On the formation and properties of interstrand DNA-DNA cross-links forged by reaction of an abasic site with the opposing guanine residue of 5′-CAp sequences in duplex DNA

Journal of the American Chemical Society

Volumn 135, Issue 3, 2013, Pages 1015-1025

  Johnson, Kevin M ^a   Price, Nathan E ^a   Wang, Jin ^c   Fekry, Mostafa I ^a   Dutta, Sanjay ^a   Seiner, Derrick R ^a   Wang, Yinsheng ^c   Gates, Kent S ^a,b  

^a UNIVERSITY OF MISSOURI   (United States)

^b University of Missouri   (United States)

^c UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO GROUP; AP-SITES; BASE PAIRS; DUPLEX DNA; GEL MOBILITY; HIGH YIELD; HIGHER YIELD; HYDROXYL RADICAL FOOTPRINTING; INTERSTRAND CROSS-LINKS; LC-MS/MS; MALDI-TOF MASS SPECTROMETRY; METHOXYAMINE; NEUTRAL PH; POLYACRYLAMIDE GELS; REACTION CONDITIONS; REDUCTIVE AMINATION; REVERSIBLE REACTION;

ALDEHYDES; AMINATION; AMINES; CROSSLINKING; DNA; EXPERIMENTS; MASS SPECTROMETRY; POSITIVE IONS;

DNA SEQUENCES;

ALDEHYDE; DOUBLE STRANDED DNA; GUANINE; IMINE; INOSINE; METHOXYAMINE;

AMINATION; AQUEOUS SOLUTION; ARTICLE; CHEMICAL REACTION; DNA CROSS LINKING; DNA SEQUENCE; GEL MOBILITY SHIFT ASSAY; MATRIX ASSISTED LASER DESORPTION IONIZATION TIME OF FLIGHT MASS SPECTROMETRY; PH;

5' UNTRANSLATED REGIONS; ALDEHYDES; CHROMATOGRAPHY, LIQUID; CROSS-LINKING REAGENTS; DNA; GUANINE; MODELS, MOLECULAR; MOLECULAR STRUCTURE; TANDEM MASS SPECTROMETRY;

EID: 84872826534     PISSN: 00027863     EISSN: 15205126     Source Type: Journal    
DOI: 10.1021/ja308119q     Document Type: Article

References (85)

