Solution structure of a duplex DNA with an abasic site in a dA tract

Biochemistry

Volumn 36, Issue 39, 1997, Pages 11629-11639

  Wang, Ke Yu ^a,b   Parker, Sharon A ^a   Goljer, Igor ^a,c   Bolton, Philip H ^a  

^a WESLEYAN UNIVERSITY   (United States)

^b GILEAD SCIENCES   (United States)

^c Varian Inc   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CURVED DNA; DOUBLE STRANDED DNA;

ARTICLE; DNA DAMAGE; DNA DETERMINATION; DNA STRUCTURE; GENE CONTROL; NUCLEAR MAGNETIC RESONANCE; PRIORITY JOURNAL; STRUCTURE ANALYSIS;

DEOXYADENOSINES; DNA; DNA DAMAGE; MAGNETIC RESONANCE SPECTROSCOPY; MODELS, CHEMICAL; MODELS, MOLECULAR; NUCLEIC ACID CONFORMATION; SOLUTIONS; STEREOISOMERISM;

EID: 0001019746     PISSN: 00062960     EISSN: None     Source Type: Journal    
DOI: 10.1021/bi971464l     Document Type: Article

References (69)

1. Cadet, J. (1994) DNA damage caused by oxidation, deamination, ultraviolet radiation and photoexcited psoralens, IARC Sci. Publ. 125, 245-276.
2. Demple, B., and Harrison, L. (1994) Repair of oxidative damage to DNA: Enzymology and biology, Annu. Rev. Biochem. 63, 915-948.
3. Barnes, D. E., Lindahl, T., and Sedgwick, B. (1993) DNA repair, Curr. Opin. Cell Biol. 5, 424-433.
4. Freidberg, E. C. (1985) DNA Repair, Freeman, New York.
5. Holmes, G. E., Bernstein, C., and Bernstein, H. (1992) Oxidative and other DNA damages as the basis of aging: A review. Mutat. Res. 275, 305-315.
6. Lindahl, T. (1994) Instability and decay of the primary structure of DNA, Nature 362, 709-715.
7. Sonntag, C. V. (1987) The chemical basis for radiation biology, Taylor-Francis, London.
8. Ward, J. F. (1991) DNA damage and repair, in Physical and chemical mechanisms in molecular radiation biology, (Glass, W. A., and Varma, M. N., Eds.) p. 403-421, Plenum Press, New York.
9. 13C, J. Am. Chem. Soc. 110, 1620-1622.
10. 13C labeling, J. Am. Chem. Soc. 110, 2690-2692.
11. Mazumder, A., Gerlt, J. A., Rabow, L., Stubbe, J., and Bolton, P. H. (1989) UV Endonuclease V from bacteriophage T4 catalyzes DNA strand cleavage at aldehydic abasic sites by a syn β-elimination reaction, J. Am. Chem. Soc. 111, 8209-8210.
12. Mazumder, A., Gerlt, J. A., Absalon, M. J., Stubbe, J., Cunningham, R. P., Withka, J. M., and Bolton, P. H. (1991) Stereochemical studies of the β-elimination reactions at aldehydic abasic sites in DNA: Endonuclease III from Escherichia coli, sodium hydroxide and Lys-Trp-Lys, Biochemistry 30, 1191-1196.
13. 17O NMR, J. Am. Chem. Soc. 111, 1894-1895.
14. Bhagwat, M., and Gerlt, J. A. (1996) 3′ and 5′ strand cleavage reactions catalyzed by the Fpg protein from Eschericha coli occur via successive β-and δ-elimination mechanisms, respectively. Biochemistry 35, 659-665.
15. Lindahl, T. (1982) DNA repair enzymes, Annu. Rev. Biochem. 51, 61-87.
16. Loeb, L. A., and Preston, D. B. (1987) Mutagenesis by apurinic/apyrimidinic sites, Annu. Rev. Genet. 20, 201-230.
17. Frederico, L. A., Kunkel, T. A., and Shaw, B. R. (1990) Sensitive genetic assay for the detection of cytosine deamination. Determination of rate constants and the activation energy, Biochemistry 29, 2532-2537.
18. Frederico, L. A., Kunkel, T. A., and Shaw, B. A. (1993) Cytosine deamination in mismatched base pairs, Biochemistry 32, 6523-6530.
19. Mosbaugh, D. W., and Bennett, S. E. (1994) Uracil-excision DNA repair, Prog. Nucleic Acid Res. 48, 316-343.
20. Cathcart, R., Schniers, E., Saul, R. L., and Ames, B. N. (1984) Thymine glycol and thymidine glycol in human and rat urine: A possible assay for oxidative DNA damage, Proc. Natl. Acad. Sci. U.S.A. 81, 5633-5637.
21. Zhou, W., and Doetsch, P. W. (1993) Effects of abasic sites and DNA single-strand breaks on prokaryotic RNA polymerases, Proc. Natl. Acad. Sci. U.S.A. 90, 6601-6605.
22. Goodman, M. F., Creighton, S., Bloom, L. B., and Petruska, J. (1993) Biochemical basis of DNA replication fidelity, Crit. Rev. Biochem. Mol. Biol. 28, 83-126.
23. Driggers, W. J., LeDoux, S. P., and Wilson, G. L. (1993) Repair of oxidative damage within the mitochondiral DNA of RINr38 cells, J. Biol. Chem. 268, 22042-22045.
