RPA repair recognition of DNA containing pyrimidines bearing bulky adducts

Journal of Molecular Recognition

Volumn 21, Issue 3, 2008, Pages 154-162

  Petruseva, Irina O ^a   Tikhanovich, Irina S ^b   Chelobanov, Boris P ^c   Lavrik, Olga I ^a  

^a INSTITUTE OF CHEMICAL BIOLOGY AND FUNDAMENTAL MEDICINE   (Russian Federation)

^b NOVOSIBIRSK STATE UNIVERSITY   (Russian Federation)

^c INSTITUTE OF PHYSIOLOGY   (Russian Federation)

Author keywords

Affinity modification; hRPA; Model NER substrates; Recognition

Indexed keywords

NUCLEOTIDE; PYRIMIDINE; PYRIMIDINE DERIVATIVE; REPLICATION FACTOR A;

ARTICLE; CHEMICAL STRUCTURE; CHEMISTRY; DNA ADDUCT; DNA PROBE; DNA REPAIR; FLUORESCENCE POLARIZATION; GENETICS; HUMAN; LIGHT; METABOLISM; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PHOTOAFFINITY LABELING;

BASE SEQUENCE; DNA ADDUCTS; DNA PROBES; DNA REPAIR; FLUORESCENCE POLARIZATION; HUMANS; LIGHT; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; NUCLEOTIDES; PHOTOAFFINITY LABELS; PYRIMIDINES; REPLICATION PROTEIN A;

EID: 44949094309     PISSN: 09523499     EISSN: 10991352     Source Type: Journal    
DOI: 10.1002/jmr.877     Document Type: Article

References (55)

