Absorption and fluorescence emission spectroscopic characters of size-expanded yDNA bases and effect of deoxyribose and base pairing

Journal of Physical Chemistry B

Volumn 113, Issue 4, 2009, Pages 1173-1181

  Zhang, Laibin ^a   Li, Huifang ^a   Chen, Xiaohua ^a   Cukier, Robert I ^b   Bu, Yuxiang ^a  

^a SHANDONG UNIVERSITY   (China)

^b MICHIGAN STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ABSORPTION; ABSORPTION SPECTROSCOPY; FLUORESCENCE; HYDROGEN; HYDROGEN BONDS; LUTETIUM; NUCLEIC ACIDS;

AB INITIO STUDIES; ABSORBANCE; BASE PAIRINGS; BASE PAIRS; BLUE SHIFTS; EMISSION ENERGIES; EXCITED SINGLET STATE; FLUORESCENCE EMISSIONS; GROUND-STATE GEOMETRIES; HYDROGEN BONDINGS; INTERACTION ENERGIES; MEASURED DATUM; NATURAL BASE; OPTICAL ABSORPTION AND EMISSIONS; RED SHIFTS;

EMISSION SPECTROSCOPY;

EID: 84962376114     PISSN: 15206106     EISSN: None     Source Type: Journal    
DOI: 10.1021/jp8094648     Document Type: Article

References (77)

