Impact of the C1′ configuration of abasic sites on DNA duplex structure

Biochemistry

Volumn 43, Issue 49, 2004, Pages 15349-15357

  De Los Santos, Carlos ^a   El khateeb, Mahmoud ^a   Rege, Pankaj ^a   Tian, Kegui ^a   Johnson, Francis ^a  

^a STONY BROOK UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALDEHYDES; COMPUTER SIMULATION; CONFORMATIONS; ENZYME KINETICS; HYDRATION; MOLECULAR DYNAMICS; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; OLIGOMERS; PLASTICITY; STRUCTURE (COMPOSITION); SYNTHESIS (CHEMICAL);

ANOMER; DNA DUPLEX STRUCTURE; LESIONS;

DNA;

ADENINE; CHLORIDE; DOUBLE STRANDED DNA; ENDONUCLEASE; ENZYME; NATURAL RESISTANCE ASSOCIATED MACROPHAGE PROTEIN; PHOSPHORAMIDIC ACID DERIVATIVE; APEX1 PROTEIN, HUMAN; APURINIC ACID; APYRIMIDINIC ACID; DNA; DNA (APURINIC OR APYRIMIDINIC SITE) LYASE; HETERODUPLEX; HYDROXYL RADICAL; OLIGODEOXYRIBONUCLEOTIDE; POLYNUCLEOTIDE;

ARTICLE; CHEMICAL STRUCTURE; MOLECULAR DYNAMICS; NUCLEAR MAGNETIC RESONANCE; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN STRUCTURE; SOLID; STEREOCHEMISTRY; CHEMISTRY; CONFORMATION; DNA DAMAGE; GENETICS; HUMAN; ISOMERISM; METABOLISM; SYNTHESIS; THERMODYNAMICS; X RAY CRYSTALLOGRAPHY;

APURINIC ACID; CRYSTALLOGRAPHY, X-RAY; DNA; DNA DAMAGE; DNA-(APURINIC OR APYRIMIDINIC SITE) LYASE; HUMANS; HYDROXYL RADICAL; ISOMERISM; MODELS, MOLECULAR; NUCLEAR MAGNETIC RESONANCE, BIOMOLECULAR; NUCLEIC ACID CONFORMATION; NUCLEIC ACID HETERODUPLEXES; OLIGODEOXYRIBONUCLEOTIDES; POLYNUCLEOTIDES; THERMODYNAMICS;

EID: 10644247699     PISSN: 00062960     EISSN: None     Source Type: Journal    
DOI: 10.1021/bi048400c     Document Type: Article

References (44)

