Ivanova Anela, Shushkov Philip, Rösch Notker
Department Chemie, Theoretische Chemie, Technische Universität München, 85747 Garching, Germany.
J Phys Chem A. 2008 Jul 31;112(30):7106-14. doi: 10.1021/jp8031513. Epub 2008 Jul 10.
The electronic coupling is one of the key parameters governing electron hole transfer along DNA helices. In this study, we established the first comprehensive data base of electronic coupling elements, calculated at the ab initio level. The data set comprises all possible Watson-Crick base pair dimers, both in standard A-DNA and B-DNA geometries. We also quantified the sensitivity of the coupling elements with respect to geometry changes by varying each of the six standard base step parameters, which specify the relative orientation of neighboring base pairs. We compare the couplings in a systematic way by discussing variations in the coupling magnitude due to geometry or nucleotide sequence in the dimer, and we analyze how the structure affects the electronic coupling in terms of general and dimer-specific trends. Furthermore, we studied how the coupling changes when one introduces the chemically modified base 7-deazaguanine in the corresponding base-pair dimers. Finally, on the basis of the calculated coupling elements, we suggest a model duplex with an enhanced capacity for hole transfer.
电子耦合是控制电子空穴沿DNA螺旋转移的关键参数之一。在本研究中，我们建立了首个从头算水平计算的电子耦合元件综合数据库。数据集包含标准A-DNA和B-DNA几何结构中所有可能的沃森-克里克碱基对二聚体。我们还通过改变六个标准碱基步参数中的每一个来量化耦合元件对几何结构变化的敏感性，这些参数指定了相邻碱基对的相对取向。我们通过讨论二聚体中由于几何结构或核苷酸序列导致的耦合强度变化，以系统的方式比较耦合情况，并根据一般趋势和二聚体特异性趋势分析结构如何影响电子耦合。此外，我们研究了在相应碱基对二聚体中引入化学修饰碱基7-脱氮鸟嘌呤时耦合如何变化。最后，基于计算得到的耦合元件，我们提出了一种具有增强空穴转移能力的模型双链体。
