物理化学学报 >> 2013, Vol. 29 >> Issue (06): 1233-1239.doi: 10.3866/PKU.WHXB201304022

理论与计算化学 上一篇    下一篇

B型DNA中鸟嘌呤-胞嘧啶碱基对内双质子转移反应

林月霞, 王红艳, 高思敏, 吴颖曦, 李汝虎   

  1. 西南交通大学物理科学与技术学院, 成都 610031
  • 收稿日期:2012-12-17 修回日期:2013-04-01 发布日期:2013-05-17
  • 通讯作者: 王红艳 E-mail:hongyanw@home.swjtu.edu.cn
  • 基金资助:

    国家自然科学基金(10974161, 11174237); 国家重点基础研究发展规划项目(973) (2013CB328904)和中央高校基本科研业务费专项基金(2010ZT06)资助

Double-Proton-Transfer Reaction in Guanine-Cytosine Base Pair Embedded in B-Form DNA

LIN Yue-Xia, WANG Hong-Yan, GAO Si-Min, WU Ying-Xi, LI Ru-Hu   

  1. School of Physical Science and Technology, Southwest Jiaotong University, Chengdu 610031, P. R. China
  • Received:2012-12-17 Revised:2013-04-01 Published:2013-05-17
  • Supported by:

    The project was supported by the National Natural Science Foundation of China (10974161, 11174237), National Key Basic Research Program of China (973) ( 2013CB328904), and Fundamental Research Funds for the Central Universities, China (2010ZT06).

摘要:

采用ONIOM(M06-2X/6-31G*:PM3)方法研究了单个鸟嘌呤-胞嘧啶(GC)碱基对和含GC碱基对的四种排序的DNA三聚体(dATGCAT, dGCGCGC, dTAGCTA, dCGGCCG)的双质子转移反应. 通过分析其双质子转移方式、质子转移过程中各结构的能量和氢键变化, 总结出环境因素对GC碱基对双质子转移机理的影响. 气相中, dCGGCCG三聚体中发生分步双质子转移, 其它四种模型中均发生协同双质子转移. 分析发现质子转移方式受上下相邻碱基对的静电相互作用和质子接受位的质子亲和势影响, dATGCAT和dGCGCGC排序有助于质子H4a转移, 而dTAGCTA和dCGGCCG排序有助于质子H1转移, 胞嘧啶的N3位较高的质子亲和势有助于质子H1转移. 水溶剂中, 上下相邻碱基对的静电相互作用被减弱, 水溶剂稳定了分步转移过程中的单质子转移产物, 因此分步转移机理占据优势, 五种模型中均出现分步双质子转移, 在此过程中能量变化趋势相似. 溶剂效应有利于单质子转移, 却增加了双质子转移反应的反应能.

关键词: 密度泛函理论, DNA三聚体, 质子转移, 静电相互作用, 质子亲和势

Abstract:

The double-proton-transfer reaction of the isolated guanine-cytosine (GC) base pair and four DNA trimers with different nucleobase sequences (dATGCAT, dGCGCGC, dTAGCTA, and dCGGCCG) are studied by quantum mechanical calculations using ONIOM(M06-2X/6-31G*:PM3). Proton-transfer patterns, energy and structural properties are analyzed to gain insight into the double-proton-transfer mechanism with consideration to environmental factors. In the gas phase, a stepwise mechanism is found for the dCGGCCG trimer, and a concerted mechanism is found in the other four models. The computational results demonstrate that electrostatic interaction of the peripheral and middle base pairs have a pronounced effect on double-proton-transfer pattern of GC base pairs. The structures with dATGCAT and dGCGCGC sequences facilitate H4a proton transfer and those with dTAGCTA and dCGGCCG sequence facilitate H1 proton transfer. The high proton affinity of cytosine at N3 facilitates H1 proton transfer. In aqueous solution, electrostatic interactions are reduced and the products of single-proton-transfer in the stepwise mechanism are stabilized. This results in a stepwise transfer pattern becoming favorable. Solvent effects favor the single-proton-transfer reaction more than gas phase conditions, but increase the reaction energy of double-proton-transfer.

Key words: Density functional theory, DNA trimer, Proton transfer, Electrostatic interaction, Proton affinity

MSC2000: 

  • O641