NMR solution structures of bistranded abasie site lesions in DNA

Biochemistry

Volumn 47, Issue 46, 2008, Pages 11909-11919

  Hazel, Raphael D ^a   Tian, Kegui ^a   De Los Santos, Carlos ^a  

^a STONY BROOK UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ANIMAL CELL CULTURE; DATA STRUCTURES; DNA; FORMING; GENES; HYDROGEN; HYDROGEN BONDS; IONIZING RADIATION; LEAD; MOLECULAR DYNAMICS; NUCLEAR MAGNETIC RESONANCE; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; NUCLEIC ACIDS; ORGANIC ACIDS; QUANTUM CHEMISTRY;

ABASIC SITES; BASE PAIRS; DNA DUPLEXES; DNA REPAIRS; ENDONUCLEASE; EXCHANGEABLE PROTONS; LESION SITES; MAJOR GROOVES; MINOR GROOVES; MOLECULAR DYNAMICS SIMULATIONS; NMR SPECTROSCOPIES; SOLUTION STRUCTURES; SPECTROSCOPIC DATUMS; STRUCTURAL DETERMINANTS; STRUCTURAL DIFFERENCES;

DYNAMICS;

DNA;

ARTICLE; DNA DAMAGE; DNA DETERMINATION; DNA STRUCTURE; HYDROGEN BOND; MOLECULAR DYNAMICS; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; NUCLEAR OVERHAUSER EFFECT; PRIORITY JOURNAL; STRUCTURE ANALYSIS;

BASE PAIRING; DNA; DNA DAMAGE; DNA-(APURINIC OR APYRIMIDINIC SITE) LYASE; HUMANS; HYDROGEN BONDING; MAGNETIC RESONANCE SPECTROSCOPY; MODELS, MOLECULAR; OXIDATION-REDUCTION; RADIATION, IONIZING;

EID: 56249148167     PISSN: 00062960     EISSN: None     Source Type: Journal    
DOI: 10.1021/bi800950t     Document Type: Article

References (50)

