Reconciliation of chemical, enzymatic, spectroscopic and computational data to assign the absolute configuration of the dna base lesion spiroiminodihydantoin

Journal of the American Chemical Society

Volumn 135, Issue 48, 2013, Pages 18191-18204

  Fleming, Aaron M ^a   Orendt, Anita M ^a   He, Yanan ^b   Zhu, Judy ^a   Dukor, Rina K ^b   Burrows, Cynthia J ^a  

^a UNIVERSITY OF UTAH   (United States)

^b BIOTOOLS INC   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ABSOLUTE CONFIGURATION; BIOLOGICAL SIGNIFICANCE; ELECTRONIC CIRCULAR DICHROISM; EXPERIMENTAL SPECTRA; ONE-ELECTRON OXIDATION; SPIROIMINODIHYDANTOIN; TIME DEPENDENT DENSITY FUNCTIONAL THEORY; VIBRATIONAL CIRCULAR DICHROISM SPECTROSCOPY;

BIOMOLECULES; DICHROISM; MOLECULES; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; PROPELLERS;

STEREOCHEMISTRY;

8 HYDROXYDEOXYGUANOSINE; DEOXYGUANOSINE; DNA BASE; GUANINE QUADRUPLEX; OLIGODEOXYNUCLEOTIDE; PURINE NUCLEOSIDE DERIVATIVE; RESTRICTION ENDONUCLEASE; SOLVENT; SPIROIMINODIHYDANTOIN 2' DEOXYRIBONUCLEOSIDE; UNCLASSIFIED DRUG;

AQUEOUS SOLUTION; ARTICLE; CHEMICAL ANALYSIS; CHEMICAL STRUCTURE; CHROMATOGRAPHY; CIRCULAR DICHROISM; CONTROLLED STUDY; CRYSTAL STRUCTURE; DENSITY FUNCTIONAL THEORY; DIASTEREOISOMER; DNA DAMAGE; ELECTRON; ENANTIOMER; HYDRATION; HYDROGEN BOND; ION EXCHANGE; ISOMER; MOLECULAR DYNAMICS; MUTAGENESIS; NUCLEAR OVERHAUSER EFFECT; OPTICAL ROTATORY DISPERSION; OXIDATION; PHOTOSENSITIZATION; REVERSED PHASE HIGH PERFORMANCE LIQUID CHROMATOGRAPHY; SOLVATION; SPECTROSCOPY; STEREOCHEMISTRY; TELOMERE;

CIRCULAR DICHROISM; DEOXYGUANOSINE; DNA; ELECTRONS; G-QUADRUPLEXES; GUANOSINE; MODELS, MOLECULAR; MOLECULAR CONFORMATION; SPIRO COMPOUNDS; STEREOISOMERISM;

EID: 84889776100     PISSN: 00027863     EISSN: 15205126     Source Type: Journal    
DOI: 10.1021/ja409254z     Document Type: Article

References (105)

