B型DNA中鸟嘌呤-胞嘧啶碱基对内双质子转移反应

引用本文: 林月霞, 王红艳, 高思敏, 吴颖曦, 李汝虎. B型DNA中鸟嘌呤-胞嘧啶碱基对内双质子转移反应[J]. 物理化学学报, 2013, 29(06): 1233-1239. doi: 10.3866/PKU.WHXB201304022 shu

Citation: 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 Physico-Chimica Sinica, 2013, 29(06): 1233-1239. doi: 10.3866/PKU.WHXB201304022 shu

B型DNA中鸟嘌呤-胞嘧啶碱基对内双质子转移反应

基金项目:
国家自然科学基金(10974161, 11174237) (10974161, 11174237)

国家重点基础研究发展规划项目(973) (2013CB328904) (973) (2013CB328904)

中央高校基本科研业务费专项基金(2010ZT06)资助 (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:

English

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

1.
School of Physical Science and Technology, Southwest Jiaotong University, Chengdu 610031, P. R. China
Received Date: 17 December 2012
Available Online: 17 May 2013
Fund Project:
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)

中央高校基本科研业务费专项基金(2010ZT06)资助

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:

1. [1]
  
  (1) Kobayashi, K.; Tagawa, S. J. Am. Chem. Soc. 2003, 125, 10213.doi: 10.1021/ja036211w
  (1) Kobayashi, K.; Tagawa, S. J. Am. Chem. Soc. 2003, 125, 10213.doi: 10.1021/ja036211w
2. [2]
  (2) Kobayashi, K.; Yamagami, R.; Tagawa, S. J. Phys. Chem. B2008, 112, 10752. doi: 10.1021/jp804005t(2) Kobayashi, K.; Yamagami, R.; Tagawa, S. J. Phys. Chem. B2008, 112, 10752. doi: 10.1021/jp804005t
3. [3]
  (3) Yamagami, R.; Kobayashi, K.; Tagawa, S. J. Am. Chem. Soc.2008, 130, 14772. doi: 10.1021/ja805127e(3) Yamagami, R.; Kobayashi, K.; Tagawa, S. J. Am. Chem. Soc.2008, 130, 14772. doi: 10.1021/ja805127e
4. [4]
  (4) Adhikary, A.; Khanduri, D.; Sevilla, M. D. J. Am. Chem. Soc.2009, 131, 8614. doi: 10.1021/ja9014869(4) Adhikary, A.; Khanduri, D.; Sevilla, M. D. J. Am. Chem. Soc.2009, 131, 8614. doi: 10.1021/ja9014869
5. [5]
  (5) rb, L.; Podolyan, Y.; Dziekonski, P.; Sokalski,W. A.;Leszczynski, J. J. Am. Chem. Soc. 2004, 126, 10119. doi: 10.1021/ja049155n(5) rb, L.; Podolyan, Y.; Dziekonski, P.; Sokalski,W. A.;Leszczynski, J. J. Am. Chem. Soc. 2004, 126, 10119. doi: 10.1021/ja049155n
6. [6]
  (6) Zoete, V.; Meuwly, M. J. Chem. Phys. 2004, 121, 4377. doi: 10.1063/1.1774152(6) Zoete, V.; Meuwly, M. J. Chem. Phys. 2004, 121, 4377. doi: 10.1063/1.1774152
7. [7]
  (7) Sevilla, M. D.; Besler, B.; Colson, A. O. J. Phys. Chem. 1995,99, 1060. doi: 10.1021/j100003a032(7) Sevilla, M. D.; Besler, B.; Colson, A. O. J. Phys. Chem. 1995,99, 1060. doi: 10.1021/j100003a032
8. [8]
  (8) Hutter, M.; Clark, T. J. Am. Chem. Soc. 1996, 118, 7574. doi: 10.1021/ja953370+(8) Hutter, M.; Clark, T. J. Am. Chem. Soc. 1996, 118, 7574. doi: 10.1021/ja953370+
9. [9]
  (9) Smets, J.; Houben, L.; Schoone, K.; Maes, G.; Adamowicz, L.Chem. Phys. Lett. 1996, 262, 789. doi: 10.1016/S0009-2614(96)01151-7(9) Smets, J.; Houben, L.; Schoone, K.; Maes, G.; Adamowicz, L.Chem. Phys. Lett. 1996, 262, 789. doi: 10.1016/S0009-2614(96)01151-7
10. [10]