1. Lindahl, T., and Nyberg, B. (1972) Rate of Depurination of Native Deoxyribonucleic Acid, Biochemistry 11, 3610-3618.
2. Nakamura, J., Walker, V. E., Upton, P. B., Chiang, S. Y., Kow, Y. W., and Swenberg, J. A. (1998) Highly Sensitive Apurinic/apyrimidinic Site Assay Can Detect Spontaneous and Chemically Induced Depurination under Physiological Conditions, Cancer Res. 58, 222-225.
3. Loeb, L. A., and Preston, B. D. (1986) Mutagenesis by apurinic/ apyrimidinic sites, Annu. Rev. Genet. 20, 201-230.
4. Kusmierek, J. T., Folkman, W., and Singer, B. (1989) Synthesis of N2,3-ethenodeoxyguanosine, N2,3-ethenodeoxyguanosine 5′-phosphate, and N2,3-ethenodeoxyguanosine 5′-triphosphate. Stability of the Glycosyl Bond in the Monomer and in Poly(dG,εdG-dC). Chem. Res. Toxicol. 2, 230-233.
5. Friedberg, E. C., Walker, G. C., and Siede, W. (1995) in DNA Repair and Mutagenesis, ASM Press, Washington, DC.
6. Strauss, B. S. (1991) The "A" Rule of Mutagen Specificity: A Consequence of DNA Polymerase Bypass of Non-Instructional Lesions? BioEssays 13, 79-84.
7. Zou, 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.
8. Weiss, B. (1976) Endonuclease II of Escherichia coli is exonuclease III, J. Biol. Chem. 251, 1896-1901.
9. Robson, C. N., and Hickson, I. D. (1991) Isolation nf cDNA Clones Encoding a Human Apurinic/Apyrimidinic Endonuclease that Corrects DNA Repair and Mutagenesis Defects in E. coli xth (Exonuclease III) Mutants, Nucleic Acids Res. 19, 5519-5523.
10. Demple, B., Herman, T., and Chen, D. S. (1991) Cloning and Expression of APE, the cDNA Encoding the Major Human Apurinic Endonuclease: Definition of a Family of DNA Repair Enzymes, Proc. Natl. Acad. Sci. U.S.A. 88, 11450-11454.
11. Nakamura, I., and Swenberg, J. A. (1999) Endogenous Apurinic/ Apyrimidinic Sites in Genomic DNA of Mammalian Tissues, Cancer Res. 59, 2522-2526.
12. Atamna, H., Cheung, I., and Ames, B. N. (2000) A Method for Detecting Abasic Sites in Living Cells: Age-Dependent Changes in Base Excision Repair, Proc. Natl. Acad. Sci. U.S.A. 97, 686-691.
13. Gelfand, C. A., Plum, G. E., Grollman, A. P., Johnson, F., and Breslauer, K. J. (1998) Thermodynamic consequences of an abasic lesion in duplex DNA are strongly dependent on base sequence, Biochemistry 37, 7321-7327.
14. Ide, H., Shimizu, H., Kimura, Y., Sakamoto, S., Makino, K., Glackin, M., Wallace, S. S., Nakamuta, H., Sasaki, M., and Sugimoto, N. (1995) Influence of α-Deoxyadenosine on the Stability and Structure of DNA. Thermodynamic and Molecular Mechanics Studies, Biochemistry 34, 6947-6955.
15. Bhagwat, M., and Gerlt, J. A. (1996) 3′- and 5′-Strand Cleavage Reactions Catalyzed by the Fpg Protein from Escherichia coli Occur Via Successive β- and δ-Elimination Mechanisms, Respectively, Biochemistry 35, 659-665.
16. Cuniasse, Ph., Sowers, L. C., Eritja, R., Kaplan, B., Goodman, N. F., Cognet, J. A. H., LeBret, M., Guschlbauer, W., and Fazakerly, G. V. (1987) An Abasic Site in DNA. Solution Conformation Determined by Proton NMR and Molecular Mechanics Calculations, Nucleic Acids Res. 15, 8003-8022.
17. Cuniasse, Ph., Fazakerly, 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.
18. Kalnick, 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.
19. Kalnick, 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.
20. Withka, J. M., Wilde, J. A., Bolton, P. H., Mazumder, A., and Gerlt, J. A. (1991) Characterization of Conformational Features of DNA Heteroduplexes Containing Aldehydic Abasic Sites, Biochemistry 30, 9931-9940.
21. 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.
22. Singh, M. P., Hill, G. C., Péoćh, D., Rayner, B., Imbach, J.-L., and Lown, W. (1994) High-field NMR and Restrained Molecular Modeling Studies on a DNA Heteroduplex Containing a Modified Apurinic Abasic Site in the Form of Covalently Linked 9-Amino-ellipticine, Biochemistry 33, 10271-10285.
23. 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.
24. Jourdan, M., Garcia, J., Defrancq, E., Kotera, M., and Lhomme, J. (1999) 2′-Deoxyribonolactone Lesion in DNA: Refined Solution Structure Determined by Nuclear Magnetic Resonance and Molecular Modeling, Biochemistry 38, 3985-3995.
25. Beger, R. D., and Bolton, P. H. (1998) Structures of Apurinic and Apyrimidinic Sites in Duplex DNAs, J. Biol. Chem. 273, 15565-15573.
26. Cline, S. D., Jones, W. R., Stone, M. P., and Osheroff, N. (1999) DNA Abasic Lesions in a Different Light: Solution Structure of an Endogenous Topoisomerase II Poison, Biochemistry 38, 15500-15507.
27. Wang, K. Y., Parker, S. A., Goljer, I., and Bolton, P. H. (1997) Solution Structure of a Duplex DNA with and Abasic Site in a dA Tract, Biochemistry 36, 11629-11639.
28. Hoehn, S., 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. Ezzitouni, A., Russ, P., and Marquez, V. E. (1997) (1S,2R)-[(Benzyloxy) methyl]cyclopent-3-enol. A Versatile Synthon for the Preparation of 4′,1′a-methano- and 1′,1′a-methanocarbocyclic Nucleosides, J. Org. Chem. 62, 4870-4873.
30. Marquez, V. E., Russ, P., Alonso, R., Siddiqui, M. A., Hernandez, S., George, C., Nicklaus, M. C., Dai, F., and Ford, H. (1999) Synthesis of Conformationally Restricted Carbocyclic Nucleosides: The Role of the O(4) Atom in the Key Hydration Step of Adenosine Deaminase, Helv. Chim. Acta 82, 2119-2129.
31. States, D. J., Habekorn, 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.
32. Plateau, P., and Gueron, M. (1982) Exchangeable Proton NMR without Base-Line Distortion, Using New Strong-Pulse Sequences, J. Am. Chem. Soc. 104, 7310-7311.
33. 1H Resonances in Oligonucleotides by Two-Dimensional NMR Spectroscopy, FEBS Lett. 208, 94-98.
34. Brünger, A. (1993) XPLOR Version 3.1: A system for X-ray Crystallography and NMK, Yale University Press, New Haven, CT.
35. Yip, P., and Case, D. A. (1989) A New Method for Refinement of Macromolecular Structures Based on Nuclear Overhauser Effect Spectra, J. Magn. Reson. 83, 643-648.
36. Brooks, B. R., Buccoleri, R. E., Olafson, B. D., States, D. J., Swaminathan, S., and Karplus, M. (1983) CHARMM: A program for macromolecular energy, minimization, and dynamics calculations, J. Comput. Chem. 4, 187-217.
37. Friedman, R. A., and Honig, B. (1992) The electrostatic contribution to DNA base-stacking interactions, Biopolymers 32, 145-159.
38. 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.
39. Rinkel, L. J., and Altona, C. (1987) Conformational analysis of the deoxyribofuranose ring in DNA by means of sums of proton-proton coupling constants: a graphical method, J. Biomol. Struct. Dyn. 4, 621-649.
40. Lavery, R., and Sklenar, H. (1988) The definition of generalized helicoidal parameters and of axis curvature for irregular nucleic acids, J. Biomol. Struct. Dyn. 6, 655-667.
41. de los Santos, C. (1999) Probing DNA Structure by NMR Spectroscopy, in Comprehensive Natural Products Chemistry (Kool, E., Ed.) Vol. 7, pp 55-80, Elsevier Science Ltd., Oxford, U.K.
42. Van de Ven, F. J. M., and Hilbers, C. W. (1988) Nucleic acids and nuclear magnetic resonance, J. Biochem. 178, 1-38.
43. Mol, C. D., Izumi, 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.
44. Wilson, D. M., III, Takeshita, M., Grollman, A. P., and Demple, B. (1995) Incision activity of human apurinic endonuclease (Ape) at abasic site analogues in DNA, J. Biol. Chem. 270, 16002-16007.