1. Cadet, J.; Douki, T.; Ravanat, J.-L. Free Radical Biol. Med. 2010, 49, 9-21
2. Halliwell, B.; Whiteman, M. Br. J. Pharmacol. 2004, 142, 231-255
3. Steenken, S.; Jovanovic, S. V. J. Am. Chem. Soc. 1997, 119, 617-618
4. Cadet, J.; Douki, T.; Gasparutto, D.; Ravanat, J.-L. Mutat. Res. 2003, 531, 5-23
5. Delaney, S.; Jarem, D. A.; Volle, C. B.; Yennie, C. J. Free Radical Res. 2012, 46, 420-441
6. Gimisis, T.; Cismas, C. Eur. J. Org. Chem. 2006, 2006, 1351-1378
7. Pratviel, G.; Meunier, B. Chem.-Eur. J. 2006, 12, 6018-6030
8. Burrows, C. J.; Muller, J. G. Chem. Rev. 1998, 98, 1109-1152
9. Mangal, D.; Vudathala, D.; Park, J.-H.; Lee, S. H.; Penning, T. M.; Blair, I. A. Chem. Res. Toxicol. 2009, 22, 788-797
10. Matter, B.; Malejka-Giganti, D.; Csallany, A. S.; Tretyakova, N. Nucleic Acids Res. 2006, 34, 5449-5460
11. Collins, A. R.; Cadet, J.; Moller, L.; Poulsen, H. E.; Vina, J. Arch. Biochem. Biophys. 2004, 423, 57-65
12. David, S. S.; O'Shea, V. L.; Kundu, S. Nature 2007, 447, 941-950
13. Steenken, S.; Jovanovic, S. V.; Bietti, M.; Bernhard, K. J. Am. Chem. Soc. 2000, 122, 2373-2374
14. Fleming, A. M.; Muller, J. G.; Dlouhy, A. C.; Burrows, C. J. J. Am. Chem. Soc. 2012, 134, 15091-15102
15. Luo, W.; Muller, J. G.; Rachlin, E. M.; Burrows, C. J. Org. Lett. 2000, 2, 613-616
16. Luo, W.; Muller, J. G.; Rachlin, E. M.; Burrows, C. J. Chem. Res. Toxicol. 2001, 14, 927-938
17. Rokhlenko, Y.; Geacintov, N. E.; Shafirovich, V. J. Am. Chem. Soc. 2012, 134, 4955-4962
18. Shafirovich, V.; Cadet, J.; Gasparutto, D.; Dourandin, A.; Geacintov, N. E. Chem. Res. Toxicol. 2001, 14, 233-241
19. Gremaud, J. N.; Martin, B. D.; Sugden, K. D. Chem. Res. Toxicol. 2010, 23, 379-385
20. Niles, J. C.; Wishnok, J. S.; Tannenbaum, S. R. Chem. Res. Toxicol. 2004, 17, 1510-1519
21. Ye, Y.; Muller, J. G.; Luo, W.; Mayne, C. L.; Shallop, A. J.; Jones, R. A.; Burrows, C. J. J. Am. Chem. Soc. 2003, 125, 13926-13927
22. Angelov, D.; Spassky, A.; Berger, M.; Cadet, J. J. Am. Chem. Soc. 1997, 119, 11373-11380
23. Cui, L.; Ye, W.; Prestwich, E.; Wishnok, J. S.; Taghizadeh, K.; Dedon, P. C.; Tannenbaum, S. R. Chem. Res. Toxicol. 2013, 26, 195-202
24. Fleming, A. M.; Burrows, C. J. Chem. Res. Toxicol. 2013, 26, 593-607
25. Muller, J. G.; Duarte, V.; Hickerson, R. P.; Burrows, C. J. Nucleic Acids Res. 1998, 26, 2247-2249
26. Hailer, M. K.; Slade, P. G.; Martin, B. D.; Sugden, K. D. Chem. Res. Toxicol. 2005, 18, 1378-1383
27. Mangerich, A.; Knutson, C. G.; Parry, N. M.; Muthupalani, S.; Ye, W.; Prestwich, E.; Cui, L.; McFaline, J. L.; Mobley, M.; Ge, Z.; Taghizadeh, K.; Wishnok, J. S.; Wogan, G. N.; Fox, J. G.; Tannenbaum, S. R.; Dedon, P. C. Proc. Natl. Acad. Sci. U.S.A. 2012, 109, E1820-E1829