  (10) Podolyan, Y.; rb, L.; Leszczynski, J. J. Phys. Chem. A 2000,104, 7346. doi: 10.1021/jp000740u(10) Podolyan, Y.; rb, L.; Leszczynski, J. J. Phys. Chem. A 2000,104, 7346. doi: 10.1021/jp000740u
11. [11]
  (11) Noguera, M.; Rodríguez-Santia , L.; Sodupe, M.; Bertran, J.J. Mol. Struct. 2001, 537, 307.(11) Noguera, M.; Rodríguez-Santia , L.; Sodupe, M.; Bertran, J.J. Mol. Struct. 2001, 537, 307.
12. [12]
  (12) Florián, J.; Leszczyński, J. J. Am. Chem. Soc. 1996, 118, 3010.doi: 10.1021/ja951983g(12) Florián, J.; Leszczyński, J. J. Am. Chem. Soc. 1996, 118, 3010.doi: 10.1021/ja951983g
13. [13]
  (13) Noguera, M.; Bertran, J.; Sodupe, M. J. Phys. Chem. A 2004,108, 333. doi: 10.1021/jp036573q(13) Noguera, M.; Bertran, J.; Sodupe, M. J. Phys. Chem. A 2004,108, 333. doi: 10.1021/jp036573q
14. [14]
  (14) Noguera, M.; Sodupe, M.; Bertrán, J. Theor. Chem. Acc. 2007,118, 113. doi: 10.1007/s00214-007-0248-z(14) Noguera, M.; Sodupe, M.; Bertrán, J. Theor. Chem. Acc. 2007,118, 113. doi: 10.1007/s00214-007-0248-z
15. [15]
  (15) Lin, Y.;Wang, H.; Gao, S.; Schaefer, H. F. J. Phys. Chem. B2011, 115, 11746. doi: 10.1021/jp205403f(15) Lin, Y.;Wang, H.; Gao, S.; Schaefer, H. F. J. Phys. Chem. B2011, 115, 11746. doi: 10.1021/jp205403f
16. [16]
  (16) Lin, Y.;Wang, H.; Gao, S.; Li, R.; Schaefer, H. F. J. Phys. Chem. B 2012, 116, 8908. doi: 10.1021/jp3048746(16) Lin, Y.;Wang, H.; Gao, S.; Li, R.; Schaefer, H. F. J. Phys. Chem. B 2012, 116, 8908. doi: 10.1021/jp3048746
17. [17]
  (17) Gupta, A.; Jaeger, H. M.; Compaan, K. R.; Schaefer, H. F.J. Phys. Chem. B 2012, 116, 5579. doi: 10.1021/jp211608b(17) Gupta, A.; Jaeger, H. M.; Compaan, K. R.; Schaefer, H. F.J. Phys. Chem. B 2012, 116, 5579. doi: 10.1021/jp211608b
18. [18]
  (18) Chen, H. Y.; Kao, C. L.; Hsu, S. C. N. J. Am. Chem. Soc. 2009,131, 15930. doi: 10.1021/ja906899p(18) Chen, H. Y.; Kao, C. L.; Hsu, S. C. N. J. Am. Chem. Soc. 2009,131, 15930. doi: 10.1021/ja906899p
19. [19]
  (19) Chen, H. Y.; Yeh, S.W.; Hsu, S. C. N.; Kao, C. L.; Dong, T. Y.Phys. Chem. Chem. Phys. 2011, 13, 2674. doi: 10.1039/c0cp01419b(19) Chen, H. Y.; Yeh, S.W.; Hsu, S. C. N.; Kao, C. L.; Dong, T. Y.Phys. Chem. Chem. Phys. 2011, 13, 2674. doi: 10.1039/c0cp01419b
20. [20]
  (20) Cerón-Carrasco, J. P.; Zúñiga, J.; Requena, A.; Perpète, E. A.;Michaux, C.; Jacquemin, D. Phys. Chem. Chem. Phys. 2011, 13,14584. doi: 10.1039/c1cp20946a(20) Cerón-Carrasco, J. P.; Zúñiga, J.; Requena, A.; Perpète, E. A.;Michaux, C.; Jacquemin, D. Phys. Chem. Chem. Phys. 2011, 13,14584. doi: 10.1039/c1cp20946a
21. [21]
  (21) Šponer, J.; Leszczynski, J.; Hobza, P. J. Mol. Struct. -Theochem2001, 573, 43. doi: 10.1016/S0166-1280(01)00537-1(21) Šponer, J.; Leszczynski, J.; Hobza, P. J. Mol. Struct. -Theochem2001, 573, 43. doi: 10.1016/S0166-1280(01)00537-1
22. [22]
  (22) Chen, H. Y.; Chao, I. ChemPhysChem 2004, 5, 1855.(22) Chen, H. Y.; Chao, I. ChemPhysChem 2004, 5, 1855.
23. [23]