1. Ward, J. F. (1998) DNA damage produced by ionizing radiation in mammalian cells: identities, mechanisms of formation and reparability. Prog. Nucleic Acids Res. Mol. Biol. 35, 95-125.
2. Halliwell, B., and Aruoma, O. I. (1991) DNA damage by oxygen derived species: Its mechanism and measurement in mammalian systems. FEBS Let. 281, 9-19.
3. Newcomb, T. G. and Loeb, L. A. (2001) Oxidative Damage and Mutagenesis, in DNA Damage and Repair, Vol. 1: DNA Repair in Higher Eukaryotes (Nickoloff, J. A., and Hoekstra, M. F., Eds.) pp 65-84, Humana Press Inc, Totowa, NJ.
4. Sutherland, B. M., Bennett, P. V., Sidorkina, O., and Laval, J. (2000) Clustered damages and total lesions induced in DNA by Ionizing radiation: oxidized bases and strand breaks. Biochemistry 39, 8026-8031.
5. Sutherland, B. M., Bennett, P. V., Sidorkina, O., and Laval, J. (2000) Clustered damages induced in isolated DNA and human cells by low doses of ionizing radiation. PNAS U.S.A. 97, 103-108.
6. David, S. S., and Williams, S. D. (1998) Chemistry of glycosylases and endonucleases involved in base-excision repair. Chem. Rev. 98, 1221-1261.
7. Wallace, S. S. (1997) in Oxidative Stress and the Molecular Biology of Antioxidant Defenses (Scandalios, J. G., Ed.) pp 49-90, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY.
8. Wilson III, D. M., Engelward, B. P., and Samson, L. (1988) Prokaryotic Base Excision Repair, in DNA Damage and Repair, Vol 1: DNA Repair in Prokaryotes and Lower Eukaryotes (Nickoloff, J. A., andHoekstra, M. F., Eds.) pp 29-64, Humana Press, Totowa, NJ.
9. Blaisdell, J. O., and Wallace, S. S. (2001) Abortive base excision repair of radiation-induced clustered DNA lesions in Escherichia coli. PNAS U.S.A. 98, 7426-7430.
10. Georgakilas, A. G., Bennet, P. V., Wilson III, D. M., and Sutherland, B. M. (2004) Processing of bistranded abasic DNA clusters in γ-irradiated human hematopoetic cells. Nucleic Acids Res. 32, 5609-5620.
11. Chaudhury, M. A., and Weinfeld, M. (1997) Reactivity of human apurinic/apyrimidinic endonuclease and Escherichia coli exonuclease III with bistranded abasic sites in DNA. J. Biol. Chem. 272, 15650-15655.
12. Chaudhury, M. A., and Weinfeld, M. (1995) The action of Escherichia coli endonuclease III on multiply damaged sites in DNA. J. Mol. Biol. 249, 914-922.
13. Harrison, L., Hatahet, Z., and Wallace, S. S. (1999) In vitro repair of synthetic ionizing radiation-induced multiply damaged DNA sites. J. Mol. Biol. 290, 667-684.
14. Weinfeld, M., Rasouli-Nia, A., Chaudhury, M. A., and Britten, R. A. (2001) Response of base excision repair enzymes to complex DNA lesions. Radiat. Res. 156, 584-589.
15. David-Cordonnier, M.-H., Cunniffe, S. M. T., Hickson, I. D., and O'Neill, P. (2002) Efficiency of incision of an AP site within clustered DNA damage by the major human AP endonucleases. Biochemistry 41, 634-642.
16. Lomax, M. E., Cunniffe, S., and O'Neill, P. (2004) Efficiency of repair of an abasic site within DNA clustered damage sites by mammalian cell nuclear extracts. Biochemistry 43, 11017-11026.
17. Tian, K., McTigue, M., and de los Santos, C. (2002) Sorting the consequences of ionizing radiation: processing of 8-oxoguanine/abasic site lesions. DNA Repair 1, 1039-1049.
18. Wilson, D. M., III, Takeshita, M., Grollman, A. P., and Demple, B. (1995) Incision activity of human apurinic endonuclease (Ape) at abasic site analogs in DNA. J. Biol. Chem. 270, 16002-16007.
19. 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 cyclic analogue of 2′-deoxyribose. Biochemistry 27, 924-931.
20. 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.
21. Cuniasse, Ph., Fazakerley, G. V., Guschlbauer, W., Kaplan, B., 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.
22. Withka, J. M., Wilde, J. A., and Bolton, P. H. (1991) Characterization of conformational features of DNA heteroduplexes containing aldehidic abasic sites. Biochemistry 30, 9931-9940.
23. Singh, M. P., Hill, G. C., Péoc'h, D., Rayner, B., Imbach, J.-L., and Lown, J. W. (1994) High-field NMR and restrained molecular modeling studies on a DNA heteroduplex containing a modefied apurinic abasic site in the form of covalently linked 9-aminoellipticine. Biochemistry 33, 10271-10285.
24. 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.
25. Wang, K. Y., Parker, S. A., Goljer, I., and Bolton, P. H. (1997) Solution structure of a duplex DNA with an abasic site in a dA tract. Biochemistry 36, 11629-11639.
26. 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(GCGTGTGCG): the unpaired thymine stacks inside the helix. Biochemistry 36, 4817-4830.
