Use of crosslinking for revealing the DNA phosphate groups forming specific contacts with the E. coli Fpg protein

Biochimie

Volumn 85, Issue 5, 2003, Pages 511-519

  Kuznetsova, Svetlana ^a   Rykhlevskaya, Anna ^a   Taranenko, Maria ^a   Sidorkina, Olga ^b   Oretskaya, Tatiana ^a   Laval, Jacques ^b  

^a MOSCOW STATE UNIVERSITY   (Russian Federation)

^b INSTITUT GUSTAVE ROUSSY   (France)

Author keywords

7,8 Dihydro 8 oxoguanosine; Crosslinking; DNA protein interaction; Fpg protein; Substituted pyrophosphate internucleotide groups

Indexed keywords

AMINO ACID; BACTERIAL PROTEIN; DNA; DOUBLE STRANDED DNA; GUANOSINE DERIVATIVE; PHOSPHATE; PYROPHOSPHORIC ACID DERIVATIVE;

AMINO ACID SYNTHESIS; ARTICLE; BINDING AFFINITY; CHEMICAL ANALYSIS; CHEMICAL STRUCTURE; CONTROLLED STUDY; DNA CONTENT; DNA CROSS LINKING; DNA PROTEIN COMPLEX; ENZYME ACTIVE SITE; ESCHERICHIA COLI; EUKARYOTE EVOLUTION; MOLECULAR RECOGNITION; NONHUMAN; NUCLEOTIDE TRANSPORT; OXIDATIVE STRESS; PROTEIN ANALYSIS; PROTEIN BINDING; PROTEIN DNA INTERACTION; PROTEIN FUNCTION;

ESCHERICHIA COLI; EUKARYOTA;

EID: 0038193778     PISSN: 03009084     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0300-9084(03)00067-1     Document Type: Article

References (33)