  (23) Ray, S. G.; Daube, S. S.; Naaman, R. Proc. Natl. Acad. Sci.2005, 102, 15. doi: 10.1073/pnas.0407020102(23) Ray, S. G.; Daube, S. S.; Naaman, R. Proc. Natl. Acad. Sci.2005, 102, 15. doi: 10.1073/pnas.0407020102
24. [24]
  (24) Yakovchuk, P.; Protozanova, E.; Frank-Kamenetskii, M. D.Nucl. Acids Res. 2006, 34, 564. doi: 10.1093/nar/gkj454(24) Yakovchuk, P.; Protozanova, E.; Frank-Kamenetskii, M. D.Nucl. Acids Res. 2006, 34, 564. doi: 10.1093/nar/gkj454
25. [25]
  (25) Kumar, A.; Sevilla, M. D. J. Phys. Chem. B 2007, 111, 5464.doi: 10.1021/jp070800x(25) Kumar, A.; Sevilla, M. D. J. Phys. Chem. B 2007, 111, 5464.doi: 10.1021/jp070800x
26. [26]
  (26) Šponer, J.; Riley, K. E.; Hobza, P. Phys Chem. Chem. Phys.2008, 10, 2595. doi: 10.1039/b719370j(26) Šponer, J.; Riley, K. E.; Hobza, P. Phys Chem. Chem. Phys.2008, 10, 2595. doi: 10.1039/b719370j
27. [27]
  (27) Matsui, T.; Sato, T.; Shigeta, Y. Int. J. Quantum Chem. 2009,109, 2168. doi: 10.1002/qua.v109:10(27) Matsui, T.; Sato, T.; Shigeta, Y. Int. J. Quantum Chem. 2009,109, 2168. doi: 10.1002/qua.v109:10
28. [28]
  (28) Chen, H. Y.; Young, P. Y.; Hsu, S. C. N. J. Chem. Phys. 2009,130, 165101. doi: 10.1063/1.3120604(28) Chen, H. Y.; Young, P. Y.; Hsu, S. C. N. J. Chem. Phys. 2009,130, 165101. doi: 10.1063/1.3120604
29. [29]
  (29) Chen, H. Y.; Hsu, S. C. N.; Kao, C. L. Phys. Chem. Chem. Phys.2010, 12, 1253. doi: 10.1039/b920603e(29) Chen, H. Y.; Hsu, S. C. N.; Kao, C. L. Phys. Chem. Chem. Phys.2010, 12, 1253. doi: 10.1039/b920603e
30. [30]
  (30) Kumar, A.; Sevilla, M. D. J. Phys. Chem. B 2011, 115, 4990.doi: 10.1021/jp200537t(30) Kumar, A.; Sevilla, M. D. J. Phys. Chem. B 2011, 115, 4990.doi: 10.1021/jp200537t
31. [31]
  (31) Gu, J.;Wang, J.; Leszczynski, J. Chem. Phys. Lett. 2011, 512,108. doi: 10.1016/j.cplett.2011.06.085(31) Gu, J.;Wang, J.; Leszczynski, J. Chem. Phys. Lett. 2011, 512,108. doi: 10.1016/j.cplett.2011.06.085
32. [32]
  (32) Cerón-Carrasco, J. P.; Requena, A.; Jacquemin, D. Theor. Chem. Acc. 2012, 131, 1188. doi: 10.1007/s00214-012-1188-9(32) Cerón-Carrasco, J. P.; Requena, A.; Jacquemin, D. Theor. Chem. Acc. 2012, 131, 1188. doi: 10.1007/s00214-012-1188-9
33. [33]
  (33) Zhang, F.;Wang, H. Y.; Lin, Y. X. Acta Phys. -Chim. Sin. 2011,27, 2799. [张凤, 王红艳, 林月霞. 物理化学学报, 2011, 27,2799.] doi: 10.3866/PKU.WHXB20112799(33) Zhang, F.;Wang, H. Y.; Lin, Y. X. Acta Phys. -Chim. Sin. 2011,27, 2799. [张凤, 王红艳, 林月霞. 物理化学学报, 2011, 27,2799.] doi: 10.3866/PKU.WHXB20112799
34. [34]
  (34) HyperChem Professional 8.0.3; Hypercube, Inc., 1115 NW 4thStreet, Gainesville, FL 32601.(34) HyperChem Professional 8.0.3; Hypercube, Inc., 1115 NW 4thStreet, Gainesville, FL 32601.
35. [35]
  (35) Zhao, Y.; Truhlar, D. G. Theor. Chem. Acc. 2007, 120, 215.(35) Zhao, Y.; Truhlar, D. G. Theor. Chem. Acc. 2007, 120, 215.
36. [36]
  (36) Zhao, Y.; Truhlar, D. G. Accounts Chem. Res. 2008, 41, 157.doi: 10.1021/ar700111a(36) Zhao, Y.; Truhlar, D. G. Accounts Chem. Res. 2008, 41, 157.doi: 10.1021/ar700111a
