Exploration of the biological micro-surrounding effect on the excited states of the size-expanded fluorescent base x-cytosine in DNA

Journal of Physical Chemistry B

Volumn 114, Issue 10, 2010, Pages 3726-3734

  Zhang, Laibin ^a   Chen, Xiaohua ^a   Liu, Haiying ^a   Han, Li ^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

FLUORESCENCE; HYDRATION; QUANTUM YIELD; SUGAR (SUCROSE);

BASE PAIRING; BASE STACKING; BLUE SHIFT; COMPUTATIONAL INVESTIGATION; DIPOLE-ALLOWED TRANSITIONS; EMISSION ENERGIES; EMISSION PROCESS; EXCITED-STATE PROPERTIES; FLUORESCENCE EMISSION; FLUORESCENCE QUANTUM YIELD; GUANINE; HYPERCHROMIC EFFECT; MEASURED DATA; NATURAL BASIS; OSCILLATOR STRENGTHS; RED SHIFT; STATIC QUENCHING;

EXCITED STATES;

CYTOSINE; DNA;

ARTICLE; BASE PAIRING; CHEMISTRY; QUANTUM THEORY; SPECTROFLUOROMETRY;

BASE PAIRING; CYTOSINE; DNA; QUANTUM THEORY; SPECTROMETRY, FLUORESCENCE;

EID: 77953957419     PISSN: 15206106     EISSN: 15205207     Source Type: Journal    
DOI: 10.1021/jp9117503     Document Type: Article

References (94)

