Acta Phys. -Chim. Sin. ›› 2013, Vol. 29 ›› Issue (06): 1233-1239.doi: 10.3866/PKU.WHXB201304022


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).


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