Spectroscopic detection of DNA quadruplexes by vibrational circular dichroism

Journal of the American Chemical Society

Volumn 133, Issue 38, 2011, Pages 15055-15064

  Andrushchenko, Valery ^a   Tsankov, Dimiter ^b   Krasteva, Maria ^c   Wieser, Helmut ^c   Bouř, Petr ^a  

^a INSTITUTE OF ORGANIC CHEMISTRY AND BIOCHEMISTRY   (Czech Republic)

^b INSTITUTE OF ORGANIC CHEMISTRY   (Bulgaria)

^c UNIVERSITY OF CALGARY   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

DNA QUADRUPLEXES; EXPERIMENTAL SPECTRA; G-QUADRUPLEXES; IR ABSORPTION; MONOPHOSPHATES; MULTI-SCALE SIMULATION; NUCLEIC ACID STRUCTURE; QUADRUPLEX STRUCTURES; QUANTUM CHEMICAL MODELING; REALISTIC SIMULATION; SPECTRAL FEATURE; SPECTROSCOPIC DETECTION; SPECTROSCOPIC TECHNIQUE; STRUCTURAL MOTIFS; STRUCTURAL VARIATIONS; VIBRATIONAL CIRCULAR DICHROISM; VIBRATIONAL CIRCULAR DICHROISM SPECTRUM;

BIOMOLECULES; CHEMICAL ANALYSIS; CONFORMATIONS; DYNAMICS; MOLECULAR DYNAMICS; NUCLEIC ACIDS; QUANTUM CHEMISTRY;

DICHROISM;

DEOXYGUANOSINE PHOSPHATE; GUANINE QUADRUPLEX;

ARTICLE; CHEMICAL MODEL; CIRCULAR DICHROISM; INFRARED SPECTROSCOPY; MOLECULAR DYNAMICS; QUANTUM MECHANICS; RADIATION ABSORPTION; SIMULATION; VIBRATIONAL CRICULAR DICHROISM;

CIRCULAR DICHROISM; DNA; G-QUADRUPLEXES; MODELS, MOLECULAR; MOLECULAR DYNAMICS SIMULATION; QUANTUM THEORY; SPECTROPHOTOMETRY, INFRARED;

EID: 80053058531     PISSN: 00027863     EISSN: 15205126     Source Type: Journal    
DOI: 10.1021/ja204630k     Document Type: Article

References (86)

