Base sequence context effects on nucleotide excision repair

Journal of Nucleic Acids

Volumn 2010, Issue , 2010, Pages

  Cai, Yuqin ^a   Patel, Dinshaw J ^b   Broyde, Suse ^a   Geacintov, Nicholas E ^a  

^a NEW YORK UNIVERSITY   (United States)

^b MEMORIAL SLOAN KETTERING CANCER CENTER   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BENZO[A]PYRENE; GUANINE DERIVATIVE;

BASE PAIRING; DNA DAMAGE; EXCISION REPAIR; GEL ELECTROPHORESIS; GENE MUTATION; HELA CELL; HUMAN; MALIGNANT NEOPLASTIC DISEASE; MOLECULAR DYNAMICS; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; REVIEW; SIGNAL TRANSDUCTION; STEREOSPECIFICITY; THERMODYNAMICS;

EID: 80455149268     PISSN: 20900201     EISSN: 2090021X     Source Type: Journal    
DOI: 10.4061/2010/174252     Document Type: Review

References (74)

1. Friedberg E. C., Walker G. C., DNA Repair and Mutagenesis 2006 Wahsington, DC, USA ASM Press
2. Gillet L. C. J., Schärer O. D., Molecular mechanisms of mammalian global genome nucleotide excision repair. Chemical Reviews 2006 106 2 253 276 2-s2.0-32644450616 10.1021/cr040483f
3. Kraemer K. H., Patronas N. J., Schiffmann R., Brooks B. P., Tamura D., DiGiovanna J. J., Xeroderma pigmentosum, trichothiodystrophy and Cockayne syndrome: a complex genotype-phenotype relationship. Neuroscience 2007 145 4 1388 1396 2-s2.0-34247169028 10.1016/j.neuroscience.2006.12.020 (Pubitemid 46602743)
4. Cleaver J. E., Cancer in xeroderma pigmentosum and related disorders of DNA repair. Nature Reviews Cancer 2005 5 7 564 573 2-s2.0-21744452376 10.1038/nrc1652 (Pubitemid 40942832)
5. Martin L. P., Hamilton T. C., Schilder R. J., Platinum resistance: the role of DNA repair pathways. Clinical Cancer Research 2008 14 5 1291 1295 2-s2.0-40949130371 10.1158/1078-0432.CCR-07-2238 (Pubitemid 351413906)
6. Li C., Wang L. E., Wie Q., DNA repair phenotype and cancer susceptibility - a mini review. International Journal of Cancer 2009 124 5 999 1007 2-s2.0-58749098419 10.1002/ijc.24126
7. Wang F., He Y., Guo H., Li J., Yang Y., Wu Z., Zheng H., Wu T., wut@mails.tjmu.edu.cn Genetic variants of nucleotide excision repair genes are associated with DNA damage in coke oven workers. Cancer Epidemiology Biomarkers and Prevention 2010 19 1 211 218 2-s2.0-34547842075 10.1158/1055-9965.EPI-09- 0270
8. Bradbury P. A., Kulke M. H., Heist R. S., Zhou W., Ma C., Xu W., Marshall A. L., Zhai R., Hooshmand S. M., Asomaning K., Su L., Shepherd F. A., Lynch T. J., Wain J. C., Christiani D. C., Liu G., Cisplatin pharmacogenetics, DNA repair polymorphisms, and esophageal cancer outcomes. Pharmacogenetics and Genomics 2009 19 8 613 625 2-s2.0-68849129048 10.1097/FPC.0b013e32832f3010
9. Nouspikel T., Nucleotide excision repair: variations on versatility. Cellular and Molecular Life Sciences 2009 66 6 994 1009 2-s2.0-62349131315 10.1007/s00018-009-8737-y
10. Sugasawa K., ksugasawa@garnet.kobe-u.ac.jp Regulation of damage recognition in mammalian global genomic nucleotide excision repair. Mutation Research 2010 685 1-2 29 37 2-s2.0-0026536763 10.1016/j.mrfmmm.2009.08.004
11. Scicchitano D. A., Transcription past DNA adducts derived from polycyclic aromatic hydrocarbons. Mutation Research 2005 577 1-2 146 154 2-s2.0-24044492238 10.1016/j.mrfmmm.2005.03.015 (Pubitemid 41225494)