37. [37]
  (37) Zhao, Y.; Truhlar, D. G. Theor. Chem. Acc. 2008, 119, 525. doi: 10.1007/s00214-007-0401-8(37) Zhao, Y.; Truhlar, D. G. Theor. Chem. Acc. 2008, 119, 525. doi: 10.1007/s00214-007-0401-8
38. [38]
  (38) Zhao, Y.; Truhlar, D. G. Chem. Phys. Lett. 2011, 502, 1. doi: 10.1016/j.cplett.2010.11.060(38) Zhao, Y.; Truhlar, D. G. Chem. Phys. Lett. 2011, 502, 1. doi: 10.1016/j.cplett.2010.11.060
39. [39]
  (39) Maseras, F.; Morokuma, K. J. Comput. Chem. 1995, 16, 1170.(39) Maseras, F.; Morokuma, K. J. Comput. Chem. 1995, 16, 1170.
40. [40]
  (40) Matsubara, T.; Sieber, S.; Morokuma, K. Int . J. Quantum Chem.1996, 60, 1101.(40) Matsubara, T.; Sieber, S.; Morokuma, K. Int . J. Quantum Chem.1996, 60, 1101.
41. [41]
  (41) Humbel, S.; Sieber, S.; Morokuma, K. J. Chem. Phys. 1996,105, 1959. doi: 10.1063/1.472065(41) Humbel, S.; Sieber, S.; Morokuma, K. J. Chem. Phys. 1996,105, 1959. doi: 10.1063/1.472065
42. [42]
  (42) Svensson, M.; Humbel, S.; Froese, R. D. J.; Matsubara, T.;Sieber, S.; Morokuma, K. J. Phys. Chem. 1996, 100, 19357. doi: 10.1021/jp962071j(42) Svensson, M.; Humbel, S.; Froese, R. D. J.; Matsubara, T.;Sieber, S.; Morokuma, K. J. Phys. Chem. 1996, 100, 19357. doi: 10.1021/jp962071j
43. [43]
  (43) Svensson, M.; Humbel, S.; Morokuma, K. J. Chem. Phys. 1996,105, 3654. doi: 10.1063/1.472235(43) Svensson, M.; Humbel, S.; Morokuma, K. J. Chem. Phys. 1996,105, 3654. doi: 10.1063/1.472235
44. [44]
  (44) Dapprich, S.; Komáromi, I.; Byun, K. S.; Morokuma, K.;Frisch, M. J. J. Mol. Struct. -Theochem 1999, 462, 1.(44) Dapprich, S.; Komáromi, I.; Byun, K. S.; Morokuma, K.;Frisch, M. J. J. Mol. Struct. -Theochem 1999, 462, 1.
45. [45]
  (45) Vreven, T.; Morokuma, K. J. Comput. Chem. 2000, 21, 1419.(45) Vreven, T.; Morokuma, K. J. Comput. Chem. 2000, 21, 1419.
46. [46]
  (46) Stewart, J. J. P. J. Comp. Chem. 1989, 10, 209.(46) Stewart, J. J. P. J. Comp. Chem. 1989, 10, 209.
47. [47]
  (47) Miertus, S.; Scrocco, E.; Tomasi, J. Chem. Phys. 1981, 55, 117.doi: 10.1016/0301-0104(81)85090-2(47) Miertus, S.; Scrocco, E.; Tomasi, J. Chem. Phys. 1981, 55, 117.doi: 10.1016/0301-0104(81)85090-2
48. [48]
  (48) Miertus, S.; Tomasi, J. Chem. Phys. 1982, 65, 239. doi: 10.1016/0301-0104(82)85072-6(48) Miertus, S.; Tomasi, J. Chem. Phys. 1982, 65, 239. doi: 10.1016/0301-0104(82)85072-6
49. [49]
  (49) Cossi, M.; Barone, V.; Cammi, R.; Tomasi, J. Chem. Phys. Lett.1996, 255, 327. doi: 10.1016/0009-2614(96)00349-1(49) Cossi, M.; Barone, V.; Cammi, R.; Tomasi, J. Chem. Phys. Lett.1996, 255, 327. doi: 10.1016/0009-2614(96)00349-1
50. [50]
  (50) Frisch, M. J.; Trucks, G.W.; Schlegel, H. B.; et al. Gaussian 09,Revision A.1; Gaussian Inc.:Wallingford, CT, 2009.
  (50) Frisch, M. J.; Trucks, G.W.; Schlegel, H. B.; et al. Gaussian 09,Revision A.1; Gaussian Inc.:Wallingford, CT, 2009.