1. M.L. Michaels, L. Pham. C. Cruz, J.H. Miller, MutM, a protein that prevents GC-TA transversions, is formamidopyrimidine-DNA glycosylase, Nucleic Acids Res. 19 (1991) 3629-3632.
2. J. Laval, J. Jurado, M. Saparbaev, Antimutagenic role of base-excision repair enzymes upon free radical-induced DNA damage, Mutat. Res. 402 (1998) 93-102.
3. T. Lindahl, Instability and decay of the primary structure of DNA, Nature 362 (1993) 709-715.
4. M. Dizdaroglu, Chemical determination of free radical-induced damage to DNA, Free Radic. Biol. Med. 10 (1991) 225-242.
5. Y. Kuchino, F. Mori, H. Kasai, H. Inoue, S. Iwai, K. Miura, E. Ohtsuka, S. Nishimura, Misreading of DNA templates containing 8-hydroxydeoxyguanosine at the modified base and at adjacent residues, Nature 327 (1987) 77-79.
6. S. Shibutani, M. Takeshita, A.P. Grollman, Insertion of specific bases during DNA synthesis past the oxidation-damaged base 8-oxodG, Nature 349 (1991) 431-434.
7. T.R. O'Connor, R.J. Graves, G. De Murcia, B. Castaing, J. Laval, Fpg protein of Escherichia coli is a zinc finger protein whose cysteine residues have a structural and/or functional role, J. Biol. Chem. 268 (1993) 9063-9070.
8. O.M. Sidorkina, J. Laval, Role of lysine-57 in the catalytic activities of Escherichia coli formamidopyrimidine-DA glycosylase (Fpg protein), Nucleic Acids Res. 26 (1998) 5351-5357.
9. L.E. Rabow, Y.W. Kow, Mechanism of action of base release by Escherichia coli Fpg protein: Role of lysine 155 in catalysis, Biochemistry 36 (1997) 5084-5096.
10. S.V. Kuznetsov, O.M. Sidorkina, J. Jurado, M. Bazin, P. Tauc, J.C. Brochon, J. Laval, R. Santus, Effect of single mutations on the structural dynamics of a DNA repair enzyme, the Escherichia coli formamidopyrimidine-DNA glycosylase: A fluorescence study using tryptophan residues as reporter groups, Eur. J. Biochem. 253 (1998) 413-420.
11. L. Rabow, R. Venkataraman, Y.W. Kow, Mechanism of action of Escherichia coli formamidopyrimidine N-glycosylase: Role of K155 in substrate binding and product release, Prog. Nucleic Acid Res. Mol. Biol. 68 (2001) 223-234.
12. 2-terminal proline acts as a nucleophile in the glycosylase/AP-lyase reaction catalyzed by Escherichia coli, J. Biol. Chem. 272 (1997) 5335-5341.
13. M. Sugahara, T. Mikawa, T. Kumasaka, M. Yamamoto, R. Kato, K. Fukuyama, Y. Inoue, S. Kuramitsu, Crystal structure of a repair enzyme of oxidatively damaged DNA, MutM (Fpg), from an extreme thermophile, Thermus thermophilus HB8, EMBO J. 19 (2000) 3857-3869.
14. R. Gilboa, D.O. Zharkov, G. Golan, A.S. Fernandes, S.E. Gerchman, E. Maty, J.H. Kycia, A.P. Grollman, G. Shoman, Structure of a formamidopyrimidine DNA glycosylase-DNA complex, J. Biol. Chem. 277 (2002) 19811-19816.
15. S.A. Kuznetsova, M.G. Ivanovskaya, Z.A. Shabarova, Chemical reactions in double-stranded nucleic acids. IX. Directed introduction of substituted pyrophosphate bonds into DNA structure, Bioorg. Khim. (Mosc.) 16 (1990) 219-225.
16. S.A. Kuznetsova, I.E. Kanevskii, V.L. Florent'ev, A.D. Mirzabekov, Z.A. Shabarova, DNA sequencing by hybridization with oligonucleotides immobilized in a gel, chemical ligation as a method of expanding the prospects for the method, Mol. Biol. (Mosc.) 28 (1994) 190-195.
17. S.A. Kuznetsova, C. Clusel, U. Edgardo, I. Elias, M. Vasseur, M. Blumenfeld, Z.A. Shabarova, Crosslinking of double-stranded oligonucleotides containing O-methyl-substituted pyrophosphate groups to the HNF1 transcription factor in nuclear cell extract, Nucleic Acids Res. 24 (1996) 4783-4790.
18. A.A. Purmal, Z.A. Shabarova, R.I. Gumport, A new affinity reagent for the site-specific, covalent attachment of DNA to active-site nucleophiles: Application to the Eco RI and RsrI restriction and modification enzymes, Nucleic Acids Res. 20 (1992) 3713-3719.
19. G.Y. Sheflyan, EA. Kubareva, S.A. Kuznetsova, A.S. Karyagina, I.I. Nikolskaya, E.S. Gromova, Z.A. Shabarova, Cross-linking of SsoII restriction endonuclease to cognate and non-cognate DNAs, FEBS Lett. 390 (1996) 307-310.
20. G.Y. Sheflyan, E.A. Kubareva, E.M. Volkov, T.S. Oretskaya, E.S. Gromova, Z.A. Shabarova, Chemical cross-linking of MvaI and EcoRII enzymes to DNA duplexes containing monosubstituted pyrophosphate internucleotide bond, Gene 157 (1995) 187-190.
21. I.A. Kozlov, E.A. Kubareva, M.G. Ivanovskaya, Z.A. Shabarova, Design of new reagents on the base of DNA duplexes for irreversible inhibition of transcription factor NK-kappa B, Antisense Nucleic Acids Drug Dev. 7 (1997) 279-289.
22. E.M. Volkov, E.A. Romanova, A. Krug, T.S. Oretskaya, V.K. Potapov, Z.A. Shabarova, Autonomic synthesis of oligodeoxyribonucleotides with end phosphate groups, Bioorg. Khim. (Mosc.) 14 (1988) 1034-1039.
23. N.A. Naryshkin, M.G. Ivanovskaya, T.S. Oretskaya, E.M. Volkov, M.J. Gait, Z.A. Shabarova, Synthesis and properties of mixed ribodeoxyribooligonucleotide duplexes containing an internucleotide trisubstituted pyrophosphate bond, Bioorg. Khim. (Mosc.) 22 (1996) 691-698.
24. M.G. Ivanovskaya, M.B. Gottikh, Z.A. Shabarova, Modification of oligo(poly)nucleotide phosphomonoester groups in aqueous solutions, Nucleosides Nucleotides 6 (1987) 913-934.
25. S. Boiteux, E. Gajewski, J. Laval, M. Dizdaroglu, Substrate specificity of the Escherichia coli Fpg protein (formamidopyrimidine-DNA glycosylase): Excision of purine lesions in DNA produced by ionizing radiation or photosensitization, Biochemistry 31 (1992) 106-110.
26. N.G. Dollinnaya, A.A. Purmal, V.L. Drutsa, Z.A. Shabarova, Synthesis and properties of concatamer DNA duplexes with modified internucleotide bonds, Vestn. Mosk. Univ. Ser. 2: Khim. 27 (1986) 520-524.
27. B. Castaing, J.L. Fourrey, N. Hervouet, M. Thomas, S. Boiteux, C. Zelver, AP site structural determinants for Fpg specific recognition, Nucleic Acids Res. 27 (1999) 608-615.
28. Z.A. Shabarova, G.Y. Sheflyan, S.A. Kuznetsova, E.A. Kubareva, O.N. Sysoev, M.G. Ivanovskaya, E.S. Gromova, Affinity modification of Eco RII restriction endonuclease by a DNA-duplex containing a monosubstituted pyrophosphate internucleotide bond, Bioorg. Khim. (Mosc.) 20 (1994) 413-419.
29. Z.A. Shabarova, Chemical development in the design of oligonucleotide probes for binding to DNA and RNA, Biochimie 70 (1988) 1323-1334.
30. B. Castaing, A. Geiger, H. Seliger, P. Nehls, J. Laval, C. Zelwer, S. Boiteux, Cleavage and binding of a DNA fragment containing a single 8-oxoguanine by wild type and mutant Fpg proteins, Nucleic Acids Res. 21 (1993) 2899-2905.
31. A.A. Purmal, S.S. Wallace, Y.W. Kow, The phosphodiester bond 3′ to a deoxyuridine residue is a crucial for substrate binding for uracil DNA N-glycosylase, Biochemistry 36 (1996) 16630-16637.
32. E.A. Kubareva, O.A. Fedorova, M.B. Gottikh, H. Tanaka, C. Malvy, Z.A. Shabarova, NF-κB p50 subunit corsslinking to DNA duplexes, containing a monosubstituted pyrophosphate internucleotide bond, FEBS Lett. 381 (1996) 35-38.
33. I.E. Kanevskii, S.A. Kuznetsova, Synthesis of reactive nucleic acid analogues and their application for the study of structure and functions of biopolymers, Russ. Chem. Rev. 67 (1998) 617-631.