12. Hanawalt P. C., Spivak G., Transcription-coupled DNA repair: two decades of progress and surprises. Nature Reviews Molecular Cell Biology 2008 9 12 958 970 2-s2.0-56749157389 10.1038/nrm2549
13. Tornaletti S., DNA repair in mammalian cells: transcription-coupled DNA repair: directing your effort where it's most needed. Cellular and Molecular Life Sciences 2009 66 6 1010 1020
14. Dreij K., Burns J. A., Geacintov N. E., Broyde S., DNA damage and transcription elongation: consequences and RNA Integrity. The Chemical Biology of DNA Damage 2010 Weinheim, Germany WILEY-VCH
15. Sugasawa K., Ng J. M. Y., Masutani C., Iwai S., Van Der Spek P. J., Eker A. P. M., Hanaoka F., Bootsma D., Hoeijmakers J. H. J., Xeroderma pigmentosum group C protein complex is the initiator of global genome nucleotide excision repair. Molecular Cell 1998 2 2 223 232 2-s2.0-0032134423 (Pubitemid 128373647)
16. Volker M., Moné M. J., Karmakar P., Van Hoffen A., Schul W., Vermeulen W., Hoeijmakers J. H. J., Van Driel R., Van Zeeland A. A., Mullenders L. H. F., Sequential assembly of the nucleotide excision repair factors in vivo. Molecular Cell 2001 8 1 213 224 2-s2.0-17944361949 10.1016/S1097-2765(01)00281- 7 (Pubitemid 32772919)
17. Riedl T., Hanaoka F., Egly J.-M., The comings and goings of nucleotide excision repair factors on damaged DNA. EMBO Journal 2003 22 19 5293 5303 2-s2.0-0141753120 10.1093/emboj/cdg489 (Pubitemid 37222048)
18. Fitch M. E., Nakajima S., Yasui A., Ford J. M., In vivo recruitment of XPC to UV-induced cyclobutane pyrimidine dimers by the DDB2 gene product. Journal of Biological Chemistry 2003 278 47 46906 46910 2-s2.0-0345306615 10.1074/jbc.M307254200 (Pubitemid 37452272)
19. Moser J., Volker M., Kool H., Alekseev S., Vrieling H., Yasui A., Van Zeeland A. A., Mullenders L. H. F., The UV-damaged DNA binding protein mediates efficient targeting of the nucleotide excision repair complex to UV-induced photo lesions. DNA Repair 2005 4 5 571 582 2-s2.0-16244423719 10.1016/j.dnarep.2005.01.001 (Pubitemid 40462045)
20. Sugasawa K., Okuda Y., Saijo M., Nishi R., Matsuda N., Chu G., Mori T., Iwai S., Tanaka K., Tanaka K., Hanaoka F., UV-induced ubiquitylation of XPC protein mediated by UV-DDB-ubiquitin ligase complex. Cell 2005 121 3 387 400 2-s2.0-21044442126 10.1016/j.cell.2005.02.035 (Pubitemid 40692299)
21. Nishi R., Alekseev S., Dinant C., Hoogstraten D., Houtsmuller A. B., Hoeijmakers J. H. J., Vermeulen W., Hanaoka F., Sugasawa K., UV-DDB-dependent regulation of nucleotide excision repair kinetics in living cells. DNA Repair 2009 8 6 767 776 2-s2.0-67349276614 10.1016/j.dnarep.2009.02.004
22. Ogi T., togi@nagasaki-u.ac.jp Limsirichaikul S., Overmeer R. M., Volker M., Takenaka K., Cloney R., Nakazawa Y., Niimi A., Miki Y., Jaspers N. G., Mullenders L. H.F., Yamashita S., Fousteri M. I., Lehmann A. R., a.r.lehmann@sussex.ac.uk Three DNA polymerases, recruited by different mechanisms, carry out NER repair synthesis in human cells. Molecular Cell 2010 37 5 714 727 2-s2.0-0030765461 10.1016/j.molcel.2010.02.009
23. Guo C., Tang T.-S., Friedberg E. C., SnapShot: nucleotide excision repair. Cell 2010 140 5 754 754.e1 2-s2.0-77649125801 10.1016/j.cell.2010.02.033
24. Gunz D., Hess M. T., Naegeli H., Recognition of DNA adducts by human nucleotide excision repair. Evidence for a thermodynamic probing mechanism. Journal of Biological Chemistry 1996 271 41 25089 25098 2-s2.0-0029840823 10.1074/jbc.271.41.25089 (Pubitemid 26337867)
