Understanding sequence effect in DNA bending elasticity by molecular dynamic simulations

Xiao-Wei Qiang,Hai-Long Dong,Kai-Xin Xiong,Wenbing Zhang,Zhi-Jie Tan

Figure 1. (a) The initial three-dimensional DNA structures with typical sequences of poly(A)-poly(T) duplex (AA-TT), poly(AT)-poly(TA) duplex (AT-TA) and generic one (GENE) for our all-atom molecular dynamics simulations, respectively. The three sequences were chosen according to the recent experiments [41, 51] and coarse-grained simulations [42]. (b) The root mean square deviations (RMSD) versus MD running time (500 ns) for the central 14-bp segment of the DNAs with three typical sequences. The black lines represent the RMSD values averaged over every 2 ns. The DNAs are in 150 mM NaCl solutions.