28. Henderson, P. T.; Delaney, J. C.; Muller, J. G.; Neeley, W. L.; Tannenbaum, S. R.; Burrows, C. J.; Essigmann, J. M. Biochemistry 2003, 42, 9257-9262
29. Delaney, S.; Neeley, W. L.; Delaney, J. C.; Essigmann, J. M. Biochemistry 2007, 46, 1448-1455
30. Delaney, S.; Delaney, J. C.; Essigmann, J. M. Chem. Res. Toxicol. 2007, 20, 1718-1729
31. Jia, L.; Shafirovich, V.; Shapiro, R.; Geacintov, N. E.; Broyde, S. Biochemistry 2005, 44, 6043-6051
32. Kornyushyna, O.; Berges, A. M.; Muller, J. G.; Burrows, C. J. Biochemistry 2002, 41, 15304-15314
33. Chen, X.; Fleming, A. M.; Muller, J. G.; Burrows, C. J. New J. Chem. 2013, 37, 3440-3449
34. Neeley, W. L.; Delaney, S.; Alekseyev, Y. O.; Jarosz, D. F.; Delaney, J. C.; Walker, G. C.; Essigmann, J. M. J. Biol. Chem. 2007, 282, 12741-12748
35. Zhao, X.; Krishnamurthy, N.; Burrows, C. J.; David, S. S. Biochemistry 2010, 49, 1658-1666
36. Krishnamurthy, N.; Zhao, X.; Burrows, C. J.; David, S. S. Biochemistry 2008, 47, 7137-7146
37. McKibbin, P. L.; Fleming, A. M.; Towheed, M. A.; Van Houten, B.; Burrows, C. J.; David, S. S. J. Am. Chem. Soc. 2013, 135, 13851-13861
38. Jia, L.; Shafirovich, V.; Geacintov, N. E.; Broyde, S. Biochemistry 2007, 46, 5305-5314
39. Durandin, A.; Jia, L.; Crean, C.; Kolbanovskiy, A.; Ding, S.; Shafirovich, V.; Broyde, S.; Geacintov, N. E. Chem. Res. Toxicol. 2006, 19, 908-913
40. Joffe, A.; Geacintov, N. E.; Shafirovich, V. Chem. Res. Toxicol. 2003, 16, 1528-1538
41. Khutsishvili, I.; Zhang, N.; Marky, L. A.; Crean, C.; Patel, D. J.; Geacintov, N. E.; Shafirovich, V. Biochemistry 2013, 52, 1354-1363
42. Ravanat, J.-L.; Cadet, J. Chem. Res. Toxicol. 1995, 8, 379-388
43. Ding, S.; Jia, L.; Durandin, A.; Crean, C.; Kolbanovskiy, A.; Shafirovich, V.; Broyde, S.; Geacintov, N. E. Chem. Res. Toxicol. 2009, 22, 1189-1193
44. Ding, S.; Kolbanovskiy, A.; Durandin, A.; Crean, C.; Shafirovich, V.; Broyde, S.; Geacintov, N. E. Chirality 2009, 21, E231-E241
45. Karwowski, B.; Dupeyrat, F.; Bardet, M.; Ravanat, J. L.; Krajewski, P.; Cadet, J. Chem. Res. Toxicol. 2006, 19, 1357-1365
46. Lonkar, P.; Dedon, P. C. Int. J. Cancer 2011, 128, 1999-2009
47. Fleming, A. M.; Muller, J. G.; Ji, I.; Burrows, C. J. Org. Biomol. Chem. 2011, 9, 3338-3348
48. Frisch, M. J. Gaussian 09, revision C.01; Gaussian, Inc.: Wallingford, CT, 2010.
49. Krishnan, R.; Binkley, J. S.; Seeger, R.; Pople, J. A. J. Chem. Phys. 1980, 72, 650-654
50. Frisch, M. J.; Pople, J. A.; Binkley, J. S. J. Chem. Phys. 1984, 80, 3265-3269
51. Becke, A. D. J. Chem. Phys. 1993, 98, 5648-5652
52. Lee, C.; Yang, W.; Parr, R. G. Phys. Rev. B 1988, 37, 785-789
53. Zhao, Y.; Truhlar, D. G. Theor. Chem. Acc. 2008, 120, 215-241
54. Yanai, T.; Tew, D. P.; Handy, N. C. Chem. Phys. Lett. 2004, 393, 51-57
