Niewieczerzał Szymon, Cieplak Marek
Institute of Physics, Polish Academy of Science, Aleja Lotników 32/48, 02-668 Warsaw, Poland.
J Phys Condens Matter. 2009 Nov 25;21(47):474221. doi: 10.1088/0953-8984/21/47/474221. Epub 2009 Nov 5.
Three coarse-grained molecular dynamics models of the double-stranded DNA are proposed and compared in the context of single molecule mechanical manipulation such as twisting and various schemes of stretching-unzipping, shearing, two-strand stretching and stretching of only one strand. The models differ in the number of effective beads (between two and five) representing each nucleotide. They all show similar behaviour, but the bigger the resolution, the more details in the force patterns. The models incorporate the effective Lennard-Jones potentials in the couplings between two strands and harmonic potentials to describe the structure of a single strand. The force patterns are shown to depend on the sequence studied. In particular, both shearing and unzipping for an all-AT sequence lead to lower forces than for an all-CG sequence. The unzipping patterns and the corresponding scenario diagrams for the contact rupture events are found to reflect the sequential information if the temperature is moderate and initial transients are discarded. The derived torque-force phase diagram is found to be qualitatively consistent with experiments and all-atom simulations.
提出了三种双链DNA的粗粒度分子动力学模型，并在单分子机械操作（如扭转以及各种拉伸-解链、剪切、双链拉伸和单链拉伸方案）的背景下进行了比较。这些模型在表示每个核苷酸的有效珠子数量（两个到五个之间）上有所不同。它们都表现出相似的行为，但分辨率越高，力模式中的细节就越多。模型在两条链之间的耦合中纳入了有效的 Lennard-Jones 势，并使用谐振势来描述单链的结构。结果表明，力模式取决于所研究的序列。特别是，对于全AT序列，剪切和解链产生的力都比全CG序列低。如果温度适中且忽略初始瞬态，发现接触破裂事件的解链模式和相应的情景图能反映序列信息。所推导的扭矩-力相图在定性上与实验和全原子模拟一致。
