasticity and cooperative extensibility of double strand DNA (dsDNA). Through the proposed model, the dynamic structural transitions of the dsDNA under external force/torque can be accurately simulated within an affordable CPU time. Moreover, the proposed dsDNA model comprises the meso-mechanics equivalent theory of single molecule dsDNA, including the base-stacking interaction between DNA adjacent base pairs, the Hydrogen bond of complementary base-pairs and electrostatic interactions along double-helix sugar-phosphate backbones. Good agreement is achieved between the numerical simulation and the single molecular manipulation experimental result, and the mechanical behavior of stretching nicked dsDNA could be revealed