25. Evans E., Moggs J. G., Hwang J. R., Egly J.-M., Wood R. D., Mechanism of open complex and dual incision formation by human nucleotide excision repair factors. EMBO Journal 1997 16 21 6559 6573 2-s2.0-0030732132 10.1093/emboj/16.21.6559 (Pubitemid 27483280)
26. Fujiwara Y., Masutani C., Mizukoshi T., Kondo J., Hanaoka F., Iwai S., Characterization of DNA recognition by the human UV-damaged DNA-binding protein. Journal of Biological Chemistry 1999 274 28 20027 20033 2-s2.0-0033538572 10.1074/jbc.274.28.20027 (Pubitemid 29327791)
27. Wood R. D., DNA damage recognition during nucleotide excision repair in mammalian cells. Biochimie 1999 81 1-2 39 44 2-s2.0-0032742715 10.1016/S0300-9084(99)80036-4
28. Sugasawa K., Okamoto T., Shimizu Y., Masutani C., Iwai S., Hanaoka F., A multistep damage recognition mechanism for global genomic nucleotide excision repair. Genes and Development 2001 15 5 507 521 2-s2.0-0035282109 10.1101/gad.866301 (Pubitemid 32205141)
29. Geacintov N. E., Broyde S., Buterin T., Naegeli H., Wu M., Yan S., Patel D. J., Thermodynamic and structural factors in the removal of bulky DNA adducts by the nucleotide excision repair machinery. Biopolymers 2002 65 3 202 210 2-s2.0-0037027367 10.1002/bip.10239
30. Sugasawa K., Shimizu Y., Iwai S., Hanaoka F., A molecular mechanism for DNA damage recognition by the xeroderma pigmentosum group C protein complex. DNA Repair 2002 1 1 95 107 2-s2.0-0036012799 10.1016/S1568-7864(01)00008-8 (Pubitemid 34475695)
31. Hess M. T., Gunz D., Luneva N., Geacintov N. E., Naegeli H., Base pair conformation-dependent excision of benzo[ a ]pyrene diol epoxide-guanine adducts by human nucleotide excision repair enzymes. Molecular and Cellular Biology 1997 17 12 7069 7076 2-s2.0-0030657472 (Pubitemid 27505936)
32. Missura M., Buterin T., Hindges R., Hübscher U., Kaspárková J., Brabec V., Naegeli H., Double-check probing of DNA bending and unwinding by XPA-RPA: an architectural function in DNA repair. EMBO Journal 2001 20 13 3554 3564 2-s2.0-0035796455 10.1093/emboj/20.13.3554 (Pubitemid 32634362)
33. Geacintov N. E., Naegeli H., Siede W., Kow Y. W., Doetsch P. W., Structural aspects of polycyclic aromatic carcinogen-damged DNA and its recognition by NER proteins. DNA Damage and Recognition 2006 London, UK Taylor & Francis
34. Yang W., Poor base stacking at DNA lesions may initiate recognition by many repair proteins. DNA Repair 2006 5 6 654 666 2-s2.0-33646768613 10.1016/j.dnarep.2006.02.004 (Pubitemid 43766519)
35. Yang W., Structure and mechanism for DNA lesion recognition. Cell Research 2008 18 1 184 197 2-s2.0-38049110204 10.1038/cr.2007.116
36. Isaacs R. J., Spielmann H. P., A model for initial DNA lesion recognition by NER and MMR based on local conformational flexibility. DNA Repair 2004 3 5 455 464 2-s2.0-1842785956 10.1016/j.dnarep.2004.01.004 (Pubitemid 38482020)
37. Buterin T., Meyer C., Giese B., Naegeli H., DNA quality control by conformational readout on the undamaged strand of the double helix. Chemistry and Biology 2005 12 8 913 922 2-s2.0-23944515285 10.1016/j.chembiol.2005.06.011 (Pubitemid 41206805)