1. For more information, see reviews: (a) Mayer, A.; Neuenhofer, S. Angew. Chem., Int. Ed. Engl. 1994, 33, 1044-1072.
2. (b) Millar, D. P. Curr. Opin. Struct. Biol. 1996, 6, 322-326.
3. (c) Manuela, J. R.; Marino, J. P. Curr. Org. Chem. 2002, 6, 775-793.
4. (d) Hawkins, M. E. Top. Fluoresc. Spectrosc. 2003, 7, 151-175.
5. Plavec, J.; Chattopadhyaya, J. Tetrahedron 1996, 52, 1597-1608.
6. (a) Ward, D. C.; Reich, E.; Stryer, L. J. Biol. Chem. 1969, 244, 1228-1237.
7. (b) Nordlund, T. M.; Andersson, S.; Nilsson, L.; Rigler, R.; Graslund, A.; McLaughlin, L. W. Biochemistry 1989, 28, 9095-9103.
8. (c) Nordlund, T. M.; Xu, D.; Evans, K. O. Biochemistry 1993, 32, 12090-12095.
9. (a) Menger, M.; Tuschl, T.; Eckstein, F.; Porschke, D. Biochemistry 1996, 35, 14710-14716.
10. (b) Allan, B. W.; Reich, N. O.; Beechem, J. M. Biochemistry 1999, 38, 5308-5314.
11. (a) Guest, C. R.; Hochstrasser, R. A.; Sowers, L. C.; Millar, D. P. Biochemistry 1991, 30, 3271-3279.
12. (b) Bandwar, R. P.; Patel, S. S. J. Biol. Chem. 2001, 276, 14075-14082.
13. (c) Ujvari, A.; Martin, C. T. Biochemistry 1996, 35, 14574-14582.
14. (d) Jia, Y.; Kumar, A.; Patel, S. S. J. Biol. Chem. 1996, 271, 30451-30458.
15. (a) Stivers, J. T. Nucleic Acids Res. 1998, 26, 3837-3844.
16. (b) Rachofsky, E. L.; Seibert, E.; Stivers, J. T.; Osman, R.; Ross, J. B. A. Biochemistry 2001, 40, 957-967.
17. Beechem, J. M.; Otto, M. R.; Bloom, L. B.; Eritja, R.; Reha-Krantz, L. J.; Goodman, M. F. Biochemistry 1998, 37, 10144-10155.
18. (a) Liu, C.; Martin, C. T. J. Mol. Biol. 2001, 308, 465-475.
19. (b) Liu, C.; Martin, C. T. J. Biol. Chem. 2002, 277, 2725-2731.
20. (a) Okamoto, A.; Tainaka, K.; Saito, I. J. Am. Chem. Soc. 2003, 125, 4972-1973.
21. (b) Okamoto, A.; Tanaka, K.; Fukuta, T.; Saito, I. ChemBioChem 2004, 5, 958-963.
22. (c) Okamoto, A.; Tainaka, K.; Saito, I. Tetrahedron Lett. 2003, 44, 6871-6874.
23. Coleman, R. S.; Madaras, M. L. J. Org. Chem. 1998, 63, 5700-5703.
24. Kool, E. T. Acc. Chem. Res. 2002, 35, 936-943.
25. Krueger, A. T.; Lu, H.; Lee, A. H.; Kool, E. T. Acc. Chem. Res. 2007, 40, 141-150.
26. Henry, A. A.; Romesberg, F. E. Curr. Opin. Chem. Biol. 2003, 7, 727-733.
27. Hirao, I. Curr. Opin. Chem. Biol. 2006, 10, 622.
28. (a) Liu, H.; Gao, J.; Lynch, S. R.; Saito, Y. D.; Maynard, L.; Kool, E. T. Science 2003, 302, 868-871.
29. (b) Gao, J.; Liu, H.; Kool, E. T. J. Am. Chem. Soc. 2004, 126, 11826-11831.
30. (c) Liu, H.; Gao, J.; Kool, E. T. J. Am. Chem. Soc. 2005, 127, 1396-1402.
31. (d) Liu, H.; Gao, J.; Kool, E. T. J. Org. Chem. 2005, 70, 639-647.
32. (e) Krueger, A. T.; Kool, E. T. J. Am. Chem. Soc. 2008, 130, 3989-3999.
33. (a) Lu, H.; He, K.; Kool, E. T. Angew. Chem. 2004, 116, 5958-5960.
34. (b) Lee, A. H. F.; Kool, E. T. J. Org. Chem. 2005, 70, 132-140.
35. (c) Lee, A. H. F.; Kool, E. T. J. Am. Chem. Soc. 2005, 127, 3332-3338.
36. Leconte, A. M.; Romesberg, F. E. Nature 2006, 444, 553-555.
37. (a) Fuentes-Cabrera, M.; Sumpter, B. G.; Wells, J. C. J. Phys. Chem. B 2005, 109, 21135-21139.
38. (b) Fuentes-Cabrera, M.; Sumpter, B. G.; Lipkowski, P.; Wells, J. C. J. Phys. Chem. B 2006, 110, 6379-6384.
39. Varsano, D.; Garbesi, A.; Felice, R. D. J. Phys. Chem. B 2007, 111, 14012-14021.
40. Huertas, O.; Blas, J. R.; Soteras, I.; Orozco, M.; Luque, F. J. J. Phys. Chem. A 2006, 110, 510-518.
