In vitro replication and repair of DNA containing a C2′-oxidized abasic site

Biochemistry

Volumn 43, Issue 48, 2004, Pages 15217-15222

  Greenberg, Marc M ^a   Weledji, Yvonne N ^a   Kroeger, Kelly M ^a   Kim, Jaeseung ^a  

^a JOHNS HOPKINS UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ENZYMES; OLIGOMERS; OXIDATION; PROTEINS;

ABASIC SITES; LESIONS; POLYMERASE;

DNA;

ALDEHYDE; DEOXYADENOSINE; DNA; ENDONUCLEASE; ENDONUCLEASE IV; EXODEOXYRIBONUCLEASE III; LYASE; OLIGONUCLEOTIDE; PHOSPHATE; UNCLASSIFIED DRUG;

ARTICLE; DNA REPAIR; DNA REPLICATION; ENZYME ACTIVITY; ENZYME ANALYSIS; EXCISION REPAIR; IN VITRO STUDY; MUTAGENICITY; OXIDATION; PRIORITY JOURNAL; PROTEIN INTERACTION; PROTEIN PROCESSING; SYNTHESIS; TECHNIQUE;

APURINIC ACID; DEOXYRIBONUCLEASE IV (PHAGE T4-INDUCED); DNA POLYMERASE I; DNA PRIMERS; DNA REPAIR; DNA REPLICATION; DNA, BACTERIAL; ESCHERICHIA COLI PROTEINS; EXODEOXYRIBONUCLEASES; NUCLEIC ACID HETERODUPLEXES; NUCLEIC ACID HYBRIDIZATION; OLIGONUCLEOTIDES; OXIDATION-REDUCTION; POLYNUCLEOTIDES; SCHIFF BASES; TEMPLATES, GENETIC;

EID: 10044231577     PISSN: 00062960     EISSN: None     Source Type: Journal    
DOI: 10.1021/bi048360c     Document Type: Article

References (28)