55. Adamo, C.; Barone, V. J. Chem. Phys. 1999, 110
56. Scalmani, G.; Frisch, M. J. J. Chem. Phys. 2010, 132
57. Tomasi, J.; Mennucci, B.; Cammi, R. Chem. Rev. 2005, 105, 2999-3094
58. Cheeseman, J. R.; Frisch, M. J.; Devlin, F. J.; Stephens, P. J. Chem. Phys. Lett. 1996, 252, 211-220
59. Dennington, R.; Keith, T.; Millam, J. GaussView, Version 5; Semichem, Inc.: Shawnee Mission, KS, 2009.
60. Autschbach, J.; Ziegler, T.; van Gisbergen, S. J. A.; Baerends, E. J. J. Chem. Phys. 2002, 116, 6930-6940
61. Stephens, P. J.; Devlin, F. J.; Cheeseman, J. R.; Frisch, M. J. J. Phys. Chem. A 2001, 105, 5356-5371
62. Mennucci, B.; Tomasi, J.; Cammi, R.; Cheeseman, J. R.; Frisch, M. J.; Devlin, F. J.; Gabriel, S.; Stephens, P. J. J. Phys. Chem. A 2002, 106, 6102-6113
63. Bauernschmitt, R.; Ahlrichs, R. Chem. Phys. Lett. 1996, 256, 454-464
64. Stratmann, R. E.; Scuseria, G. E.; Frisch, M. J. J. Chem. Phys. 1998, 109, 8218-8224
65. Scalmani, G.; Frisch, M. J.; Mennucci, B.; Tomasi, J.; Cammi, R.; Barone, V. J. Chem. Phys. 2006, 124, 1-15
66. Wang, Y.; Patel, D. J. Structure 1993, 1, 263-282
67. Phan, A. T.; Kuryavyi, V.; Luu, K. N.; Patel, D. J. Nucleic Acids Res. 2007, 35, 6517-6525
68. Parkinson, G. N.; Lee, M. P. H.; Neidle, S. Nature 2002, 417, 876-880
69. Crean, C.; Geacintov, N. E.; Shafirovich, V. Angew. Chem., Int. Ed. 2005, 44, 5057-5060
70. Munk, B. H.; Burrows, C. J.; Schlegel, H. B. J. Am. Chem. Soc. 2008, 130, 5245-5256
71. McCallum, J. E. B.; Kuniyoshi, C. Y.; Foote, C. S. J. Am. Chem. Soc. 2004, 126, 16777-16782
72. He, Y.; Bo, W.; Dukor, R. K.; Nafie, L. A. Appl. Spectrosc. 2011, 65, 699-723
73. Stephens, P. J.; McCann, D. M.; Devlin, F. J.; Flood, T. C.; Butkus, E.; Stoncius, S.; Cheeseman, J. R. J. Org. Chem. 2005, 70, 3903-3913
74. Polavarapu, P. L.; Scalmani, G.; Hawkins, E. K.; Rizzo, C.; Jeirath, N.; Ibnusaud, I.; Habel, D.; Nair, D. S.; Haleema, S. J. Nat. Prod. 2011, 74, 321-328
75. Vass, E.; Hollósi, M.; Forró, E.; Fülöp, F. Chirality 2006, 18, 733-740
76. Monde, K.; Taniguchi, T.; Miura, N.; Kutschy, P.; Curillova, Z.; Pilatova, M.; Mojzis, J. Bioorg. Med. Chem. 2005, 13, 5206-5212
77. Devlin, F. J.; Stephens, P. J.; Osterle, C.; Wiberg, K. B.; Cheeseman, J. R.; Frisch, M. J. J. Chem. Soc. 2002, 67, 8090-8096
78. Polavarapu, P. L. Chirality 2012, 24, 909-920
79. Sebek, J.; Gyurcsik, B.; Sebestik, J.; Kejik, A.; Bednarova, L.; Bour, P. J. Phys. Chem. A 2007, 111, 2750-2760
80. Jacquemin, D.; Perpete, E. A.; Ciofini, I.; Adamo, C.; Valero, R.; Zhao, Y.; Truhlar, D. G. J. Chem. Theory Comput. 2010, 6, 2071-2085
81. Lassen, P. R.; Skytte, D. M.; Hemmingsen, L.; Nielsen, S. F. k.; Freedman, T. B.; Nafie, L. A.; Christensen, S. B. g. J. Nat. Prod. 2005, 68, 1603-1609
