Citation: ZHANG Feng, WANG Hong-Yan, LIN Yue-Xia. Effects of Cu²⁺ on Proton Transfer Processes in an Adenine-Thymine Anion Base Pair[J]. Acta Physico-Chimica Sinica, ;2011, 27(12): 2799-2804. doi: 10.3866/PKU.WHXB20112799 shu

Effects of Cu²⁺ on Proton Transfer Processes in an Adenine-Thymine Anion Base Pair

1.
School of Physical Science and Technology, Southwest Jiaotong University, Chengdu 610031, P. R. China

Corresponding author: LIN Yue-Xia,
Received Date: 28 June 2011
Available Online: 27 September 2011
Fund Project: 国家自然科学基金(10974161, 11004160) (10974161, 11004160)中央高校基本科研业务费专项基金(SWJTU09CX079, 2010ZT06)资助项目 (SWJTU09CX079, 2010ZT06)

The proton-transfer processes of the adenine-thymine (A-T) base pair anion (AT)^- and the Cu²⁺ cationized (A-T) base pair anion were investigated using the B3LYP/DZP ++ method. A single protontransfer process was found for the (A-T) base pair anion in which proton H₂₆ at the N₂₅ site of thymine transferred to the N₁₀ site of adenine. The metal cation Cu²⁺ can coordinate to the N₄ and N₁₃ sites of adenine as well as the O₂₄ and O₂₈ sites of thymine in (AT)^- by coordination interactions. For Cu²⁺ coordinated to the O₂₄ and O₂₈ sites of thymine the single proton transfer from thymine to adenine is possible. However, when Cu²⁺ interacts with the N4 or N13 of adenine the double proton-transferred product was found to be stable.
- Density functional theory,
- Base pair,
- Proton-transfer,
- Coordination,
- DNA damage
1. [1]
  (1) Thompson, C. K.; Conwell, E. J. Phys. Chem. Lett. 2010, 1, 1403.
2. [2]
  (2) Noguera, M.; Sodupe, M.; Bertrán, J. Theor. Chem. Acc. 2007, 118, 113.
3. [3]
  (3) Wang, H. Y.; Zhang, J. D.; Schaefer, H. F. ChemPhysChem. 2010, 11, 622.
4. [4]
  (4) Xie, H. J.; Xia, F.; Cao, Z. X. J. Phys. Chem. A 2007, 111 (20), 4384.
5. [5]
  (5) Lind, M. C.; Richardson, N. A.; Wheeler, S. E.; Schaefer, H. F. J. Phys. Chem. B 2007, 111 (19), 5525.
6. [6]
  (6) Xu, Z.; Li, N.; Cui, Y. P. J. Chem. Chin. Univ. 2009. 30 (3), 588. [徐仲, 李宁, 崔燕平. 高等学校化学学报. 2009, 3, 588.]
7. [7]
  (7) Shimizua, N.; Kawano, S.; Tachikawa, M. J. Mole. Struc. 2005, 735-736, 243.
8. [8]
  (8) Villani, G. Chem. Phys. 2005, 316, 1.
9. [9]
  (9) Zhang, Y. Theoretical Investigation of Metal Cations Interact with DNA Base Pair. Ph. D. Dissertation, Huazhong University of Science and Technology,Wuhan, 2004. [张愚. 金属离子与DNA碱基对相互作用的理论研究[D]. 武汉: 华中科技大学, 2004.]
10. [10]
  (10) Burda, J. V.; Sponer, J.; Hobza, P. J. Phys. Chem.1996, 100 (17), 7250.
11. [11]
  (11) Burda, J. V.; Sponer, J.; Leszczynski, J.; Hobza, P. J. Phys. Chem. 1997, 101 (46), 9670.
12. [12]
  (12) Noguera, M.; Bertrán, J.; Sodupe, M. J. Phys. Chem. B 2008, 112 (15), 4817.
13. [13]
  (13) Kumar, A.; Sevilla, M. D.; Sándor, S. J. Phys. Chem . B 2008, 112 (16), 5189.
14. [14]
  (14) Zhang, J. D.; Chen, Z. F.; Schaefer, H. F. J. Phys. Chem. A 2008, 112 (27), 6217.
15. [15]
  (15) Richardson, N. A.;Wesolowski, S. S.; Schaefer, H. F. J. Phys. Chem. B 2003, 107 (3), 848.
16. [16]
  (16) Xie, Y. M.; Schaefer, H. F. J. Chem. Phys. 2007, 127, 155107.
17. [17]
  (17) Radisic, D.; Bowen, K. H.; Dabkowska, I.; Storoniak, P.; Rak, J.; Gutowski, M. J. Am. Chem. Soc. 2005, 127, 6443.
18. [18]
  (18) Frisch, M. J.; Trucks, G.W.; Schlegel, H. B.; et al . Gaussian 03, Revision A. 01; Gaussian Inc.: Pittsburgh, PA, 2003.
19. [19]
  (19) Becke, A. D. J. Chem. Phys. 1993, 98, 5648.
20. [20]
  (20) Lee, C.; Yang,W. T.; Parr, R. G. Phys. Rev. 1988, 37, 785.
21. [21]
  (21) Kumar, A.; Sevilla, M. D. J. Phys. Chem. B 2009, 113 (33), 11359.
22. [22]
  (22) Latajka, Z.; Bouteiller, Y. J. Chem. Phys. 1994, 101, 9793.
23. [23]
  (23) Lee, C.; Fitzgerald, G.; Planas, M.; Novoa, J. J. J. Phys. Chem. 1996, 100, 7398.
24. [24]
  (24) Huzinaga, S. J. Chem. Phys. 1965, 42, 1293.
25. [25]
  (25) Dunning, T. H. J. Chem. Phys. 1970, 53, 2823.
26. [26]
  (26) Wachters, A. J. H. J. Chem. Phys. 1970, 52, 1033.
27. [27]
  (27) Hood, D. M.; Pitzer, R. M.; Schaefer, H. F. J. Chem. Phys. 1979, 71, 705.
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通讯作者: 陈斌, bchen63@163.com

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沈阳化工大学材料科学与工程学院沈阳 110142

Effects of Cu2+ on Proton Transfer Processes in an Adenine-Thymine Anion Base Pair

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通讯作者: 陈斌, bchen63@163.com

Effects of Cu²⁺ on Proton Transfer Processes in an Adenine-Thymine Anion Base Pair