41. Frisch, M. J.; Trucks, G. W.; Schlegel, H. B.; Scuseria, G. E.; Robb, M. A.; Cheeseman, J. R.; Montgomery, J. A., Jr.; Vreven, T.; Kudin, K.; Mennucci, B.; Cossi, M.; Scalmani, G.; Rega, N.; Petersson, G. A.; Nakatsuji, H.; Hada, M.; Ehara, M.; Toyota, K.; Fukuda, R.; Hasegawa, J.; Ishida, M.; Nakajima, T.; Honda, Y.; Kitao, O.; Nakai, H.; Klene, M.; Li, X.; Knox, J. E.; Hratchian, H. P.; Cross, J. B.; Adamo, C.; Jaramillo, J.; Gomperts, R.; Stratmann, R. E.; Yazyev, O.; Austin, A. J.; Cammi, R.; Pomelli, C.; Ochterski, J. W.; Ayala, P. Y.; Morokuma, K.; Voth, G. A.; Salvador, P.; Dannenberg, J. J.; Zakrzewski, V. G.; Dapprich, S.; Daniels, A. D.; Strain, M. C.; Farkas, O.; Malick, D. K.; Rabuck, A. D.; Raghavachari, K.; Foresman, J. B.; Ortz, J. V.; Cui, Q.; Baboul, A. F.; Clifford, S.; Cioslowski, J.; Stefanov, B. B.; Liu, G.; Liashenko, A.; Piskorz, P.; Komaromi, I.; Martin, R. L.; Fox, D. J.; Keith, T.; Al-Laham, M. A.; Peng, C. Y.; Nanyakkara, A.; Challacombe, M.; Gill, P. M. W.; Johnson, B.; Chen, W.; Wong, M. W.; Gonzalez, C.; Pople, J. A. Gaussian 03, revision B.03; Gaussian, Inc.: Pittsburgh, PA, 2003.
42. Beck, A. D. J Chem. Phys. 1993, 98, 5648-5652.
43. Lee, C.; Yang, W.; Parr, R. G. Phys. Rev. B: Condens. Matter. 1988, 37, 785-789.
44. Foresman, J. B.; Head-Gordon, M.; Pople, J. A.; Frisch, M. J. J. Phys. Chem. 1992, 96, 135-149.
45. (a) Broo, A.; Holmen, A. J. Phys. Chem. A 1997, 101, 3589-3600.
46. (b) Holmén, A.; Broo, A.; Norden, B. J. Am. Chem. Soc. 1997, 119, 12240-12250.
47. (a) Shukla, M. K.; Leszczynski, J. J. Phys. Chem. A 2002, 106, 4709-4717.
48. (b) Shukla, M. K.; Leszczynski, J. J. Phys. Chem. B 2005, 109, 17333-17339.
49. (a) Thompson, K. C.; Miyake, N. J. Phys. Chem. B 2005, 109, 6012-6019.
50. (b) Hardman, S. J. O.; Thompson, K. C. Biochemistry 2006, 45, 9145-9155.
51. Zhang, L.; Bu, Y. J. Phys. Chem. B 2008, 112, 10723-10731.
52. (a) Jödicke, C. J.; Luthi, H. P. J. Chem. Phys. 2002, 117, 4146-4156.
53. (b) Jödicke, C. J.; Lüthi, H. P. J. Chem. Phys. 2003, 119, 12852-12865.
54. (c) Jödicke, C. J.; Luthi, H. P. J. Am. Chem. Soc. 2003, 125, 252-264.
55. (a) Zhao, G. J.; Han, K. L. J. Phys. Chem. A 2007, 111, 2469-2474.
56. (b) Zhao, G. J.; Liu, J. Y.; Zhou, L. C.; Han, K. L. J. Phys. Chem. B 2007, 111, 8940-8945.
57. (c) Zhao, G. J.; Han, K. L. J. Phys. Chem. A 2007, 111, 9218-9223.
58. Kumar, A.; Sevilla, M. D. J. Am. Chem. Soc. 2008, 130, 2130-2131.
59. Gorelsky, S. I. SWizard Program; CCRI, University Of Ottawa: Ottawa, Canada, 2008; http://www.sg-chem.net/.
60. (a) Sponer, J.; Hobza, P. J. Phys. Chem. 1994, 98, 3161-3164.
61. (b) Hobza, P.; Sponer, J. Chem. Rev. 1999, 99, 3247-3276.
62. (a) Shukla, M. K.; Leszczynski, J. J. Comput. Chem. 2004, 25, 768-778.
63. (b) We also calculated the absorption spectra of natural bases at the same level of theory used in the present paper, and the detailed information are given in the Supporting Information.
64. So, R.; Alavi, S. J. Comput. Chem. 2007, 28, 1776-1782.
65. Kasha, M. Faraday Discuss. 1950, 9, 14-19.
66. Merchán, M.; Serrano-Andrés, L. J. Am. Chem. Soc. 2003, 125, 8108-8109.
67. (a) Miertus, S.; Scrocco, E.; Tomasi, J. Chem. Phys. 1981, 55, 117-129.
68. (b) Miertus, S.; Tomasi, J. Chem. Phys. 1982, 65, 239-245.
69. (a) Shukla, M. K.; Leszczynski, J. J. Phys. Chem. A 2002, 106, 8642-8650.
70. (b) Shukla, M. K.; Leszczynski, J. J. Phys. Chem. A 2002, 106, 11338-11346.
71. 1 excited states are optimized at the CIS level, which is at the same level of the HF method, the ground-state geometries used for comparisons are optimized using the latter method.
72. Broo, A. J. Phys. Chem. A 1998, 102, 526-531.
73. Ismail, N.; Blancafort, L.; Olivucci, M.; Kohler, B.; Robb, M. A. J. Am. Chem. Soc. 2002, 124, 6818-6819.
74. Mulliken, R. S. J. Chem. Phys. 1977, 66, 2448-2451.
75. (a) Mennucci, B.; Toniolo, A.; Tomasi, J. J. Phys. Chem. A 2001, 105, 7126-7134.
76. (b) Mishra, S. K.; Shukla, M. K.; Mishra, P. C. Spectrochim. Acta, Part A 2000, 56, 1355-1365.
77. Dreuw, A.; Head-Gordon, M. Chem. Rev. 2005, 105, 4009-4037.