Model calculations for the misincorporation of nucleotides opposite five-membered exocyclic DNA adduct: N 2,3-ethenoguanine

Journal of Physical Chemistry B

Volumn 115, Issue 35, 2011, Pages 10537-10546

  Srinivasadesikan, Venkatesan ^a   Sahu, Prabhat K ^a   Lee, Shyi Long ^a  

^a NATIONAL CHUNG CHENG UNIVERSITY   (Taiwan)

Author keywords

[No Author keywords available]

Indexed keywords

CHLORINE COMPOUNDS; ELECTRONIC PROPERTIES; HYDROGEN; HYDROGEN BONDS; NUCLEOTIDES;

BASE-PAIRING; CALCULATION MODELS; DNA ADDUCTS; DNA DAMAGES; DNA NUCLEOTIDES; DNA REPLICATIONS; GEOMETRIC CHARACTERISTICS; HYDROGEN-BONDING STRENGTH; MODEL CALCULATIONS; MOLECULAR LEVELS; MUTAGENIC PROCESS; OPTIMIZED GEOMETRIES; POLARIZABILITIES; REACTION ENTHALPIES; SINGLE-POINT ENERGY;

DNA;

EID: 80052333115     PISSN: 15206106     EISSN: 15205207     Source Type: Journal    
DOI: 10.1021/jp202738v     Document Type: Article

References (61)