38. Malta E., Moolenaar G. F., Goosen N., Base flipping in nucleotide excision repair. Journal of Biological Chemistry 2006 281 4 2184 2194 2-s2.0-33644855067 10.1074/jbc.M508901200 (Pubitemid 43845809)
39. Truglio J. J., Karakas E., Rhau B., Wang H., Dellavecchia M. J., Van Houten B., Kisker C., Structural basis for DNA recognition and processing by UvrB. Nature Structural and Molecular Biology 2006 13 4 360 364 2-s2.0-33744948123 10.1038/nsmb1072 (Pubitemid 43873508)
40. Clement F. C., Camenisch U., Fei J., Kaczmarek N., Mathieu N., Naegeli H., naegelih@vetpharm.uzh.ch Dynamic two-stage mechanism of versatile DNA damage recognition by xeroderma pigmentosum group C protein. Mutation Research 2010 685 1-2 21 28 2-s2.0-0033065080 10.1016/j.mrfmmm.2009.08.005
41. Min J.-H., Pavletich N. P., Recognition of DNA damage by the Rad4 nucleotide excision repair protein. Nature 2007 449 7162 570 575 2-s2.0-34948892722 10.1038/nature06155 (Pubitemid 47525148)
42. Luch A., Nature and nurture - lessons from chemical carcinogenesis. Nature Reviews Cancer 2005 5 2 113 125 2-s2.0-13444273224 10.1038/nrc1546 (Pubitemid 40215860)
43. Buening M. K., Wislocki P. G., Levin H., Tumorigenicity of the optical enantiomers of the diastereomeric benzo[ a ]pyrene 7,8-diol-9,10-epoxides in newborn mice: exceptional activity of (+)-7 β8 α -dihydroxy-9 α10 α -epoxy-7,8,9,10-tetrahydrobenzo[ a ]pyrene. Proceedings of the National Academy of Sciences of the United States of America 1978 75 11 5358 5361 2-s2.0-0000933858 (Pubitemid 9079793)
44. Weinstein I. B., Jeffrey A. M., Jennette K. W., Benzo[ a ]pyrene diol epoxides as intermediates in nucleic acid binding in vitro and in vivo. Science 1976 193 4253 592 594 2-s2.0-0017063932
45. Koreeda M., Moore P. D., Wislocki P., Binding of benzo[ a ]pyrene 7,8-diol-9,10-epoxides to DNA,RNA, and protein of mouse skin occurs with high stereoselectivity. Science 1978 199 4330 778 781 2-s2.0-0018137343 (Pubitemid 8291348)
46. Weinstein I. B., Jeffrey A. M., Jennette K. W., Benzo[ a ]pyrene diol epoxides as intermediates in nucleic acid binding in vitro and in vivo. Science 1976 193 4253 592 594 2-s2.0-0017063932
47. Wei D., Maher V. M., Mccormick J. J., Site-specific rates of excision repair of benzo[ a ]pyrene diol epoxide adducts in the hypoxanthine phosphoribosyltransferase gene of human fibroblasts: correlation with mutation spectra. Proceedings of the National Academy of Sciences of the United States of America 1995 92 6 2204 2208 2-s2.0-0028940079 10.1073/pnas.92.6.2204
48. Fernandes A., Liu T., Amin S., Geacintov N. E., Grollman A. P., Moriya M., Mutagenic potential of stereoisomeric bay region (+)- and (-)- cis-anti -benzo[ a ]pyrene diol epoxide- N2-2′ -deoxyguanosine adducts in Escherichia coli and Simian kidney cells. Biochemistry 1998 37 28 10164 10172 2-s2.0-0032516459 10.1021/bi980401f (Pubitemid 28366371)
49. Seo K. Y., Nagalingam A., Tiffany M., Loechler E. L., Mutagenesis studies with four stereoisomeric N2 -dG benzo[ a ]pyrene adducts in the identical 5′ -CGC sequence used in NMR studies: G→T mutations dominate in each case. Mutagenesis 2005 20 6 441 448 2-s2.0-29144536834 10.1093/mutage/gei061 (Pubitemid 41816531)
