Shimazaki Tomomi, Asai Yoshihiro, Yamashita Koichi
Department of Chemical System Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo, Tokyo 113-8656, Japan.
J Phys Chem B. 2005 Jan 27;109(3):1295-303. doi: 10.1021/jp047456d.
Recently, the electronic properties of DNA have been extensively studied, because its conductivity is important not only to the study of fundamental biological problems, but also in the development of molecular-sized electronics and biosensors. We have studied theoretically the reorganization energies, the activation energies, the electronic coupling matrix elements, and the rate constants of hole transfer in B-form double-helix DNA in water. To accommodate the effects of DNA nuclear motions, a subset of reaction coordinates for hole transfer was extracted from classical molecular dynamics (MD) trajectories of DNA in water and then used for ab initio quantum chemical calculations of electron coupling constants based on the generalized Mulliken-Hush model. A molecular mechanics (MM) method was used to determine the nuclear Franck-Condon factor. The rate constants for two types of mechanisms of hole transfer-the thermally induced hopping (TIH) and the super-exchange mechanisms-were determined based on Marcus theory. We found that the calculated matrix elements are strongly dependent on the conformations of the nucleobase pairs of hole-transferable DNA and extend over a wide range of values for the "rise" base-step parameter but cluster around a particular value for the "twist" parameter. The calculated activation energies are in good agreement with experimental results. Whereas the rate constant for the TIH mechanism is not dependent on the number of A-T nucleobase pairs that act as a bridge, the rate constant for the super-exchange process rapidly decreases when the length of the bridge increases. These characteristic trends in the calculated rate constants effectively reproduce those in the experimental data of Giese et al. [Nature 2001, 412, 318]. The calculated rate constants were also compared with the experimental results of Lewis et al. [Nature 2000, 406, 51].
近年来，DNA的电子特性受到了广泛研究，因为其导电性不仅对基础生物学问题的研究至关重要，而且在分子尺寸电子学和生物传感器的发展中也具有重要意义。我们从理论上研究了水中B型双螺旋DNA的重组能、活化能、电子耦合矩阵元以及空穴转移的速率常数。为了考虑DNA核运动的影响，从水中DNA的经典分子动力学（MD）轨迹中提取了空穴转移反应坐标的一个子集，然后用于基于广义穆利肯-胡什模型的电子耦合常数的从头算量子化学计算。采用分子力学（MM）方法确定核弗兰克-康登因子。基于马库斯理论确定了空穴转移的两种机制——热诱导跳跃（TIH）和超交换机制的速率常数。我们发现，计算得到的矩阵元强烈依赖于可进行空穴转移的DNA核碱基对的构象，对于“上升”碱基步长参数，其值分布在很宽的范围内，但对于“扭曲”参数则聚集在一个特定值附近。计算得到的活化能与实验结果吻合良好。虽然TIH机制的速率常数不依赖于作为桥梁的A-T核碱基对的数量，但当桥梁长度增加时，超交换过程的速率常数迅速下降。计算得到的速率常数中的这些特征趋势有效地重现了吉泽等人[《自然》2001年，412卷，318页]实验数据中的趋势。计算得到的速率常数还与刘易斯等人[《自然》2000年，406卷，51页]的实验结果进行了比较。