1. Carcinogenesis 1987, 8, 745 - 747
2. Blair, I. A. Exp. Gerontol. 2001, 36, 1473-1481
3. Burcham, P. C. Mutagenesis 1998, 13, 287-305
4. Choi, J. H.; Pfeifer, G. P. Mutat. Res. 2004, 568, 245-256
5. Gros, L.; Ishchenko, A. A; Saparbaev, M. Mutat. Res. 2003, 531, 219-229
6. Douki, T.; Odin, F.; Caillat, S.; Favier, A.; Cadet, J. Free Radical Biol. Med. 2004, 37, 62-70
7. Speina, E; Kierzek, A. M.; Tudek, B. Mutat. Res. 2003, 531, 205-217
8. Mishina, Y.; Yang, C.-G.; He, C. J. Am. Chem. Soc. 2005, 127, 14594-14595
9. Green, T.; Hathway, D. E. Chem.-Biol. Interact. 1978, 22, 211-224
10. Eberle, G.; Barbin, A.; Laib, R. J.; Ciroussel, F.; Thomale, J.; Bartsch, H.; Rajewsky, M. F. Carcinogenesis 1989, 10, 209-212
11. Fedtke, N.; Boucheron, J. A.; Walker, V. E.; Swenberg, J. A. Carcinogenesis 1990, 11, 1287-1292
12. Guengerich, F. P.; Mason, P. S.; Stott, W. T.; Fox, T. R.; Watanabe, P. G. Cancer Res. 1981, 41, 4391-4398
13. Guengerich, F. P.; Kim, D. H. Chem. Res. Toxicol. 1991, 4, 413-421
14. Guengerich, F. P. Chem. Res. Toxicol. 1992, 5, 2-5
15. Bartsch, H.; Barbin, A.; Marion, M. J.; Nair, J.; Guichard, Y. Drug Metab. Rev. 1994, 26, 349-371
16. Nair, U.; Bartsch, H.; Nair, J. Free Radical Biol. Med. 2007, 43, 1109-1120
17. Lee, S. H.; Oe, T.; Blair, I. A. Chem. Res. Toxicol. 2002, 15, 300-304
18. Petrova, K. V.; Jalluri, R. S.; Kozekov, I. D.; Rizzo, C. J. Chem. Res. Toxicol. 2007, 20, 1685-1692
19. Lee, S. H.; Arora, J. A.; Oe, T.; Blair, I. A. Chem. Res. Toxicol. 2005, 18, 780-786
20. Lee, S. H.; Blair, I. A. Chem. Res. Toxicol. 2000, 13, 698-702
21. Kawai, Y.; Uchida, K.; Osawa, T. Free Radical Biol. Med. 2004, 36, 529-541
22. Lee, S. H.; Silva Elipe, M. V.; Arora, J. S.; Blair, I. A. Chem. Res. Toxicol. 2005, 18, 566-578
23. Creech, J. L.; Johnson, M. N. J. Occup. Med. 1974, 16, 150-151
24. Singer, B.; Spengler, S. J.; Chavez, F.; Kusmierek, J. T. Carcinogenesis 1987, 8, 745-747
25. Cheng, K. C.; Preston, B. D.; Cahill, D. S.; Dosanjh, M. K.; Singer, B.; Loeb, L. A. Proc. Natl. Acad. Sci. U.S.A. 1991, 88, 9974-9978
26. Loft, S.; Poulsen, H. E. J. Mol. Med. 1996, 74, 297-312
27. Schofield, M. J.; Hsieh, P. Annu. Rev. Microbiol. 2003, 57, 579
28. Berashevich, J.; Chakraborty, T. J. Chem. Phys. 2009, 130, 015101
29. Sahu, P. K.; Kuo, C.-W; Lee, S.-L. J. Phys. Chem. B 2007, 111, 2991-2998
30. Sahu, P. K.; Wang, C.-H; Lee, S.-L. J. Phys. Chem. B 2009, 113, 14529-14535
31. Sahu, P. K.; Jhong, M.-L.; Srinivasadesikan, V.; Lee, S.-L. J. Chem. Inf. Model. 2011, in press.
32. Parr, R. G.; Yang, W. Density-Functional Theory of Atoms and Molecules; Oxford Science: Oxford, U.K., 1989.
33. Magalhaes, A. L.; Madail, S. R. R. S.; Ramos, M. J. Theor. Chem. Acc. 2000, 105, 68-76
34. Fuqiang, B.; Kathryn, N. R.; James, W. G.; Russell, J. B. Theor. Chem. Acc. 2002, 108, 1-11
35. Loos, P. F.; Assfeld, X.; Rivail, J. L. Theor. Chem. Acc. 2007, 118, 165-171
36. Becke, A. D. Phys. Rev. A 1988, 38, 3098-3100
37. Becke, A. D. J. Chem. Phys. 1993, 98, 5648-5652
38. Becke, A. D. J. Chem. Phys. 1997, 107, 8554-8560
39. Lee, C.; Yang, W.; Parr, R. G. Phys. Rev. B 1988, 37, 785-789
40. Schmider, H. L.; Becke, A. D. J. Chem. Phys. 1998, 108, 9624-9631
41. Zhao, Y.; Truhlar, D. G. Theor. Chem. Acc. 2008, 120, 215-241
42. Head-Gordon, M.; Pople, J. A.; Frisch, M. J. Chem. Phys. Lett. 1988, 153, 503-506
43. Saebo, S.; Almloef, J. Chem. Phys. Lett. 1989, 154, 83-89
44. Frisch, M. J.; Head-Gordon, M.; Pople, J. A. Chem. Phys. Lett. 1990, 166, 275-280
45. Frisch, M. J.; Head-Gordon, M.; Pople, J. A. Chem. Phys. Lett. 1990, 166, 281-289
46. van Duijineveldt, F. B.; van Duijineveldt-van de Rijdt, J. C. M.; van Lenthe, J. H. Chem. Rev. 1994, 94, 1873-1885
47. Boys, S. F.; Bernardi, F. Mol. Phys. 1970, 19, 553-566
48. Barone, V.; Cossi, M. J. Phys. Chem. A 1998, 102, 1995-2001
49. Frisch, M. J.; Trucks, G. W.; Schlegel, H. B.; Scuseria, G. E.; Robb, M. A.; Cheeseman, J. R.; Scalmani, G.; Barone, V.; Mennucci, B.; Petersson, G. A.; Nakatsuji, H.; Caricato, M.; Li, X.; Hratchian, H. P.; Izmaylov, A. F.; Bloino, J.; Zheng, G.; Sonnenberg, J. L.; Hada, M.; Ehara, M.; Toyota, K.; Fukuda, R.; Hasegawa, J.; Ishida, M.; Nakajima, T.; Honda, Y.; Kitao, O.; Nakai, H.; Vreven, T.; Montgomery, J. A., Jr.; Peralta, J. E.; Ogliaro, F.; Bearpark, M.; Heyd, J. J.; Brothers, E.; Kudin, K. N.; Staroverov, V. N.; Kobayashi, R.; Normand, J.; Raghavachari, K.; Rendell, A.; Burant, J. C.; Iyengar, S. S.; Tomasi, J.; Cossi, M.; Rega, N.; Millam, J. M.; Klene, M.; Knox, J. E.; Cross, J. B.; Bakken, V.; Adamo, C; Jaramillo, J.; Gomperts, R. E.; Stratmann, O.; Yazyev, A. J.; Austin, R.; Cammi, C.; Pomelli, J. W.; Ochterski, R.; Martin, R. L.; Morokuma, K.; Zakrzewski, V. G.; Voth, G. A.; Salvador, P.; Dannenberg, J. J.; Dapprich, S.; Daniels, A. D.; Farkas, O.; Foresman, J. B.; Ortiz, J. V.; Cioslowski, J.; Fox, D. J. Gaussian 09, revision A.1; Gaussian, Inc.: Wallingford, CT, 2009.
50. Leontis, N. B.; Stombaugh, J.; Westhof, E. Nucleic Acids Res. 2002, 30, 3497-3531
51. Lemieux, S.; Major, F. Nucleic Acids Res. 2002, 30, 4250-4263
52. Das, J.; Mukherjee, S.; Mitra, A.; Bhattacharyya, D. J. Biomol. Struct. Dyn. 2006, 24, 149-161
53. Lu, X.-J.; Olson, W. K. Nat. Protocols 2008, 3, 1213-1227
54. Volk, D. E.; Thiviyanathan, V.; Somasunderam, A; Gorenstein, D. G. Org. Biomol. Chem. 2006, 4, 1741-1745
55. Czyznikowska, Z.; Gra, R. W.; Zaleny, R.; Lipkowski, P.; Jarzembska, K. N.; Dominiak, P. M.; Leszczynski, J. J. Phys. Chem. B 2010, 114, 9629-9644
56. Mallajosyula, S. S.; Datta, A.; Pati, S. K. Synth. Met. 2005, 155, 398-401
57. Sponer, J.; Jurecka, P.; Hobza, P. J. Am. Chem. Soc. 2004, 126, 10142-10151
58. Mo, Y. J. Mol. Model. 2006, 12, 665-672
59. Roy, A.; Panigrahi, S.; Bhattacharyya, M.; Bhattacharyya, D. J. Phys. Chem. B 2008, 112, 3786-3796
60. Hobza, P.; Kabelac, M.; Sponer, J.; Mejzlik, P.; Vondrasek, J. J. Comput. Chem. 1997, 18, 1136-1150
61. Bernstein, H.; Byerly, H.; Hopf, F.; Michod, R. Science 1985, 229, 1277-1281