扫一扫看文章

计量

PDF下载量: 548
文章访问数: 1389
HTML全文浏览量: 61

通讯作者: 陈斌, bchen63@163.com

1.
沈阳化工大学材料科学与工程学院沈阳 110142

B型DNA中鸟嘌呤-胞嘧啶碱基对内双质子转移反应

English

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

CCS Chemistry：嵌段共聚物自组装成 “三明治”二维有机材料，实现纳米级压力传感功能

CCS Chemistry：颜徐州、鲍哲南：你的皮肤可能是一片SPMs

CCS Chemistry：工作高效不疲劳，只须让催化剂动起来

CCS Chemistry：静电组装导向聚合- 聚电解质纳米凝胶量化制备新策略

CCS Chemistry：金黄色葡萄球菌醛基脱氢酶是如何识别特异性底物的？

计量

通讯作者: 陈斌, bchen63@163.com

中国化学会秘书处

B型DNA中鸟嘌呤-胞嘧啶碱基对内双质子转移反应

English

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

CCS Chemistry：嵌段共聚物自组装成 “三明治”二维有机材料，实现纳米级压力传感功能

CCS Chemistry：颜徐州、鲍哲南： 你的皮肤可能是一片SPMs

CCS Chemistry：工作高效不疲劳，只须让催化剂动起来

CCS Chemistry：静电组装导向聚合- 聚电解质纳米凝胶量化制备新策略

CCS Chemistry：金黄色葡萄球菌醛基脱氢酶是如何识别特异性底物的？

计量

文章相关

通讯作者: 陈斌, bchen63@163.com

中国化学会秘书处

CCS Chemistry：颜徐州、鲍哲南：你的皮肤可能是一片SPMs