1. Strauss, B. S. (1991) The "A Rule" of Mutagen Specificity: a Consequence of DNA Polymerase Bypass of Non-Instructional Lesions?, BioEssays 13, 79-84.
2. Kroeger, K. M., Hashimoto, M., Kow, Y. W., and Greenberg, M. M. (2003) Cross-Linking of 2-Deoxyribonolactone and Its β-E-limination Product by Base Excision Repair Enzymes, Biochemistry 42, 2449-2455.
3. Kroeger, K. M., Jiang, Y. L., Kow, Y. W., Goodman, M. F., and Greenberg, M. M. (2004) Mutagenic Effects of 2-Deoxyribonolactone in Escherichia coli. An Abasic Lesion That Disobeys the A-Rule, Biochemistry 43, 6723-6733.
4. Hashimoto, M., Greenberg, M. M., Kow, Y. W., Hwang, J.-T., and Cunningham, R. P. (2001) The 2-Deoxyribonolactone Lesion Produced in DNA by Neocarzinostatin and Other DNA Damaging Agents Forms Cross-links with the Base-Excision Repair Enzyme Endonuclease III, J. Am. Chem. Soc. 123, 3161-3162.
5. Greenberg, M. M., Weledji, Y. N., Kroeger, K. M., Kim, J., and Goodman, M. F. (2004) In Vitro Effects of a C4′-Oxidized Abasic Site on DNA Polymerases, Biochemistry 43, 2656-2663.
6. Kim, J., Weledji, Y. N., and Greenberg, M. M. (2004) Independent Generation and Characterization of a C2′-Oxidized Abasic Site in Chemically Synthesized Oligonucleotides, J. Org. Chem. 69, 6100-6104.
7. von Sonntag, C. (1987) The Chemical Basis of Radiation Biology, Taylor & Francis, London.
8. Dizdaroglu, M., Schulte-Frohlinde, D., and Von Sonntag, C. (1977) γ-Radiolysis of DNA in Oxygenated Aqueous Solution. Structure of an Alkali-Labile Site, Z. Naturforsch. 32c, 1021-1022.
9. Hissung, A., Isildar, M., and von Sonntag, C. (1981) Radiolysis of Aqueous Solutions of Nucleosides Halogenated at the Sugar Moiety, Int. J. Radiat. Biol. 39, 185-193.
10. Sugiyama, H., Tsutsumi, Y., Fujimoto, K., and Saito, I. (1993) Photoinduced Deoxyribose C2′ Oxidation in DNA. Alkali-Dependent Cleavage of Erythrose-Containing Sites via a Retroaldol Reaction, J. Am. Chem. Soc. 115, 4443-4448.
11. Sugiyama, H., Fujimoto, K., and Saito, I. (1995) Stereospecific 1,2-Hydride Shift in Ribonolactone Formation in the Photoreaction of 2′-Iododeoxyuridine, J. Am. Chem. Soc. 117, 2945-2946.
12. Sugiyama, H., Fujimoto, K., and Saito, I. (1996) Evidence for Intrastrand C2′ Hydrogen Abstraction in Photoirradiation of 5-Halouracil-Containing Oligonucleotides by Using Stereospecifically C2′-Deuterated Deoxyadenosine, Tetrahedron Lett. 37, 1805-1808.
13. Kool, E. T. (2002) Active Site Tightness and Substrate Fit in DNA Replication, Annu. Rev. Biochem. 71, 191-219.
14. Collins, C., Awada, M. M., Zhou, X., and Dedon, P. C. (2003) Analysis of 3′-Phosphoglycoladehyde Residue in Oxidized DNA by Gas Chromatography/Negative Chemical Ionization/Mass Spectroscopy, Chem. Res. Toxicol. 16, 1560-1566.
15. Maniatis, T., Fritsch, E. F., and Sambrook, J. (1982) Molecular Cloning, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY.
16. Kim, J., Gil, J. M., and Greenberg, M. M. (2003) Synthesis and Characterization of Oligonucleotides Containing the C4′-Oxidized Abasic Site Produced by Bleomycin and Other DNA Damaging Agents, Angew. Chem., Int. Ed. 42, 5882-5885.
17. Greenberg, M. M., Weledji, Y. N., Kim, J., and Bales, B. C. (2004) Repair of Oxiidzed Abasic Sites by Exonuclease III, Endonuclease IV, and Endonuclease III, Biochemistry 43, 817-8183.
18. Kow, Y. W., and Wallace, S. S. (1987) Mechanism of Action of Escherichia coli Endonuclease III, Biochemistry 26, 8200-8206.
19. Ide, H., and Kotera, M. (2004) Human DNA Glycosylases Involved in the Repair of Oxidatively Damaged DNA, Biol. Pharm. Bull. 27, 480-485.
20. Asagoshi, K., Odawara, H., Nakano, H., Miyano, T., Terato, H., Ohyama, Y., Seki, S., and Ide, H. (2000) Comparison of Substrate Specificities of Escherichia coli Endonuclease III and Its Mouse Homologue (mNTH1) Using Defined Oligonucleotide Substrates, Biochemistry 39, 11389-11398.
21. Katafuchi, A., Nakano, T., Masaoka, A., Terato, H., Iwai, S., Hanaoka, F., and Ide, H. (2004) Differential Specificity of Human and Escherichia coli Endonuclease III and VIII Homologues for Oxidative Base Lesions, J. Biol. Chem. 279, 14464-14471.
22. Shibutani, S., Takeshita, M., and Grollman, A. P. (1997) Translesional Synthesis on DNA Templates Containing a Single Abasic Site, J. Biol. Chem. 272, 13916-13922.
23. Berthet, N., Roupioz, Y., Constant, J. F., Kotera, M., and Lhomme, J. (2001) Translesional Synthesis on DNA Templates Containing the 2′-Deoxyribonolactone Lesion, Nucleic Acids Res. 29, 2725-2732.
24. Lawrence, C. W., Borden, A., Banerjee, S. K., and LeClerc, J. E. (1990) Mutation Frequency and Spectrum Resulting From a Single Abasic Site in a Single Stranded Vector, Nucleic Acids Res. 18, 2153-2157.
25. Wilson, D. M. I., and Barsky, D. (2001) The Major Human Abasic Endonuclease: Formation, Consequences and Repair of Abasic Lesions in DNA, Mutat. Res. 485, 283-307.
26. Takeuchi, M. L. R., Demple, B., and Takeshita, M. (1994) Interactions of Escherichla coli Endonuclease IV and Exonuclease III with Abasic Sites in DNA, J. Biol. Chem. 269, 21907-21914.
27. Xu, Y. J., DeMottt, M. S., Hwang, J. T., Greenberg, M. M., and Demple, B. (2003) Action of Human Apurinic Endonuclease (Apel) on Cl′-Oxidized Deoxyribose Damage in DNA. DNA Repair 2, 175-185.
28. Matsumoto, Y. K., K. (1995) Excision of Deoxyribose Phosphate Residues by DNA Polymerase Beta During DNA Repair, Science 269, 699-702.