24. Leadon, S., and Lawrence, D. A. (1992) Strand-selective repair of DNA damage in the yeast GAL 7 gene required RNA polymerase II, J. Biol. Chem. 267, 23175-23182.
25. Weeda, G., and Hoeijmakers, J. H. J. (1993) Genes controlling nucleotide excision repair in eukaryotic cells, BioEssays 15, 249-258.
26. Selby, C. P., and Sancar, A. (1993) Molecular mechanism of transcription-repair coupling, Science 260, 53-58.
27. Chen, R.-H., Maher, V. M., Brouwer, J., Putte, J. v. d., and McCormick, J. J. (1992) Preferential repair and strand-specific repair of benzo-A-pyrene diol epoxide adducts in the HPRT gene of diploid human fibroblasts, Proc. Natl. Acad. Sci. U.S.A. 89, 5413-5417.
28. Elledge, S. J. (1996) Cell cycle checkpoints: Preventing an identity crisis, Science 274, 1664-1672.
29. Nasmyth, K. (1996) Viewpoint: Putting the cell cycle in order, Science 274, 1643-1645.
30. Sherr, C. J. (1996) Cancer cell cycles, Science 274, 1672-1677.
31. Stillman, B. (1996) Cell cycle control of DNA replication, Science 274, 1659-1664.
32. Hollander, M. C., Zhan, Q., Bae, I., and Fornace, A. J. (1997) Mamallian GADD34 an apoptosis and DNA damage-inducible gene, J. Biol. Chem. 272, 13731-13737.
33. Leadon, S. A., and Cooper, P. K. (1993) Preferential repair of ionizing radiation-induced damage in the transcribed strand of an active human gene is defective in Cockayne syndrome, Proc. Natl. Acad. Sci. U.S.A. 90, 10499-10503.
34. Klupp, B. G., Baumeister, J., Karger, A., Visser, N., and Mettenleiter, T. C. (1994) Identification and characterization of a novel structural glycoprotein in pseudorabies virus, gL, J. Virol. 68, 3868-3878.
35. Stuart, D. T., Upton, D. C., Higman, M. A., Niles, E. G., and McFadden, G. (1993) A pox virus-encoded uracil DNA glycosylase is essential for virus viability, J. Virol. 67, 2503-2512.
36. Rao, K. S., and Loeb, L. A. (1992) DNA damage and repair in brain: relationship to aging, Mutat. Res. 275, 317-329.
37. Millins, A. K., Carpenter, M. S., and DeLange, A. M. (1994) The vaccina virus-encoded uracil DNA glycosylase has an essential role in viral DNA replication. Virology 198, 504-513.
38. Chen, Y.-H., and Bogenhagen, D. F. (1993) Effects of DNA lesions on transcription elongation by T7 RNA polymerase, J. Biol. Chem. 268, 5849-5855.
39. Sanchez, G., and Mamet-Bradley, M. D. (1994) Transcription by T7 RNA polymerase of DNA containing abasic sites, Environ. Mol. Mutagen. 23, 32-36.
40. Cai, H., Bloom, L. B., Eritja, R., and Goodman, M. F. (1993) Kinetics of deoxyribonucleotide insertion and extension at abasic template lesions in different sequence contexts using HIV-1 reverse transcriptase, J. Biol. Chem. 265, 23567-23572.
41. Kingma, P. S., and Osheroff, N. (1997) Spontaneous DNA damage stimulate topoisomerase II-mediated DNA cleavage, J. Biol. Chem. 272, 7488-7493.
42. Maccabee, M., Evans, J. S., Glackin, M. P., Hatahet, S., and Wallace, S. S. (1994) Pyrimidine ring fragmentation products. Effects of lesion structure and sequence context on mutagenesis, J. Mol. Biol. 236, 514-530.
43. Shibutani, S., and Grollman, A. P. (1993) Molecular mechanism of transcription-repair coupling, J. Biol. Chem. 268, 11703-11710.
44. Sandell, L. L., and Zakian, V. (1993) Loss of a yeast telomere: Arrest, recovery, and chromosome loss, Cell 75, 729-739.
45. Harrington, R. E. (1992) DNA curving and bending in protein-DNA recognition, Mol. Microbiol. 6, 2549-2555.
46. Ohyama, T. (1996) Bent DNA in the human adenovirus type 2 E1 A enhancer is an architechtural element for transcription stimulation, J. Biol. Chem. 271, 27823-27828.
47. Tsai, M.-M., Fu, Y.-H. F., and Deonier, R. C. (1990) Intrinsic bends and integration host factor binding at F plasmid oriT, J. Bacteriol. 172, 4603-4609.
48. Cobbett, C., Dickson, B., and Farmer, L. (1989) The role of a static bend in the DNA of the aroF regulatory region of Escherichia coli, Gene 75, 185-191.
49. Lavigne, M., Roux, P., Buc, H., and Schaeffer, F. (1997) DNA curvature controls termination of plus strand DNA synthesis at the centre of HIV-1 genome, J. Mol. Biol. 266, 507-524.