1. (a) Henry, A. A.; Romesberg, F. E. Curr. Opin. Chem. Biol. 2003, 7, 727.
2. (b) Cobb, A. J. A. Org. Biomol. Chem 2007, 5, 3260-3275.
3. (a) Egholm, M.; Buchart, O.; Christensen, L.; Behrens, C.; Freier, S. M.; Driver, D. A.; Berg, R. H.; Kim, S. K.; Norden, B.; Nielsen, P. E. Nature 1993, 365, 566-568.
4. (b) Nielsen, P. E.; Egholm, M.; Buchart, O. Bioconjugate Chem. 1994, 5, 3-7.
5. Petersen, M.; Wengel, J. Trends Biotechnol. 2003, 27, 74-81.
6. (a) Eschenmoser, A. Science 1999, 284, 2118-2124.
7. (b) Schoning, K.; Scholz, P.; Guntha, S.; Wu, X.; Krishnamurthy, R.; Eschenmoser, A. Science 2000, 290, 1347-1351.
8. (a) Ward, D. C.; Reich, E.; Stryer, L. J. Biol. Chem.1969, 244, 1228-1237.
9. (b) Nordlund, T. M.; Andersson, S.; Nilsson, L.; Rigler, R.; Graslund, A.; McLaughlin, L. W. Biochemistry 1989, 28, 9095-9103.
10. (c) Nordlund, T. M.; Xu, D.; Evans, K. O. Biochemistry 1993, 32, 12090-12095.
11. (a) Menger, M.; Tuschl, T.; Eckstein, F.; Porschke, D. Biochemistry 1996, 35, 14710-14716.
12. (b) Allan, B. W.; Reich, N. O.; Beechem, J. M. Biochemistry 1999, 38, 5308-5314.
13. (a) Guest, C. R.; Hochstrasser, R. A.; Sowers, L. C.; Millar, D. P. Biochemistry 1991, 30, 3271-3279.
14. (b) Bandwar, R. P.; Patel, S. S. J. Biol. Chem. 2001, 276, 14075-14082.
15. (c) Ujvari, A.; Martin, C. T. Biochemistry 1996, 35, 14574-14582.
16. (d) Jia, Y.; Kumar, A.; Patel, S. S. J. Biol. Chem. 1996, 271, 30451-30458.
17. (a) Stivers, J. T. Nucleic Acids Res. 1998, 26, 3837-3844.
18. (b) Rachofsky, E. L.; Seibert, E.; Stivers, J. T.; Osman, R.; Ross, J. B. A. Biochemistry 2001, 40, 957-967.
19. (a) Liu, C.; Martin, C. T. J. Mol. Biol. 2001, 308, 465-475.
20. (b) Liu, C.; Martin, C. T. J. Biol. Chem., 2002, 277, 2725-2731.
21. Coleman, R. S.; Madaras, M. L. J. Org. Chem. 1998, 63. 5700-5703.
22. (a) Okamoto, A.; Tainaka, K.; Saito, I. J. Am. Chem. Soc. 2003, 125, 4972-4973.
23. (b) Okamoto, A.; Tanaka, K.; Fukuta, T.; Saito, I. ChemBioChem 2004, 5, 958-963.
24. (c) Okamoto, A.; Tainaka, K.; Saito, I. Tetrahedron Lett. 2003, 44, 6871-6874.
25. (a) Kool, E. T. Acc. Chem. Res. 2002, 35, 936-943.
26. (b) Henry, A. A.; Romesberg, F. E. Curr. Opin. Chem. Biol. 2003, 7, 727-733.
27. (c) Hirao, I. Curr. Opin. Chem. Biol. 2006, 10, 622.
28. (d) Krueger, A. T.; Lu, H.; Lee, A. H.; Kool, E. T. Acc. Chem Res. 2007, 40, 141-150.
29. (a) Liu, H.; Gao, J.; Lynch, S. R.; Saito, Y. D.; Maynard, L.; Kool, E. T. Science 2003, 302, 868-871.
30. (b) Gao, J.; Liu, H.; Kool, E. T. J. Am. Chem. Soc. 2004, 126, 11826-11831.
31. (c) Liu, H.; Gao, J.; Kool, E. T. J. Org. Chem. 2005, 70, 639-647.
32. (d) Liu, H.; Gao, J.; Maynard, L.; Saito, D.; Kool, E. T. J. Am. Chem. Soc. 2004, 126, 1102-1109.
33. (e) Liu, H.; Gao, J.; Kool, E. T. J. Am. Chem. Soc. 2005, 127, 1396-1402.
34. (f) Krueger, A. T.; Kool, E. T. J. Am. Chem. Soc. 2008, 130, 3989-3999.
35. (a) Lu, H.; He, K.; Kool, E. T. Angew. Chem., Int. Ed. 2004, 43, 5834-5836.
36. (b) Lee, A. H. F.; Kool, E. T. J. Org. Chem. 2005, 70, 132-140.
37. (c) Lee, A. H. F.; Kool, E. T. J. Am. Chem. Soc. 2005, 127, 3332-3338.
38. Lee, A. H. F.; Kool, E. T. J. Am. Chem. Soc. 2006, 128, 9219-9230.
39. (a) Zhang, J.; Cukier, R. I.; Bu, Y. J. Phys. Chem. B 2007, 111, 8335-8341.
40. (b) Han, L.; Li, H.; Cukier, R. I.; Bu, Y. J. Phys. Chem. B 2009, 113, 4407-4412.
41. (a) Mayer, A.; Neuenhofer, S. Angew. Chem. Int. Ed. Engl. 1994, 33, 1044-1072.
42. (b) Millar, D. P. Curr. Opin. Struct. Biol. 1996, 6, 322-326.
43. (a) Manuela, J. R.; Marino, J. P. Curr. Org. Chem. 2002, 6, 775-793.
44. (b) Hawkins, M. E. Top. Fluoresc. Spectrosc. 2003, 7, 151-175.
45. Leconte, A. M.; Romesberg, F. E. Nature 2006, 444, 553-555.
46. (a) Fuentes-Cabrera, M.; Sumpter, B. G.; Wells, J. C. J. Phys. Chem. B 2005, 109, 21135-21139.
47. (b) Fuentes-Cabrera, M.; Sumpter, B. G.; Lipkowski, P.; Wells, J. C. J. Phys. Chem. B 2006, 110, 6379-6384.
48. (c) Vazquez-Mayagoita, A.; Huertas, O.; Fuentes-Cabrera, M.; Sumpter, B. G.; Orozco, M.; Luque, F. J. J. phys. Chem. B 2008, 112, 2179-2186.
49. Varsano, D.; Garbesi, A.; Felice, R. D. J. Phys. Chem. B 2007, 111, 14012-14021.
50. (a) Zhang, L.; Li, H.; Chen, X.; Cukier, R. I.; Bu, Y. J. Phys. Chem. B 2009, 113, 1173-1181.