50. Cosman M., de los Santos C., Fiala R., Hingerty B. E., Singh S. B., Ibanez V., Margulis L. A., Live D., Geacintov N. E., Broyde S., Patel D. J., Solution conformation of the major adduct between the carcinogen (+)- anti -benzo[ a ]pyrene diol epoxide and DNA. Proceedings of the National Academy of Sciences of the United States of America 1992 89 5 1914 1918 2-s2.0-0026527186
51. Rodríguez F. A., Cai Y., Lin C., Tang Y., Kolbanovskiy A., Amin S., Patel D. J., Broyde S., Geacintov N. E., Exocyclic amino groups of flanking guanines govern sequence-dependent adduct conformations and local structural distortions for minor groove-aligned benzo[ a ]pyrenyl-guanine lesions in a GG mutation hotspot context. Nucleic Acids Research 2007 35 5 1555 1568 2-s2.0-34247213435 10.1093/nar/gkm022 (Pubitemid 46603434)
52. Cai Y., Patel D. J., Geacintov N. E., Broyde S., Differential nucleotide excision repair susceptibility of bulky DNA adducts in different sequence contexts: hierarchies of recognition signals. Journal of Molecular Biology 2009 385 1 30 44 2-s2.0-57749188239 10.1016/j.jmb.2008.09.087
53. Kropachev K., Kolbanovskii M., Cai Y., Rodríguez F., Kolbanovskii A., Liu Y., Zhang L., Amin S., Patel D., Broyde S., Geacintov N. E., The sequence dependence of human nucleotide excision repair efficiencies of benzo[ a ]pyrene-derived DNA lesions: insights into the structural factors that favor dual incisions. Journal of Molecular Biology 2009 386 5 1193 1203 2-s2.0-60849122212 10.1016/j.jmb.2008.12.082
54. Xu J., Sequence dependence of carcinogen-induced DNA bending, Ph.D. thesis 1999 New York, NY, USA New York University
55. Gorin A. A., Zhurkin V. B., Olson W. K., B-DNA twisting correlates with base-pair morphology. Journal of Molecular Biology 1995 247 1 34 48 2-s2.0-0028931709 10.1006/jmbi.1994.0120
56. Dickerson R. E., DNA bending: the prevalence of kinkiness and the virtues of normality. Nucleic Acids Research 1998 26 8 1906 1926 2-s2.0-0032522139 10.1093/nar/26.8.1906 (Pubitemid 28291723)
57. Olson W. K., Gorin A. A., Lu X.-J., Hock L. M., Zhurkin V. B., DNA sequence-dependent deformability deduced from protein-DNA crystal complexes. Proceedings of the National Academy of Sciences of the United States of America 1998 95 19 11163 11168 2-s2.0-0032530555 10.1073/pnas.95.19.11163 (Pubitemid 28450099)
58. Geacintov N. E., Cosman M., Hingerty B. E., Amin S., Broyde S., Patel D. J., NMR solution structures of stereoisomeric covalent polycyclic aromatic carcinogen-DNA adducts: Principles, patterns, and diversity. Chemical Research in Toxicology 1997 10 2 111 146 2-s2.0-0031041812 10.1021/tx9601418 (Pubitemid 27091881)
59. Xu R., Mao B., Amin S., Geacintov N. E., Bending and circularization of site-specific and stereoisomeric carcinogen-DNA adducts. Biochemistry 1998 37 2 769 778 2-s2.0-0032512426 10.1021/bi971785x (Pubitemid 28123812)
60. Tsao H., Mao B., Zhuang P., Xu R., Amin S., Geacintov N. E., Sequence dependence and characteristics of bends induced by site-specific polynuclear aromatic carcinogen-deoxyguanosine lesions in oligonucleotides. Biochemistry 1998 37 14 4993 5000 2-s2.0-0032492642 10.1021/bi980291c (Pubitemid 28235691)
61. Ruan Q., Liu T., Kolbanovskiy A., Liu Y., Ren J., Skorvaga M., Zou Y., Lader J., Malkani B., Amin S., Van Houten B., Geacintov N. E., Sequence context- and temperature-dependent nucleotide excision repair of a benzo[ a ]pyrene diol epoxide-guanine DNA adduct catalyzed by thermophilic UvrABC proteins. Biochemistry 2007 46 23 7006 7015 2-s2.0-34250177258 10.1021/bi700294k (Pubitemid 46906429)