1. Gates, K. S.; Nooner, T.; Dutta, S. Chem. Res. Toxicol. 2004, 17, 839-856
2. Gates, K. S. Chem. Res. Toxicol. 2009, 22, 1747-1760
3. Amosova, O.; Coulter, R.; Fresco, J. R. Proc. Natl. Acad. Sci. U.S.A. 2006, 103, 4392-4397
4. Lindahl, T.; Nyberg, B. Biochemistry 1972, 11, 3610-3618
5. Nakamura, J.; Swenberg, J. A. Cancer Res. 1999, 59, 2522-2526
6. Nakamura, J.; Walker, V. E.; Upton, P. B.; Chiang, S. Y.; Kow, Y. W.; Swenberg, J. A. Cancer Res. 1998, 58, 222-225
7. Park, J.-H.; Troxel, A. B.; Harvey, R. G.; Penning, T. M. Chem. Res. Toxicol. 2006, 19, 719-728
8. Rusyn, I.; Asakura, S.; Y., L.; Kosyk, O.; Koc, H.; Nakamura, J.; Upton, P. B.; Swenberg, J. A. DNA Repair 2005, 4, 1099-1110
9. Viswesh, V.; Gates, K. S.; Sun, D. Chem. Res. Toxicol. 2010, 23, 99-107
10. Torres, M. C.; Rieger, R. A.; Iden, C. R. Chem. Res. Toxicol. 1996, 9, 1313-1318
11. Masta, A.; Gray, P. J.; Phillips, D. R. Nucleic Acids Res. 1994, 22, 3880-3886
12. Wang, Z.; Chandrasena, E. R.; Yuan, Y.; Peng, K.-w.; van Breemen, R. B.; Thatcher, G. R. J.; Bolton, J. L. Chem. Res. Toxicol. 2010, 23, 1365-1373
13. De Bont, R.; van Larebeke, N. Mutagenesis 2004, 19, 169-185
14. Marnett, L. J.; Burcham, P. C. Chem. Res. Toxicol. 1993, 6, 771-785
15. Gates, K. S. In Reviews of Reactive Intermediates; Platz, M. S.; Moss, R. A.; Jones, M. J., Eds.; John Wiley and Sons, Inc.: Hoboken, 2007; pp 333-378.
16. Guillet, M.; Bioteux, S. Mol. Cell. Biol. 2003, 23, 8386-8394
17. David, S. S.; Williams, S. D. Chem. Rev. 1998, 98, 1221-1261
18. Loeb, L. A.; Preston, B. D. Ann. Rev. Genet. 1986, 20, 201-230
19. Boiteux, S.; Guillet, M. DNA Repair 2004, 3, 1-12
20. Lhomme, J.; Constant, J.-F.; Demeunynck, M. Biopolymers 2000, 52, 65-83
21. Wilson, D. M., III; Barsky, D. Mutat. Res. 2001, 485, 283-307
22. Evans, A. R.; Limp-Foster, M.; Kelley, M. R. Mutat. Res. 2000, 461, 83-108
23. Yu, S.-L.; Lee, S.-K.; Johnson, R. E.; Prakash, L.; Prakash, S. Mol. Cell. Biol. 2003, 23, 382-388
24. Auerbach, P.; Bennett, R. A. O.; Bailey, E. A.; Krokan, H. E.; Demple, B. Proc. Natl. Acad. Sci. U.S.A. 2005, 102, 17711-17716
25. Schaaper, R. M.; Loeb, L. A. Proc. Natl. Acad. Sci. U.S.A. 1981, 78, 1773-1777
26. Taylor, A. F.; Weiss, B. J. Bacteriol. 1982, 151, 351-357
27. Wilde, J. A.; Bolton, P. H.; Mazumdar, A.; Manoharan, M.; Gerlt, J. A. J. Am. Chem. Soc. 1989, 111, 1894-1896
28. Wang, M.; McIntee, E. J.; Cheng, G.; Shi, Y.; Villalta, P. W.; Hecht, S. S. Chem. Res. Toxicol. 2000, 13, 1149-1157
29. Riggins, J. N.; Daniels, J. S.; Rouzer, C. A.; Marnett, L. J. J. Am. Chem. Soc. 2004, 126, 8237-8243
30. Chaw, Y. F. M.; Crane, L. E.; Lange, P.; Shapiro, R. Biochemistry 1980, 19, 5525-5531
31. Stone, M. P.; Cho, Y. J.; Huang, H.; Kim, H. Y.; Kozekov, I. D.; Kozekova, A.; Wang, H.; Minko, I. G.; Lloyd, R. S.; Harris, T. M.; Rizzo, C. J. Acc. Chem. Res. 2008, 41, 793-804
32. Kozekov, I. D.; Nechev, L. V.; Moseley, M. S.; Harris, C. M.; Rizzo, C. J.; Stone, M. P.; Harris, T. M. J. Am. Chem. Soc. 2003, 125, 50-61
33. Dutta, S.; Chowdhury, G.; Gates, K. S. J. Am. Chem. Soc. 2007, 129, 1852-1853
34. Hopkins, P. B.; Millard, J. T.; Woo, J.; Weidner, M. F.; Kirchner, J. J.; Sigurdsson, S. T.; Raucher, S. Tetrahedron 1991, 47, 2475-2489
35. Hoehn, S. T.; Turner, C. J.; Stubbe, J. Nucleic Acids Res. 2001, 29, 3413-3423
36. Chen, J.; Dupradeau, F.-Y.; Case, D. A.; Turner, C. J.; Stubbe, J. Nucleic Acids Res. 2008, 36, 253-262
37. de los Santos, C.; El-khateeb, M.; Rege, P.; Tian, K.; Johnson, F. Biochemistry 2004, 43, 15349-15357
38. Beger, R. D.; Bolton, P. H. J. Biol. Chem. 1998, 273, 15565-15573
39. Schärer, O. D. ChemBioChem 2005, 6, 27-32
40. Noll, D. M.; Mason, T. M.; Miller, P. S. Chem. Rev. 2006, 106, 277-301
41. Hlavin, E. M.; Smeaton, M. B.; Miller, P. S. Environ. Mol. Mutagen. 2010, 51, 604-624
42. Muniandy, P. A.; Liu, J.; Majumdar, A.; Liu, S.-t.; Seidman, M. M. Crit. Rev. Biochem. Mol. Biol. 2010, 45, 23-49