51. (b) Zhang, L.; Li, H.; Li, J.; Chen, X.; Bu, Y. J. Comput. Chem. 2010, 31, 825-836.
52. Delaney, J. C.; Gao, J.; Liu, H.; Shrivastav, N.; Essigmann, J. M.; Kool, E. T. Angew. Chem. Int. Ed. 2009, 48, 4524-4527.
53. 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.; Ortiz, 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 E.0l; Gaussian, Inc.: Pittsburgh, PA, 2003.
54. Beck, A. D. J. Chem. Phys. 1993, 98, 5648-5652.
55. Lee, C.; Yang, W.; Parr, R. G. Phys. Rev. B: Condens. Matter. 1988, 37, 785-789.
56. Foresman, J. B.; Head-Gordon, M.; Pople, J. A.; Frisch, M. J. J. Phys. Chem. 1992, 96, 135-149.
57. Case, D. A.; Darden, T. A.; Cheatham, T. E., III; Simmerling, C. L.; Wang, J.; Duke, R. E.; Luo, R.; Merz, K. M.; Wang, B.; Pearlman, D. A.; Crowley, M.; Brozell, S.; Tsui, V.; Gohlke, H.; Mongan, J.; Hornak, V.; Cui, G.; Beroza, P.; Schafmeister, C.; Caldwell, J. W.; Ross, W. S.; Kollman, P. A. AMBER 8; University of California: San Francisco, CA, 2004.
58. Gorelsky, S. I. SWizard Program; CCRI, University Of Ottawa: Ottawa, Canada, 2009. http://www.sg-chem.net/swizard/.
59. Sobolewski, A. L.; Domcke, W.; Dedonder-Lardeux, C.; Jouvet, C. Phys. Chem. Chem. Phys. 2002, 4, 1093-1100.
60. (a) Kabelac, M.; Hobza, P. Chem.- Eur. J. 2001, 7, 2067-2074.
61. (b) Kabelac, M.; Ryjacek, F.; Hobza, P. Phys. Chem. Chem. 2000, 2, 4906-4909.
62. (c) Sivanesan, D.; Sumathi, I.; Welsh, W. J. Chem. Phys. Lett. 2003, 367, 351-360.
63. (a) Leszczynski, J. In Advances in Molecular Structure and Research; Hargittai, M., Hargittai, I., Eds.; JAI Press Inc.: Stamford, CT, 2000; Vol.6.
64. (b) Gorb, L.; Leszczynski, J. J. Am. Chem. Soc. 1998, 720, 5024-5032.
65. (c) Sponer, J.; Hobza, P.; Leszczynski, J. In Computational Chemistry: Reviews of Current Trends; Leszczynski, J., Ed.; World Scientific: Singapore, 2000; Vol.5.
66. (d) Trygubenko, S. A.; Bogdan, T. V.; Rueda, M.; Orozco, M.; Luque, F. J.; Sponer, J.; Slavicek, P.; Hobza, P. Phys. Chem. Chem. Phys. 2002, 4, 4192-4203.
67. (e) Hanu, M.; Ryjacek, F.; Kabelac, M.; Kubar, T.; Bogdan, T. V.; Trygubenko. S. A.; Hobza, P. J. Am. Chem. Soc. 2003, 125, 7678-7688.
68. (a) Shukla, M. K.; Leszczynski, J. J. Phys. Chem. B 2005, 109, 17333-17339.
69. (b) Shukla, M. K.; Leszczynski, J. J. Phys. Chem. B 2008, 112, 5139-5152.
70. (c) Shukla, M. K.; Leszczynski, J. Chem. Phys. Lett. 2009, 478, 254-259.
71. Merchán, M.; Serrano-Andrés, L. J. Am. Chem. Soc. 2003, 125, 8108-8109.
72. So, R.; Alavi, S. J. Comput. Chem. 2007, 28, 1776-1782.
73. Dreuw, A.; Head-Gordon, M. Chem. Rev. 2005, 105, 4009-4037.
74. Yanai, T.; Tew, D. P.; Handy, N. C. Chem. Phys. Lett. 2004, 393, 51-57.
75. (a) Kobayashi, R.; Amos, R. D. Chem. Phys. Lett. 2006, 420, 106109.
76. (b) Cai, Z.; Crossley, M. J.; Reimers, J. R.; Kobayashi, R.; Amos, R. J. Phys. Chem. B 2006, 110, 15624-15632.
77. Jensen, L.; Govind, N. J. Phys. Chem. A 2009, 113, 9761-9765.
78. (a) Makarov, V.; Pettitt, B. M.; Feig, M. Acc. Chem. Res. 2002, 35, 376-384.
79. (b) Auffinger, P.; Westhof, E. J. Mol. Biol. 2000, 300, 1113-1131.
80. (a) Schneider, B.; Berman, H. M. Biophys. J. 1995, 69, 2661.
81. (b) Coutinho, K.; Ludwig, V.; Canuto, S. phys. Rev. E 2004, 69, 061902.
82. (a) Kumar, A.; Mishra, P. C.; Suhai, S. J. Phys. Chem. A 2005, 109, 3971-3979.
83. (b) Kumar, A.; Sevilla, M. D.; Suhai, S. J. Phys. Chem. B 2008, 112, 5189-5198.
84. Thompson, K. C.; Miyake, N. J. phys. Chem. B 2005, 109, 6012-6019.
85. (a) Jean, J. M.; Hall, K. B. Biochemistry 2002, 41, 13152-13161.
86. (b) Jean, J. M.; Hall, K. B. Proc. Natl. Acad. Sci. U.S.A. 2001, 98, 37-41.
87. Kenfack, C. A.; Burger, A.; Mely, Y. J. Phys. Chem. B 2006, 110, 26327-26336.
88. (a) Santoro, F.; Barone, V.; Improta, R. Proc. Natl. Acad. Sci. U.S.A. 2007, 104, 9931-9936.
89. (b) Santoro, F.; Barone. V.; Improta, R. J. Comput. Chem. 2008, 29, 957-964.
90. (c) Improta, R. Phys. Chem. Chem. Phys. 2008, 10, 2656-2664.
91. Sugiyama, H.; Saito, I. J. Am. Chem. Soc. 1996, 118, 7063-7068.
92. Cantor, C R.; Schimmel, P. R. Biophysical Chemistry Part II: Techniques for the study of biological Stucture and Function; Freeman: New York, 1980.
93. Strickler, S. J.; Berg, R. A. J. Chem. Phys. 1962, 37, 814-822.
94. Atkins, P. W.; De Paula, J. Physical Chemistry, 7th ed.; Oxford University Press: New York, 2001.