Woźniak Aleksander P, Leś Andrzej, Adamowicz Ludwik
Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093, Warsaw, Poland.
Pharmaceutical Research Institute, Rydygiera 8, 01-793, Warsaw, Poland.
J Mol Model. 2019 Mar 14;25(4):97. doi: 10.1007/s00894-019-3976-9.
The phenomenon of DNA hole transport (HT) has attracted of scientists for several decades, mainly due to its potential application in molecular electronics. As electron holes mostly localize on purine bases in DNA, the majority of scientific effort has been invested into chemically modifying the structures of adenine and guanine in order to increase their HT-mediating properties. In this work we examine an alternative, never yet explored, way of affecting the HT efficiency by forcing electron holes to localize on pyrimidine bases and move between them. Using an enhanced and revised version of our previously developed QM/MM model, we perform simulations of HT through polyadenine, polycytosine, polyguanine, and polythymine stacks according to a multistep hopping mechanism. From these simulations, kinetic parameters for HT are obtained. The results indicate a particularly high efficiency of cytosine→cytosine hopping, which is about ten times higher than the G → G hopping. We also discuss possible improvement of cytosine HT by modifying the oxidoreductive properties of complementary guanine residues.
几十年来，DNA空穴传输（HT）现象一直吸引着科学家们，这主要是由于其在分子电子学中的潜在应用。由于电子空穴大多定位于DNA中的嘌呤碱基上，因此大部分科研工作都投入到对腺嘌呤和鸟嘌呤结构进行化学修饰，以增强它们介导空穴传输的特性。在这项工作中，我们研究了另一种尚未探索过的方法，即通过迫使电子空穴定位于嘧啶碱基并在它们之间移动来影响空穴传输效率。我们使用之前开发的QM/MM模型的增强和修订版本，根据多步跳跃机制对通过聚腺嘌呤、聚胞嘧啶、聚鸟嘌呤和聚胸腺嘧啶堆积体的空穴传输进行模拟。从这些模拟中，获得了空穴传输的动力学参数。结果表明胞嘧啶→胞嘧啶跳跃的效率特别高，大约比鸟嘌呤→鸟嘌呤跳跃高十倍。我们还讨论了通过修饰互补鸟嘌呤残基的氧化还原特性来提高胞嘧啶空穴传输的可能性。