43. Zheng, H.; Wang, X.; Warren, A. J.; Legerski, R. J.; Nairn, R. S.; Hamilton, J. W.; Li, L. Mol. Cell. Biol. 2003, 23, 754-761
44. Greenberg, R. B.; Alberti, M.; Hearst, J. E.; Chua, M. A.; Saffran, W. A. J. Biol. Chem. 2001, 276, 31551-31560
45. Shen, X.; Li, L. Environ. Mol. Mutagen. 2010, 51, 493-499
46. Ho, T. V.; Schärer, O. D. Environ. Mol. Mutagen. 2010, 51, 552-566
47. Rajski, S. R.; Williams, R. M. Chem. Rev. 1998, 98, 2723-2795
48. Niedernhofer, L. J.; Garinis, G. A.; Raams, A.; Lalai, A. S.; Robinson, A. R.; Appeldoorn, E.; Odijk, H.; Oostendorp, R.; Ahmad, A.; van Leeuwen, W.; Theil, A. F.; Vermeulen, W.; van der Horst, G. T. J.; Meinecke, P.; Kleijer, W. J.; Vijg, J.; Jaspers, N. G. J.; Hoeijmakers, J. H. J. Nature 2006, 444, 1038-1043
49. Bergstrahl, D. T.; Sekelsky, J. Trends Genet. 2007, 24, 70-76
50. Grillari, J.; Katinger, H.; Voglauer, R. Nucleic Acids Res. 2007, 35, 7566-7576
51. Sambrook, J.; Fritsch, E. F.; Maniatis, T. Molecular Cloning: A Lab Manual; Cold Spring Harbor Press: Cold Spring Harbor, NY, 1989.
52. Sczepanski, J. T.; Jacobs, A. C.; Majumdar, A.; Greenberg, M. M. J. Am. Chem. Soc. 2009, 131, 11132-11139
53. Luce, R. A.; Hopkins, P. B. Methods Enzymol. 2001, 340, 396-412
54. Maxam, A. M.; Gilbert, W. Methods Enzymol. 1980, 65, 499-560
55. Lavanant, H.; Lange, C. Rapid Commun. Mass Spectrom. 2002, 16, 1928-1933
56. Koomen, J. M.; Russell, W. K.; Tichy, S. E.; Russell, D. H. J. Mass Spectrom. 2002, 37
57. Wang, J.; Yuan, B.; Guerrero, C.; Bahde, R.; Gupta, S.; Wang, Y. Anal. Chem. 2011, 83, 2201-2209
58. Borch, R. F.; Hassid, A. I. J. Org. Chem. 1972, 37, 1673-1674
59. Manoharan, M.; Andrade, L. K.; Cook, P. D. Org. Lett. 1999, 1, 311-314
60. Dohno, C.; Okamoto, A.; Saito, I. J. Am. Chem. Soc. 2005, 127, 16681-16684
61. Angelov, T.; Guainazzi, A.; Schärer, O. D. Org. Lett. 2009, 11, 661-664
62. Varshney, U.; van de Sande, J. H. Biochemistry 1991, 30, 4055-4061
63. Eftedal, I.; Guddal, P. H.; Slupphaug, G.; Volden, G.; Krokan, H. E. Nucleic Acids Res. 1993, 11, 2095-2101
64. Nilsen, H.; Yazdankhah, S. P.; Eftedal, I.; Krokan, H. E. FEBS Lett. 1995, 362, 205-209
65. Rosa, S.; Fortini, P.; Karran, P.; Bignami, M.; Dogliotti, E. Nucleic Acids Res. 1991, 19, 5569-5574
66. Coombs, M. M.; Livingston, D. C. Biochim. Biophys. Acta 1969, 174, 161-173
67. Pogozelski, W. K.; McNeese, T. J.; Tullius, T. D. J. Am. Chem. Soc. 1995, 117, 6428-6433
68. Huang, H.; Solomon, M. S.; Hopkins, P. B. J. Am. Chem. Soc. 1992, 114, 9240-9241
69. Sczepanski, J. T.; Jacobs, A. C.; Greenberg, M. M. J. Am. Chem. Soc. 2008, 130, 9646-9647
70. Sczepanski, J. T.; Heimstra, C. N.; Greenberg, M. M. Bioorg. Med. Chem. 2011, 19, 5788-5793
71. Holton, S.; Runquist, O. J. Org. Chem. 1961, 26, 5193-5195
72. Dirksen, A.; Dawson, P. E. Bioconjugate Chem. 2008, 19, 2543-2548
73. Thygesen, M. B.; Munch, H.; Sauer, J.; Cló, E.; Jorgensen, M. R.; Hindsgaul, O.; Jensen, K. J. J. Org. Chem. 2010, 75, 1752-1755
74. Wang, Y.; Wang, Y. Anal. Chem. 2003, 75, 6306-6313
75. Cao, H.; Hearst, J. E.; Corash, L.; Wang, Y. Anal. Chem. 2008, 80, 2932-2938
76. Lai, C.; Cao, H.; Hearst, J. E.; Corash, L.; Luo, H.; Wang, Y. Anal. Chem. 2008, 80, 8790-8798
77. Sanderson, P. N.; Sweatman, B. C.; Farrant, R. D.; Lindon, J. C. Carbohydr. Res. 1996, 284, 51-60
78. Regulus, P.; Duroux, B.; Bayle, P.-A.; Favier, A.; Cadet, J.; Ravanat, J.-L. Proc. Natl. Acad. Sci. U.S.A. 2007, 104, 14032-14037
79. Kallen, R. G.; Jencks, W. P. J. Biol. Chem. 1966, 241, 5851-5863
80. Bomann, M. D.; Guch, I. C.; DiMare, M. J. Org. Chem. 1995, 60, 5995-5996
81. Abdel-Magid, A., F.; Carson, K. G.; Harris, B. D.; Maryanoff, C. A.; Shah, R. D. J. Org. Chem. 1996, 61, 3849-3862
82. Zhang, X.-a.; Song, D.; Lippard, S. J. J. Org. Chem. 2008, 73, 734-737
83. Dallmann, A.; Dehmel, L.; Peters, T.; Mügge, C.; Griesinger, C.; Tuma, J.; Ernsting, N. P. Angew. Chem., Int. Ed. 2010, 49, 5989-5992
84. Belowich, M. E.; Stoddart, J. F. Chem. Rev. 2012, 41, 2003-2024
85. McGhee, J. D.; von Hippel, P. H. Biochemistry 1975, 14, 1281-1296