G-quadruplex DNA cleavage preference and identification of a perylene diimide G-quadruplex photocleavage agent using a rapid fluorescent assay

Bioorganic and Medicinal Chemistry

Volumn 20, Issue 24, 2012, Pages 6904-6918

  Schoonover, Michelle ^a   Kerwin, Sean M ^a  

^a UNIVERSITY OF TEXAS AT AUSTIN   (United States)

Author keywords

c Myc promoter; G quadruplex DNA; Perylene diimide; Photocleavage; Porphyrins

Indexed keywords

GUANINE QUADRUPLEX; MYC PROTEIN; NUCLEIC ACID; OLIGONUCLEOTIDE; PERYLENE; PERYLENE DIIMIDE G QUADRUPLEX PHOTOCLEAVAGE AGENT; UNCLASSIFIED DRUG;

ARTICLE; CHEMICAL BINDING; DNA CLEAVAGE; DNA STRUCTURE; FLUORESCENCE ANALYSIS; NUCLEIC ACID STRUCTURE; OXIDATIVE STRESS; PHOTOCHEMISTRY; POLYACRYLAMIDE GEL ELECTROPHORESIS; PROMOTER REGION;

BASE SEQUENCE; DNA CLEAVAGE; FLUORESCENCE RESONANCE ENERGY TRANSFER; G-QUADRUPLEXES; GENES, MYC; HUMANS; IMIDES; MOLECULAR STRUCTURE; NUCLEIC ACID CONFORMATION; PERYLENE; PHOTOCHEMICAL PROCESSES; PROMOTER REGIONS, GENETIC; SPECTROMETRY, FLUORESCENCE;

EID: 84870052913     PISSN: 09680896     EISSN: 14643391     Source Type: Journal    
DOI: 10.1016/j.bmc.2012.10.017     Document Type: Article

References (67)