1. Howard, F. B.; Frazier, J.; Miles, H. T. Biopolymers 1977, 16, 791-809
2. Gellert, M.; Lipsett, M. N.; Davies, D. R. Proc. Natl. Acad. Sci. U.S.A. 1962, 48, 2013-2018
3. Davis, J. T. Angew. Chem, Int. Ed. 2004, 43, 668-698
4. Gottarelli, G.; Spada, G. P.; Garbesi, A. In Comprehensive Supramolecular Chemistry; Lehn, J.-M.; Atwood, J. L.; MacNicol, D. D.; Davies, J. A. D.; Vögtle, F.; Sauvage, J.-P.; Housseini, M. W., Eds.; Pergamon: Oxford, U.K., 1996; Vol. 9.
5. Forman, S. L.; Fettinger, J. C.; Pieraccini, S.; Gottarelli, G.; Davis, J. T. J. Am. Chem. Soc. 2000, 122, 4060-4067
6. Simonsson, T. Biol. Chem. 2001, 382, 621-628
7. Keniry, M. A. Biopolymers 2000, 56, 123-146
8. Han, H. Y.; Hurley, L. H. Trends Pharmacol. Sci. 2000, 21, 136-142
9. Burge, S.; Parkinson, G. N.; Hazel, P.; Todd, A. K.; Neidle, S. Nucleic Acids Res. 2006, 34, 5402-5415
10. Blackburn, E. H. Cell 1994, 77, 621-623
11. Kilpatrick, M. W.; Torri, A.; Kang, D. S.; Engler, J. A.; Wells, R. D. J. Biol. Chem. 1986, 261, 1350-1354
12. Sen, D.; Gilbert, W. Nature 1988, 334, 364-366
13. Simonsson, T.; Pecinka, P.; Kubista, M. Nucleic Acids Res. 1998, 26, 1167-1172
14. Neidle, S.; Read, M. A. Biopolymers 2000, 56, 195-208
15. Helder, M. N.; Wisman, G. B.; van der Zee, G. J. Cancer Invest. 2002, 20, 82-101
16. Huppert, J. L. Philos. Trans. R. Soc., A 2007, 365, 2969-2984
17. Oganesian, L.; Bryan, T. M. BioEssays 2007, 29, 155-165
18. Ueyama, H.; Takagi, M.; Takenaka, S. J. Am. Chem. Soc. 2002, 124, 14286-14287
19. Alberti, P.; Mergny, J. L. Proc. Natl. Acad. Sci. U.S.A. 2003, 100, 1569-1573
20. Miles, H. T.; Frazier, J. Biochim. Biophys. Acta 1964, 79, 216-220
21. Howard, F. B.; Miles, H. T. J. Biol. Chem. 1965, 240, 801-805
22. Miles, H. T.; Frazier, J. Biochem. Biophys. Res. Commun. 1972, 49, 199-204
23. Guzman, M. R.; Liquier, J.; Brahmachari, S. K.; Taillandier, E. Spectrochim. Acta, Part A 2006, 64, 495-503
24. Gramlich, V.; Klump, H.; Herbeck, R.; Schmid, E. D. FEBS Lett. 1976, 69, 15-18
25. Simard, C.; Savoie, R. Biopolymers 1994, 34, 91-100
26. Miura, T.; Thomas, G. J. Biochemistry 1995, 34, 9645-9654
27. Annamalai, A.; Keiderling, T. A. J. Am. Chem. Soc. 1987, 109, 3125-3132
28. Xiang, T.; Goss, D. J.; Diem, M. Biophys. J. 1993, 65, 1255-1261
29. Petrovic, A. G.; Polavarapu, P. L. J. Phys. Chem. B 2008, 112, 2245-2254
30. Nový, J.; Böhm, S.; Králová, J.; Král, V.; Urbanová, M. Biopolymers 2008, 89, 144-152
31. Andrushchenko, V. V.; van de Sande, J. H.; Wieser, H.; Kornilova, S. V.; Blagoi, Y. P. J. Biomol. Struct. Dyn. 1999, 17, 545-560
32. Andrushchenko, V.; Blagoi, Y.; van de Sande, J. H.; Wieser, H. J. Biomol. Struct. Dyn. 2002, 19, 889-906
33. Andrushchenko, V.; Tsankov, D.; Wieser, H. J. Mol. Struct. 2003, 661, 541-560
34. Polyanichko, A. M.; Andrushchenko, V. V.; Chikhirzhina, E. V.; Vorob'ev, V. I.; Wieser, H. Nucleic Acids Res. 2004, 32, 989-996
35. Tsankov, D.; Krasteva, M.; Andrushchenko, V.; van de Sande, J. H.; Wieser, H. Biophys. Chem. 2006, 119, 1-6
36. Zhong, W. X.; Gulotta, M.; Goss, D. J.; Diem, M. Biochemistry 1990, 29, 7485-7491
37. Zhong, W. X.; Gulotta, M. S.; Goss, D. J.; Diem, M. Biophys. J. 1990, 57, A457-A457
38. Wang, L.; Keiderling, T. A. Biochemistry 1992, 31, 10265-10271
39. Keiderling, T. A. In Circular Dichroism and the Conformational Analysis of Biomolecules; Fasman, G. D., Ed.; Plenum Press: New York, 1996; pp 555-597.
40. Stephens, P. J.; Devlin, F. J.; Gasparrini, F.; Ciogli, A.; Spinelli, D.; Cosimelli, B. J. Org. Chem. 2007, 72, 4707-4715
41. Freedman, T. B.; Cao, X. L.; Dukor, R. K.; Nafie, L. A. Chirality 2003, 15, 743-758
42. Bouř, P.; Sopková, J.; Bednárová, L.; Maloň, P.; Keiderling, T. A. J. Comput. Chem. 1997, 18, 646-659
43. Andrushchenko, V.; Bouř, P. Chirality 2010, 22, E96-E114