82. Poopari, M. R.; Dezhahang, Z.; Xu, Y. Phys. Chem. Chem. Phys. 2013, 15, 1655-1665
83. Mennucci, B.; Cappelli, C.; Cammi, R.; Tomasi, J. Chirality 2011, 23, 717-729
84. Stephens, P. J.; McCann, D. M.; Devlin, F. J.; Flood, T. C.; Butkus, E.; Stoncius, S.; Cheeseman, J. R. J. Org. Chem. 2005, 70, 3903-3913
85. Mukhopadhyay, P.; Zuber, G.; Goldsmith, M.-R.; Wipf, P.; Beratan, D. N. ChemPhysChem 2006, 7, 2483-2486
86. Pikulska, A.; Hopmann, K. H.; Bloino, J.; Pecul, M. J. Phys. Chem. B 2013, 117, 5136-5147
87. Mennucci, B.; Martinex, J. M. J. Phys. Chem. B 2005, 109, 9818-9829
88. Mennucci, B.; Martinez, J. M. J. Phys. Chem. B 2005, 109, 9830-9838
89. Si, Y.; Yang, G.; Hu, M.; Wang, M. Chem. Phys. Lett. 2011, 502, 266-270
90. Kongsted, J.; Pedersen, T. B.; Jensen, L.; Hansen, A. E.; Mikkelsen, K. V. J. Am. Chem. Soc. 2005, 128, 976-982
91. Isborn, C. M.; Mar, B. D.; Curchod, B. F. E.; Tavernelli, I.; Martinez, T. J. J. Phys. Chem. B 2013, 117, 12189-12201
92. Pecul, M.; Marchesan, D.; Ruud, K.; Coriani, S. J. Chem. Phys. 2005, 122, 024106
93. Kongsted, J.; Pedersen, T. B.; Osted, A.; Hansen, A. E.; Mikkelsen, K. V.; Christiansen, O. J. Phys. Chem. A 2004, 108, 3632-3641
94. Fidler, J.; Rodger, P. M.; Rodger, A. J. Am. Chem. Soc. 1994, 116, 7266-7273
95. Verdolino, V.; Cammi, R.; Munk, B. H.; Schlegel, H. B. J. Phys. Chem B 2008, 112, 16860-16873
96. Jia, L.; Shafirovich, V.; Shapiro, R.; Geacintov, N. E.; Broyde, S. Biochemistry 2005, 44, 13342-13353
97. Krishnamurthy, N.; Muller, J. G.; Burrows, C. J.; David, S. S. Biochemistry 2007, 46, 9355-9365
98. Hazra, T. K.; Muller, J. G.; Manuel, R. C.; Burrows, C. J.; Lloyd, R. S.; Mitra, S. Nucleic Acids Res. 2001, 29, 1967-1974
99. Leipold, M. D.; Workman, H.; Muller, J. G.; Burrows, C. J.; David, S. S. Biochemistry 2003, 42, 11373-11381
100. Bandaru, V.; Zhao, X.; Newton, M. R.; Burrows, C. J.; Wallace, S. S. DNA Repair 2007, 6, 1629-1641
101. Hailer, M. K.; Slade, P. G.; Martin, B. D.; Rosenquist, T. A.; Sugden, K. D. DNA Repair 2005, 4, 41-50
102. Sejersted, Y.; Hildrestrand, G. A.; Kunke, D.; Rolseth, V. y.; Krokeide, S. Z.; Neurauter, C. G.; Suganthan, R.; Atneosen-Asegg, M.; Fleming, A. M.; Saugstad, O. D.; Burrows, C. J.; Luna, L.; Bjoras, M. Proc. Natl. Acad. Sci. U.S.A. 2011, 108, 18802-18807
103. Liu, M.; Bandaru, V.; Bond, J. P.; Jaruga, P.; Zhao, X.; Christov, P. P.; Burrows, C. J.; Rizzo, C. J.; Dizdaroglu, M.; Wallace, S. S. Proc. Natl. Acad. Sci. U.S.A. 2010, 107, 4925-4930
104. Krokeide, S. Z.; Laerdahl, J. K.; Salah, M.; Luna, L.; Cederkvist, F. H.; Fleming, A. M.; Burrows, C. J.; Dalhus, B.; Bjoras, M. DNA Repair 2013, /10.1016/j.dnarep.2013.04.026
105. Zhou, J.; Liu, M.; Fleming, A. M.; Burrows, C. J.; Wallace, S. S. J. Biol. Chem. 2013, 288, 27263-27272-27272