1. T. Simonsson Biol. Chem. 382 2001 621
2. G.N. Parkinson S. Neidle, S. Balasubramanian, Quadruplex Nucleic Acids 2006 The Royal Society of Chemistry Cambridge 1 30
3. P.A. Rachwal, T. Brown, and K.R. Fox Biochemistry 46 2007 3036
4. N. Maizels Nat. Struct. Mol. Biol. 13 2006 1055
5. T.M. Ou, Y.J. Lu, J.H. Tan, Z.S. Huang, K.Y. Wong, and L.Q. Gu ChemMedChem 3 2008 690
6. S. Neidle FEBS J. 277 2010 1118
7. P. Rawal, V.B.R. Kummarasetti, J. Ravindran, N. Kumar, K. Halder, R. Sharma, M. Mukerji, S.K. Das, and S. Chowdhury Genome Res. 16 2006 644
8. A. Verma, V.K. Yadav, R. Basundra, A. Kumar, and S. Chowdhury Nucleic Acids Res. 37 2006 4194
9. A. Verma, K. Halder, R. Halder, V.K. Yadav, P. Rawal, R.K. Thakur, F. Mohd, A. Sharma, and S. Chowdhury J. Med. Chem. 51 2008 5641
10. A. Siddiqui-Jain, C.L. Grand, D.J. Bearss, and L.H. Hurley Proc. Natl. Acad. Sci. U.S.A. 99 2002 11593
11. S. Kendrick, and L.H. Hurley Pure Appl. Chem. 82 2010 1609
12. J. Huppert, A. Bugaut, S. Kumari, and S. Balasubramanian Nucleic Acids Res. 36 2007 6260
13. J.L. Huppert FEBS J. 277 2010 3452
14. P. Mani, V.K. Yadav, S.K. Das, and S. Chowdhury Plos One 4 2009 e4399
15. M. Nambiar, G. Goldsmith, B.T. Moorthy, M.R. Lieber, M.V. Joshi, B. Choudhary, R.V. Hosur, and S.C. Raghavan Nucleic Acids Res. 39 2011 936
16. C. Sissi, B. Gatto, and M. Palumbo Biochimie 93 2011 1219
17. M. Fry Front. Biosci. 12 2007 4336
18. B. Tuesuwan, J.T. Kern, P.W. Thomas, M.L. Rodriguez, J. Li, W.M. David, and S.M. Kerwin Biochemistry 2008 1896 47
19. H. Sun, A. Yabuki, and N. Maizels Proc. Natl. Acad. Sci. U.S.A. 98 2001 12444
20. V.I. Bashkirov, H. Scherthan, J.A. Solinger, J.M. Buerstedde, and W.D. Heyer J. Cell Biol. 136 1997 761
21. A. Heller Faraday Discuss. 116 2010 1
22. D. Grygoryev, and J.D. Zimbrick Radiat. Res. 173 2010 110
23. S. Delaney, and J.K. Barton Biochemistry 42 2004 14159
24. T. Ndlebe, and G.B. Schuster Org. Biomol. Chem. 4 2006 4015
25. V.A. Szalai, and H.H. Thorp J. Am. Chem. Soc. 122 2000 4524
26. A. Pothukuchy, C.L. Mazzitelli, M.L. Rodriguez, B. Tuesuwan, M. Salazar, J.S. Brodbelt, and S.M. Kerwin Biochemistry 44 2005 2163
27. Y.C. Huang, A.K.H. Cheng, H.Z. Yu, and D. Sen Biochemistry 48 2009 6794
28. M.Y. Kim, W.H. Duan, M. Gleason-Guzman, and L.H. Hurley J. Med. Chem. 46 2003 571
29. W.H. Duan, A. Rangan, H. Vankayalapati, M.Y. Kim, Q.P. Zeng, D.K. Sun, H.Y. Han, O.Y. Fedoroff, D. Nishioka, S.Y. Rha, E. Izbicka, D.D. Von Hoff, and L.H. Hurley Mol. Cancer Ther. 1 2001 103
30. F.X.G. Han, R.T. Wheelhouse, and L.H. Hurley J. Am. Chem. Soc. 121 1999 3561
31. H.Y. Han, D.R. Langley, A. Rangan, and L.H. Hurley J. Am. Chem Soc. 123 2001 8902
32. W. Tuntiwechapikul, and M. Salazar Biochemistry 40 2001 13652
33. C. Vialas, G. Pratviel, and B. Meunier Biochemistry 39 2000 9514
34. K.W. Zheng, D. Zhang, L.X. Zhang, Y.H. Hao, X.A. Zhou, and Z. Tan J. Am. Chem. Soc. 133 2011 1475
35. M. Schoonover, and S.M. Kerwin S. Sheardy, S. Winkle, Frontiers in Nucleic Acids ACS Symp. Series Vol. 1082 2011 Oxford Univ. Press Oxford 13 32
36. J.B. Biggins, J.R. Prudent, D.J. Marshall, M. Ruppen, and J.S. Thorson Proc. Natl. Acad. Sci. U.S.A. 97 2000 13537