62. Breslauer K. J., Frank R., Blocker H., Marky L. A., Predicting DNA duplex stability from the base sequence. Proceedings of the National Academy of Sciences of the United States of America 1986 83 11 3746 3750 2-s2.0-0001550068 (Pubitemid 16062362)
63. SantaLucia J. Jr., Allawi H. T., Seneviratne P. A., Improved nearest-neighbor parameters for predicting DNA duplex stability. Biochemistry 1996 35 11 3555 3562 2-s2.0-0029968822 10.1021/bi951907q (Pubitemid 26092574)
64. Cai Y., Patel D. J., Geacintov N. E., Broyde S., Dynamics of a benzo[ a ]pyrene-derived guanine DNA lesion in TGT and CGC sequence contexts: enhanced mobility in TGT explains conformational heterogeneity, flexible bending, and greater susceptibility to nucleotide excision repair. Journal of Molecular Biology 2007 374 2 292 305 2-s2.0-35548986675 10.1016/j.jmb.2007.09.034 (Pubitemid 350007650)
65. Gardiner E. J., Hunter C. A., Packer M. J., Palmer D. S., Willett P., Sequence-dependent DNA Structure: a database of octamer structural parameters. Journal of Molecular Biology 2003 332 5 1025 1035 2-s2.0-0042386600 10.1016/j.jmb.2003.08.006 (Pubitemid 37108796)
66. Cai Y., Kropachev K., Xu R., Tang Y., Kolbanovskii M., Kolbanovskii A., Amin S., Patel D. J., Broyde S., Geacintov N. E., ng1@nyu.edu Distant neighbor base sequence context effects in human nucleotide excision repair of a benzo[ a ]pyrene-derived DNA lesion. Journal of Molecular Biology 2010 399 3 397 409 2-s2.0-77951857971 10.1016/j.jmb.2010.04.004
67. Johnson R. C., Stella S., Rice P. A., Correll C. C., Bending and compaction of DNA by proteins. Protein-Nucleic Acid Interactions 2008 Cambridge, UK The Royal Society of Chemistry
68. Calladine C. R., Mechanics of sequence-dependent stacking of bases in B-DNA. Journal of Molecular Biology 1982 161 2 343 352 2-s2.0-0020385863 (Pubitemid 13253157)
69. el Hassan M. A., Calladine C. R., Conformational characteristics of DNA: empirical classifications and a hypothesis for the conformational behaviour of dinucleotide steps. Philosophical Transactions of the Royal Society A 1997 355 1722 43 100 2-s2.0-3142518260
70. el Hassan M. A., Calladine C. R., Two distinct modes of protein-induced bending in DNA. Journal of Molecular Biology 1998 282 2 331 343 2-s2.0-0032544507 10.1006/jmbi.1998.1994 (Pubitemid 28418787)
71. Packer M. J., Dauncey M. P., Hunter C. A., Sequence-dependent DNA structure: dinucleotide conformational maps. Journal of Molecular Biology 2000 295 1 71 83 2-s2.0-0034614483 10.1006/jmbi.1999.3236 (Pubitemid 30025902)
72. Okonogi T. M., Alley S. C., Reese A. W., Hopkins P. B., Robinson B. H., Sequence-dependent dynamics of duplex DNA: the applicability of a dinucleotide model. Biophysical Journal 2002 83 6 3446 3459 2-s2.0-0036928374 (Pubitemid 36041961)
73. Schärer O. D., A molecular basis for damage recognition in eukaryotic nucleotide excision repair. ChemBioChem 2008 9 1 21 23 2-s2.0-38149019888 10.1002/cbic.200700619
74. Buterin T., Hess M. T., Luneva N., Geacintov N. E., Amin S., Kroth H., Seidel A., Naegeli H., Unrepaired fjord region polycyclic aromatic hydrocarbon-DNA adducts in ras codon 61 mutational hot spots. Cancer Research 2000 60 7 1849 1856 2-s2.0-0034029834 (Pubitemid 30207643)