Bascom Gavin, Andricioaei Ioan
Department of Chemistry, University of California , Irvine, California 92617, United States.
J Phys Chem C Nanomater Interfaces. 2014 Dec 18;118(50):29441-29447. doi: 10.1021/jp5081274. Epub 2014 Oct 21.
We study the conformational equilibrium between B-to-A forms of ds-DNA adsorbed onto a single-walled carbon nanotube (SWNT) using free energy profile calculations based on all-atom molecular dynamics simulations. The potential of mean force (PMF) of the B-to-A transition of ds-DNA in the presence of an uncharged (10,0) carbon nanotube for two dodecamers with poly-AT or poly-GC sequences is calculated as a function of a root-mean-square-distance (ΔRMSD) difference metric for the B-to-A transition. The calculations reveal that in the presence of a SWNT DNA favors B-form DNA significantly in both poly-GC and poly-AT sequences. Furthermore, the poly-AT DNA:SWNT complex shows a higher energy penalty for adopting an A-like conformation than poly-GC DNA:SWNT by several kcal/mol. The presence of a SWNT on either poly-AT or poly-GC DNA affects the PMF of the transition such that the B form is favored by as much as 10 kcal/mol. In agreement with published data, we find a potential energy minimum between A and B-form DNA at ΔRMSD ≈ -1.5 Å and that the presence of the SWNT moves this minimum by as much as ΔRMSD = 3 Å.
我们基于全原子分子动力学模拟，通过自由能分布计算，研究了吸附在单壁碳纳米管（SWNT）上的双链DNA（ds-DNA）从B型到A型的构象平衡。对于具有聚AT或聚GC序列的两个十二聚体，计算了在存在不带电的（10,0）碳纳米管的情况下ds-DNA从B型到A型转变的平均力势（PMF），该PMF是B型到A型转变的均方根距离（ΔRMSD）差异度量的函数。计算结果表明，在存在SWNT的情况下，无论是聚GC序列还是聚AT序列，DNA都显著倾向于B型DNA。此外，聚AT DNA:SWNT复合物采用类似A型构象时的能量惩罚比聚GC DNA:SWNT高几个千卡/摩尔。聚AT或聚GC DNA上存在SWNT会影响转变的PMF，使得B型受到高达10千卡/摩尔的青睐。与已发表的数据一致，我们发现在ΔRMSD≈ -1.5 Å处，A型和B型DNA之间存在势能最小值，并且SWNT的存在会使这个最小值移动多达ΔRMSD = 3 Å。
