B型DNA中鸟嘌呤-胞嘧啶碱基对内双质子转移反应

doi:10.3866/PKU.WHXB201304022

Abstract

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

LIN Yue-Xia, WANG Hong-Yan, GAO Si-Min, WU Ying-Xi, LI Ru-Hu. Double-Proton-Transfer Reaction in Guanine-Cytosine Base Pair Embedded in B-Form DNA[J]. Acta Phys. -Chim. Sin. 2013, 29(06), 1233-1239. doi: 10.3866/PKU.WHXB201304022

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

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