37. M.W. Freyer, R. Buscaglia, K. Kaplan, D. Cashman, L.H. Hurley, and E.A. Lewis Biophys. J. 92 2007 2007
38. G.N. Parkinson, R. Ghosh, and S. Neidle Biochemistry 46 2007 2390
39. A. Arora, and S. Maiti J. Phys. Chem. B. 112 2008 8151
40. H.J. Zhang, X.F. Wang, P. Wang, X.C. Ai, and J.P. Zhang Photochem. Photobiol. Sci. 7 2008 956
41. V. Gabelica, E.S. Baker, M.P. Teulade-Fichou, E. De Pauw, and M.T. Bowers J. Am. Chem. Soc. 129 2007 895
42. D.T. Croke, L. Perrouault, M.A. Sari, J.P. Battioni, D. Mansuy, C. Helene, and L.D. Trung J. Photochem. Photobiol. B. 18 2006 41
43. K. Aoki, Y. Ishikawa, M. Oyama, Y. Tomisugi, and T. Uno Chem. Pharm. Bull. 51 2003 899
44. J. Seenisamy, E.M. Rezler, T.J. Powell, D. Tye, V. Gokhale, C.S. Joshi, A. Siddiqui-Jain, and L.H. Hurley J. Am. Chem. Soc. 126 2004 8702
45. S. Cogoi, and L.E. Xodo Nucleic Acids Res. 34 2006 2536
46. J. Bernadou, G. Pratviel, F. Bennis, M. Girardet, and B. Meunier Biochemistry 28 1989 7268
47. A. De Cian, L. Guittat, M. Kaiser, B. Sacca, S. Amrane, A. Bourdoncle, P. Alberti, M.P. Teulade-Fichou, L. Lacroix, and J.L. Mergny Methods 42 2007 183
48. B. Guyen, C.M. Schultes, P. Hazel, J. Mann, and S. Neidle Org. Biomol. Chem. 2 2004 981
49. J.L. Mergny, and J.C. Maurizot ChemBioChem 2 2001 124
50. D. Renciuk, I. Kejnovska, P. Skolakova, K. Bednarova, J. Motlova, and M. Vorlickova Nucleic Acids Res. 37 2009 6625
51. A. Ambrus, D. Chen, J.X. Dai, T. Bialis, R.A. Jones, and D.Z. Yang Nucleic Acids Res. 34 2006 2723
52. Y. Wang, and D.J. Patel Structure 1 1993 263
53. A. Ambrus, D. Chen, J.X. Dai, R.A. Jones, and D.Z. Yang Biochemistry 44 2005 2048
54. S.M. Kerwin M. Greenberg, Radical and Radical Ion Reactivity in Nucleic Acid Chemistry 2009 Wiley New York 389 419
55. C. Pivetta, L. Lucatello, A.P. Krapcho, B. Gatto, M. Palumbo, and C. Sissi Bioorg. Med. Chem. 16 2008 9331
56. J.T. Kern, and S.M. Kerwin Bioorg. Med. Chem. Lett. 12 2002 3395
57. M. Franceschin, C.M. Lombardo, E. Pascucci, D. D'Ambrosio, E. Micheli, A. Bianco, G. Ortaggi, and M. Savino Bioorg. Med. Chem. 16 2008 2292
58. V. Casagrande, E. Salvati, A. Alvino, A. Bianco, A. Ciammaichella, C. D'Angelo, L. Ginnari-Satriani, A.M. Serrilli, S. Iachettini, C. Leonetti, S. Neidle, G. Ortaggi, M. Porru, A. Rizzo, M. Franceschin, and A. Biroccio J. Med. Chem. 54 2011 1140
59. L. Rossetti, M. Franceschin, A. Bianco, G. Ortaggi, and M. Savino Bioorg. Med. Chem. Lett. 12 2002 2527
60. O.Y. Fedoroff, M. Salazar, H.Y. Han, V.V. Chemeris, S.M. Kerwin, and L.H. Hurley Biochemistry 37 1998 12367
61. T.A. Zeidan, R. Carmieli, R.F. Kelley, T.M. Wilson, F.D. Lewis, and M.R. Wasielewski J. Am. Chem. Soc. 130 2008 13945
62. C. Li, and H. Wonneberger Adv. Mater. 24 2012 613
63. J.E. Rogers, and L.A. Kelly J. Am. Chem. Soc. 121 1999 3854
64. K. Kawai, Y. Osakada, E. Matsutani, and T. Majima J. Phys. Chem. B. 114 2010 10195
65. P. Ragazzon, and J.B. Chaires Methods 43 2007 313
66. V.V. Borovkov, J.M. Lintuluoto, and Y. Inoue Synlett 1999 61
67. A.M. Maxam, and W. Gilbert Methods Enzymol. 65 1980 499