44. Bouř, P.; Andrushchenko, V.; Kabeláč, M.; Maharaj, V.; Wieser, H. J. Phys. Chem. B 2005, 109, 20579-20587
45. Andrushchenko, V.; Wieser, H.; Bouř, P. J. Phys. Chem. B 2004, 108, 3899-3911
46. Andrushchenko, V.; Wieser, H.; Bouř, P. J. Phys. Chem. B 2002, 106, 12623-12634
47. Tsankov, D.; Eggimann, T.; Wieser, H. Appl. Spectrosc. 1995, 49, 132-138
48. Wang, Y.; Patel, D. J. J. Mol. Biol. 1993, 234, 1171-1183
49. Case, D. A.; AMBER 9; University of California: San Francisco, 2006.
50. Perez, A.; Marchan, I.; Svozil, D.; Šponer, J.; Cheatham, T. E.; Laughton, C. A.; Orozco, M. Biophys. J. 2007, 92, 3817-3829
51. Jorgensen, W. L.; Chandrasekhar, J.; Madura, J. D.; Impey, R. W.; Klein, M. L. J. Chem. Phys. 1983, 79, 926-935
52. Frisch, M. J.; Gaussian 03, revision D.02; Gaussian, Inc.: Wallingford, CT, 2004.
53. Becke, A. D. J. Chem. Phys. 1993, 98, 1372-1377
54. Klamt, A.; Jonas, V.; Burger, T.; Lohrentz, J. C. W. J. Phys. Chem. A 1998, 102, 5074-5085
55. Perdew, J. P.; Wang, Y. Phys. Rev. B 1992, 45, 13244-13249
56. Becke, A. D. Phys. Rev. A 1988, 38, 3098-3100
57. Andrushchenko, V.; Bouř, P. J. Phys. Chem. B 2009, 113, 283-291
58. Grimme, S. J. Comput. Chem. 2006, 27, 1787-1799
59. Bouř, P.; Keiderling, T. A. J. Chem. Phys. 2002, 117, 4126-4132
60. Andrushchenko, V.; Leonenko, Z.; Cramb, D.; van de Sande, J. H.; Wieser, H. Biopolymers 2001, 61, 243-260
61. Tsuboi, M.; Kyogoku, Y.; Shimanouchi, T. Biochim. Biophys. Acta 1962, 55, 1-12
62. Tsuboi, M. Appl. Spectrosc. Rev. 1969, 3, 45-90
63. Tsuboi, M. In Basic Principles in Nucleic Acid Chemistry; Ts'o, P. O. P., Ed.; Academic Press: New York, 1974; Vol. 1, pp 399-452.
64. Taillandier, E.; Liquier, J.; Taboury, J. A. Adv. Infrared Raman Spectrosc. 1985, 12, 65-114
65. Theophanides, T.; Tajmir-Riahi, H. A. In Spectroscopy of Biological Molecules; Sandorfy, C.; Theophanides, T., Eds.; Reidel: Dordrecht, The Netherlands, 1984; pp 137-152.
66. Birke, S. S.; Diem, M. Biophys. J. 1995, 68, 1045-1049
67. Gulotta, M.; Goss, D. J.; Diem, M. Biopolymers 1989, 28, 2047-2058
68. Wang, L.; Keiderling, T. A. Nucleic Acids Res. 1993, 21, 4127-4132
69. Wang, L.; Yang, L.; Keiderling, T. A. Biophys. J. 1994, 67, 2460-2467
70. Bonazzi, S.; Capobianco, M.; Demorais, M. M.; Garbesi, A.; Gottarelli, G.; Mariani, P.; Bossi, M. G. P.; Spada, G. P.; Tondelli, L. J. Am. Chem. Soc. 1991, 113, 5809-5816
71. Gottarelli, G.; Proni, G.; Spada, G. P. Enantiomer 1996, 1, 201-209
72. Andrushchenko, V.; Bouř, P. J. Comput. Chem. 2008, 29, 2693-2703
73. Andrushchenko, V.; van de Sande, J. H.; Wieser, H. Biopolymers 2003, 69, 529-545
74. Špačková, N.; Berger, I.; Šponer, J. J. Am. Chem. Soc. 1999, 121, 5519-5534
75. Chowdhury, S.; Bansal, M. J. Phys. Chem. B 2001, 105, 7572-7578
76. Štefl, R.; Cheatham, T. E.; Špačková, N.; Fadrna, E.; Berger, I.; Koca, J.; Šponer, J. Biophys. J. 2003, 85, 1787-1804
77. Phillips, K.; Dauter, Z.; Murchie, A. I. H.; Lilley, D. M. J.; Luisi, B. J. Mol. Biol. 1997, 273, 171-182
78. Haider, S.; Parkinson, G. N.; Neidle, S. J. Mol. Biol. 2002, 320, 189-200
79. Saenger, W. Principles of Nucleic Acid Structure; Springer-Verlag: New York, 1984.
80. Arnott, S.; Chandras., R.; Marttila, C. M. Biochem. J. 1974, 141, 537-543
81. Patel, P. K.; Hosur, R. V. Nucleic Acids Res. 1999, 27, 2457-2464
82. Schultze, P.; Smith, F. W.; Feigon, J. Structure 1994, 2, 221-233
83. Keniry, M. A.; Strahan, G. D.; Owen, E. A.; Shafer, R. H. Eur. J. Biochem. 1995, 233, 631-643
84. Aboulela, F.; Murchie, A. I. H.; Norman, D. G.; Lilley, D. M. J. J. Mol. Biol. 1994, 243, 458-471
85. Hazel, P.; Parkinson, G. N.; Neidle, S. J. Am. Chem. Soc. 2006, 128, 5480-5487
86. Callender, R.; Deng, H. Annu. Rev. Biophys. Biomol. Struct. 1994, 23, 215-245