27. Beger, R. D., and Bolton, P. H. (1998) Structures of Apurinic and Apyrimidinic Sites in Duplex DNAs. J. Biol. Chem. 273, 1565-1573.
28. Hoehn, S. T., Turner, C. J., and Stubbe, J. (2001) Solution structure of an oligonucleotide containing an abasic site: evidence for an unusual deoxyribose conformation. Nucleic Acids Res. 29, 3413-3423.
29. 1′(OH) conformation on duplex DNA containing abasic sites. Biochemistry 43, 15349-15357.
30. Chen, J., Dupradeau, F. Y., Case, D. A., Turner, C. J., and Stubbe, J. (2007) Nuclear magnetic resonance structural studies and molecular modeling of duplex DNA containing normal and 4′-oxidized abasic sites. Biochemistry 46, 3096-3107.
31. Chen, J., Dupradeau, F. Y., Case, D. A., Turner, C. J., and Stubbe, J. (2008) DNA oligonucleotides with A, T, G or C opposite an abasic site: structure and dynamics. Nucleic Acids Res. 36, 253-162.
32. Lin, Z., Hung, K.-N., Grollman, A. P., and de los Santos, C. (1998) Solution structure of duplex DNA containing an extrahelical abasic site analog determined by NMR spectroscopy and molecular dynamics. Nucleic Acid Res. 26, 2385-2391.
33. Cuniasse, Ph., Sowers, L. C., Eritja, R., Kaplan, B., Goodman, M. F., Cognet, J. A. H., Le Bert, M., Guschlbauer, W., and Fazakerley, G. V. (1989) Abasic frameshift in DNA. Solution conformation determined by proton NMR and molecular mechanics calculations. Biochemistry 28, 2018-2026.
34. Lin, Z., and de los Santos, C. (2001) NMR characterization of clustered bistrand abasic site lesions: effect of orientation on their solution structure. J. Mol. Biol. 308, 341-352.
35. States, D. J., Haberkorn, R. A., and Ruben, D. J. (1982) A two-dimensional nuclear Overhauser experiment with pure absorption phase in four quadrants. J. Magn. Reson. 48, 286-292.
36. Plateau, P., and Gueron, M. (1982) Exchangeable proton NMR without baseline distortion, using new strong-pulse sequences. J. Am. Chem. Soc. 104, 7310-7311.
37. Brunger, A. (1993) X-PLOR, version 3.1, A System for X-ray Crystallography and NMR, Yale University Press, New Haven, CT.
38. Lavery, R., and Sklenar, H. (1988) The definition of generalized helicoidal parameters and axis of curvature for irregular nucleic acids. J. Biomol. Struct. Dyn. 6, 63-91.
39. Lavery, R., and Sklenar, H. (1989) Defining the structure of irregular nucleic acids: conventions and principles. J. Biomol. Struct. Dyn. 6, 655-667.
40. Brooks, B., Bruccoleri, R., Olafson, B., States, D., Swaminathan, S., and Karplus, M. (1983) CHARMM: a program for macromolecular energy, minimization, and dynamics calculations. J. Comput. Chem. 4, 187-217.
41. Majumdar, A., and Hosur, R. V. (1992) Simulation of 2D NMR spectra for determination of solution conformations of nucleic acids. Prog. NMR Spectrosc. 24, 109-158.
42. Rinkel, L. J., and Altona, C. (1987) Conformational analysis of deoxyrybofuranos ring in DNA by means of sums of proton-proton coupling constants: a graphical method. J. Biomol. Struct. Dyn. 4, 621-649.
43. Ryckert, J.-P., Ciccoti, G., and Berendsen, H. J. C. (1977) Numerical integration of Cartesian equations of motion of a system with constraints-molecular-dynamics of N-alkanes. J. Comput. Phys. 23, 327-341.
44. van de Ven., F. J., and Hilbers, C. W. (1988) Nucleic acids and nuclear magnetic resonance. Eur. J. Biochem. 178, 1-38.
45. de los Santos, C. (1999) Probing DNA Structure by NMR Spectroscopy, in Comprehensive Natural Products Chemistry, Vol. 7: DNA and Aspects of Molecular Biology (Kool, E., Barton, D., Nakanishi, K., and Meth-Cohn, O., Eds.) pp 55-80, Elsevier Science Ltd., Oxford, UK.
46. Hare, D. R., Wemmer, D. E., Chou, S. H., Drobny, G., and Reid, B. (1983) Assignment of the non-exchangeable proton resonances of d(C-G-C-G-A-A-T-T-C-G-C- G) using two-dimensional nuclear magnetic resonance methods. J. Mol. Biol. 171, 319-336.
47. Gorman, M. A., Morera, S., Rothwell, D. G., de La Fortelle, E., Mol, C. D., Tainer, J. A., Hickson, I. D., and Freemont, P. S. (1997) The crystal structure of the human DNA repair endonuclease HAPE1 suggests the recognition of extra-helical deoxyribose at DNA abasic sites. EMBO J. 16, 6548-6558.
48. Mol, C. D., Izuml, T., Mitra, S., and Tainer, J. A. (2000) DNA-bound structures and mutants reveal abasic DNA binding by APE1 DNA repair and coordination. Nature 403, 451-456.
49. Ferrin, T. E., Huang, C. C., Jarvis, L. E., and Lngridge, R. (1988) The MIDAS display system. J. Mol. Graphics 6, 13-27.
50. Huang, C. C., Pettersen, T. E., Ferrin, T. E., and Lngridge, R. (1991) Conic: A faster render for space-filling molecules with shadows. J. Mol. Graphics 9, 230-236.