50. Price, M. A., and Tullius, T. D. (1993) How the structure of an adenine tract depends on sequence context: a new model for the structure of TnAn DNA sequences, Biochemistry 32, 127-136.
51. Harrington, R. E. (1993) Studies of DNA bending and flexibility using gel electrophoresis, Electrophoresis 14, 732-746.
52. Koo, H.-S., Wu, H.-M., and Crothers, D. M. (1986) DNA bending at adenine.thymine tracts, Nature 320, 501-506.
53. Nadeau, J. G., and Crothers, D. M. (1989) Structural basis for DNA bending, Proc. Natl. Acad. Sci. U.S.A. 86, 2622-2626.
54. DiGabriele, A. D., Sanderson, M. R., and Steitz, T. A. (1989) Crystal lattice packing is important in determing the bend of a DNA dodecamer containing an adenine tract, Proc. Natl. Acad. Sci. U.S.A. 86, 1816-1820.
55. DiGabriele, A., and Steitz, T. A. (1993) A DNA dodecamer containing an adenine tract crystallizes in a unique lattice and exhibits a new bend, J. Mol. Biol. 231, 1024-1039.
56. Young, M. A., Goljer, I., Kumar, S., Srinivasan, J., Beveridge, D. L., and Bolton, P. H. (1995) Structure determination and analysis of local bending in an A-tract DNA duplex: comparison of results from crystallography, nuclear magnetic resonance and molecular dynamics simulations on d(CG-CAAAAATGCG), Methods Enzymol. 261, 121-144.
57. Goljer, I., Kumar, S., and Bolton, P. H. (1995) Refined solution structure of a DNA heteroduplex containing an aldehydic abasic site, J. Biol. Chem. 270, 22980-22987.
58. Goljer, I., Withka, J. M., Kao, J. Y., and Bolton, P. H. (1992) Effects of the presence of an aldehydic abasic site on the thermal stability and rate of helix opening and closing of duplex DNA, Biochemistry 31, 11614-11619.
59. Withka, J. M., Wilde, J. A., Bolton, P. H., Mazumder, A., and Gerlt, J. A. (1991) Characterization of conformational features of a DNA heteroduplex containing an aldehydic abasic site, Biochemists 30, 9931-9936.
60. Devchand, P. R., McGhee, J. D., and Sande, J. H. v. d. (1993) Uracil-DNA glycosylase as a probe for protein-DNA interactions, Nucleic Acids Res. 21, 3437-3443.
61. Kumar, N. V., and Varshney, U. (1994) Inefficient excision of uracil from loop regions of DNA oligomers by E. coli uracil DNA glycosylase, Nucleic Acids Res. 22, 3737-3741.
62. Kung, H. C., and Bolton, P. H. (1997) Solution structure of a duplex DNA containing a thymine glycol, J. Biol. Chem. 272, 9227-9236.
63. Withka, J. M., Srinivasan, J., and Bolton, P. H. (1992) Problems with, and alternatives to the NMR R factor, J. Magn. Reson. 98, 611-616.
64. Kalnik, M. W., Chang, C. N., Grollman, A. P., and Patel, D. J. (1988) NMR studies of abasic sites in DNA duplexes: Deoxyadenosine stacks into the helix opposite the cyclic analogue of 2-deoxyribose, Biochemistry 27, 924-931.
65. Kalnik, M. W., Chang, C. N., Johnson, F., Grollman, A. P., and Patel, D. J. (1989) NMR studies of abasic sites in DNA duplexes: Deoxyadenosine stacks into the helix opposite acyclic lesions, Biochemistry 28, 3373-3383.
66. Cuniasse, P., Fazakerley, G. V., Guschlbauer, W., Kaplan, B. E., and Sowers, L. C. (1990) The abasic site as a challenge to DNA polymerase. A nuclear magnetic resonance study of G, C and T opposite a model abasic site, J. Mol. Biol. 213, 303-314.
67. Cuniasse, P., Sowers, L. C., Eritja, R., Kaplan, B., Goodman, M. F., Cognet, J. A., LeBret, M., Guschlbauer, W., and Fazakerley, G. V. (1987) An abasic site in DNA. Solution conformation determined by proton NMR and molecular mechanics calculations, Nucleic Acids Res. 15, 8003-8022.
68. Coppel, Y., Berthet, N., Coulombeau, C., Coulombeau, C., Garcia, J., and Lhomme, J. (1997) Solution conformation of an abasic DNA undecamer duplex d(CGCACXCACGC)· d(GCGTGTGTGCG): The unpaired thymine stacks inside the helix, Biochemistry 36, 4817-4830.
69. Mullen, G. P., and Wilson, S. H. (1997) DNA polymerase β in abasic site repair: A structurally conserved helix-hairpin-helix motif in lesion detection by base excision repair enzymes, Biochemistry 36, 4713-4717.