Ferreira Izabela, Amarante Tauanne D, Weber Gerald
Departamento de Física, Universidade Federal de Minas Gerais, 31270-901 Belo Horizonte-MG, Brazil.
J Chem Phys. 2015 Nov 7;143(17):175101. doi: 10.1063/1.4934783.
DNA base pairs are known to open more easily at the helix terminal, a process usually called end fraying, the details of which are still poorly understood. Here, we present a mesoscopic model calculation based on available experimental data where we consider separately the terminal base pairs of a DNA duplex. Our results show an important reduction of hydrogen bond strength for terminal cytosine-guanine (CG) base pairs which is uniform over the whole range of salt concentrations, while for AT base pairs, we obtain a nearly 1/3 reduction but only at low salt concentrations. At higher salt concentrations, terminal adenine-thymine (AT) pair has almost the same hydrogen bond strength than interior bases. The calculated terminal stacking interaction parameters display some peculiarly contrasting behavior. While there is mostly no perceptible difference to internal stacking, for some cases, we observe an unusually strong dependence with salt concentration which does not appear follow any pattern or trend.
已知DNA碱基对在螺旋末端更容易打开，这一过程通常称为末端磨损，其细节仍知之甚少。在这里，我们基于现有实验数据进行了介观模型计算，其中我们分别考虑了DNA双链体的末端碱基对。我们的结果表明，末端胞嘧啶-鸟嘌呤（CG）碱基对的氢键强度显著降低，在整个盐浓度范围内都是均匀的，而对于腺嘌呤-胸腺嘧啶（AT）碱基对，我们只在低盐浓度下得到了近1/3的降低。在较高盐浓度下，末端腺嘌呤-胸腺嘧啶（AT）对的氢键强度几乎与内部碱基相同。计算得到的末端堆积相互作用参数显示出一些特别鲜明的对比行为。虽然与内部堆积大多没有明显差异，但在某些情况下，我们观察到其对盐浓度有异常强烈的依赖性，且似乎不遵循任何模式或趋势。