1. Bochkareva E, Korolev S, Lees-Miller SP, Bochkarev A. 2002. Structure of the RPA trimerization core and its role in the multistep DNA-binding mechanism of RPA. EMBO J. 21: 1855-1863.
2. Bujalowski W. 2006. Thermodynamic and kinetic methods of analyses of protein-nucleic acid interactions from simpler to more complex systems. Chem. Rev. 106: 556-606.
3. Buterin T, Hess MT, Gunz D, Geacintov NE, Mullenders LH, Naegeli H. 2002. Trapping of DNA nucleotide excision repair factors by nonrepairable carcinogen adducts. Cancer Res. 62: 4229-4235.
4. Buterin T, Hess MT, Luneva N, Geacintov NE, Amin S, Kroth H, Seidel A, Naegeli H. 2000. Unrepaired fjord region polycyclic aromatic hydrocarbon-DNA adducts in ras codon 61 mutational hot spots. Cancer Res. 60: 1849-1856.
5. Buterin T, Meyer C, Giese B, Naegeli H. 2005. DNA quality control by conformational readout on the undamaged strand of the double helix. Chem. Biol. 12: 913-922.
6. Chelobanov BP, Laktionov PP, Kharkova MV, Rykova EY, Vlassov VV. 2004. Isolation of nucleic acid binding proteins: an approach for isolation of cell surface, nucleic acid binding proteins. Ann. N. Y. Acad. Sci. 1022: 239-243.
7. de Laat WL, Appeldoorn E, Sugasawa K, Weterings E, Jaspers NGJ, Hoeijmakers JHJ. 1998. DNA-binding polarity of human replication protein A positions nucleases in nucleotide excision repair. Genes Dev. 12: 2598-2609.
8. DellaVecchia MJ, Croteau DL, Skorvaga M, Dezhurov SV, Lavrik OI, Van Houten B. 2004. Analyzing the handoff of DNA from UvrA to UvrB utilizing DNA-protein photoaffinity labeling. J. Biol. Chem. 279: 45245-46256.
9. Dezhurov SV, Khodyreva SN, Plekhanova ES, Lavrik OI. 2005. A new highly efficient photoreactive analogue of dCTP. Synthesis, characterization, and application in photoaffinity modification of DNA binding proteins. Bioconjug. Chem. 16: 215-222.
10. Dip R, Camenisch U, Naegeli H. 2004. Mechanisms of DNA damage recognition and strand discrimination in human nucleotide excision repair. DNA Repair (Amst.) 3: 1409-1423.
11. Fanning E, Klimovich V, Nager AR. 2006. A dynamic model for replication protein A (RPA) function in DNA processing pathways. Nucleic Acids Res. 34: 4126-4137.
12. Geacintov NE, Broyde S, Buterin T, Naegeli H, Wu M, Yan S, Patel DJ. 2002. Thermodynamic and structural factors in the removal of bulky DNA adducts by the nucleotide excision repair machinery. Biopolymers 65: 202-210.
13. Gillet LC, Alzeer J, Scharer OD. 2005. Site-specific incorporation of N-(deoxyguanosin-8-yl)-2-acetylaminofluorene (dG-AAF) into oligonucleotides using modified 'ultra-mild' DNA synthesis. Nucleic Acids Res. 33: 1961-1969.
14. Gillet LC, Scharer OD. 2006. Molecular mechanisms of mammalian global genome nucleotide excision repair. Chem. Rev. 106: 253-276.
15. Gunz D, Hess MT, Naegeli H. 1996. Recognition of DNA adducts by human nucleotide excision repair. J. Biol. Chem. 271: 25089-25098.
16. Henricksen LA, Umbricht CB, Wold MS. 1994. Recombinant replication protein A: expression, complex formation, and functional characterization. J. Biol. Chem. 269: 11121-11132.
17. Hermanson-Miller IL, Turchi JJ. 2002. Strand-specific binding of RPA and XPA to damaged duplex DNA. Biochemistry 41: 2402-2408.
18. Hess MT, Gunz D, Luneva N, Geacintov N, Naegeli H. 1997. Base pair conformation-dependent excision of benzo[a]pyrene diol epoxide-guanine adducts by human nucleotide excision repair enzymes. Mol. Cell. Biol. 17: 7069-7076.
19. Hey T, Lipps G, Krauss G. 2001. Binding of XPA and RPA to damaged DNA investigated by fluorescence anisotropy. Biochemistry 40: 2901-2910.
20. Huang JC, Hsu DS, Kazantsev A, Sancar A. 1994. Substrate spectrum of human excinuclease: repair of abasic sites, methylated bases, mismatches, and bulky adducts. Proc. Natl. Acad. Sci. USA 91: 12213-12217.
21. Iakoucheva LM, Walker RK, van Houten B, Ackerman EJ. 2002. Equilibrium and stop-flow kinetic studies of fluorescently labeled DNA substrates with DNA repair proteins XPA and replication protein A. Biochemistry 41: 131-143.
22. Iftode C, Daniely Y, Borowiec JA. 1999. Replication protein A (RPA): the eukaryotic SSB. Crit. Rev. Biochem. Mol. Biol. 34: 141-180.
23. Kerr ID, Wadsworth RI, Cubeddu L, Blankenfeldt W, Naismith JH, White MF. 2003. Insights into ssDNA recognition by the OB fold from a structural and thermodynamic study of Sulfolobus SSB protein. EMBO J. 22: 2561-2570.
24. Khodyreva SN, Lavrik OI. 2005. Photoaffinity labeling technique for studying DNA replication and DNA repair. Curr. Med. Chem. 12: 641-655. Review.
25. Kolpashchikov DM, Rechkunova NI, Dobrikov MI, Khodyreva SN, Lebedeva NA, Lavrik OI. 1999. Sensitized photomodification of mammalian DNA polymerase beta. A new approach for highly selective affinity labeling of polymerases. FEBS Lett. 448: 141-144.
26. Laemmli UK. 1970. Cleavage of structural proteins during the assembly of the head of bacteriophage T4. Nature 227: 680-685.
27. Lao Y, Gomes XV, Ren Y, Taylor JS, Wold MS. 2000. Replication protein A interactions with DNA. III. Molecular basis of recognition of damaged DNA. Biochemistry 39: 850-859.
28. Lavrik OI, Kolpashchikov DM, Weisshart K, Nasheuer HP, Khodyreva SN, Favre A. 1999. RPA subunit arrangement near the 3′-end of primer is modulated by the length of the template strand and cooperative protein interactions. Nucleic Acids Res. 27: 4235-4240.
29. Lavrik OI, Pestryakov PE, Nazarkina JK, Khodyreva SN. 2003. Study of human replication protein A by photoaffinity labeling technique. In Chemical Probes in Biology, Schneider M (ed.). Kluwer Academic Publishers: Dordrecht, the Netherlands 181-192.
30. Liu Y, Yang Z, Utzat CD, Liu Y, Geacintov NE, Basu AK, Zou Y. 2005. Interactions of human replication protein A with single-stranded DNA adducts. Biochem. J. 385: 519-526.
31. Maillard O, Solyom S, Naegeli H. 2007. An aromatic sensor with aversion to damaged strands confers versatility to DNA repair. PLoS Biol. 5: e79.
32. Majka J, Binz SK, Wold MS, Burgers PM. 2006. Replication protein A directs loading of the DNA damage checkpoint clamp to 5′-DNA junctions. J. Biol. Chem. 281: 27855-27861.
33. Maltseva EA, Rechkunova NI, Gillet LC, Petruseva IO, Scharer OD, Lavrik OI. 2007. Crosslinking of the NER damage recognition proteins XPC-HR23B, XPA and RPA to photoreactive probes that mimic DNA damages. Biochim. Biophys. Acta 1770: 781-789.
34. Maltseva EA, Rechkunova NI, Petruseva IO, Silnikov VN, Vermeulen W, Lavrik OI. 2006. Interaction of nucleotide excision repair factors RPA and XPA with DNA containing bulky photoreactive groups imitating damages. Biochemistry (Moscow) 71: 270-278.
35. Mass G, Nethanel T, Lavrik OI, Wold MS, Kaufmann G. 2001. Replication protein A modulates its interface with the primed DNA template during RNA-DNA primer elongation in replicating SV40 chromosomes. Nucleic Acids Res. 29: 3892-3899.
36. Missura M, Buterin T, Hindges R, Hubscher U, Kasparkova J, Brabec V, Naegeli H. 2001. Double-check probing of DNA bending and unwinding by XPA-RPA: an architectural function in DNA repair. EMBO J. 20: 3554-3564.
37. Mou TC, Shen M, Abdalla S, Delamora D, Bochkareva E, Bochkarev A, Gray DM. 2006. Effects of ssDNA sequences on non-sequence-specific protein binding. Chirality 18: 370-382.
38. Osterman LA. 1981. Methods of Investigation of Proteins and Nucleic Acids. Electrophoresis and Ultracentrifugation. Nauka: Russia; 56-59.
39. Patrick SM, Turchi JJ. 2001. Stopped-flow kinetic analysis of replication protein A-binding DNA. J. Biol. Chem. 276: 22630-22637.
40. Reardon JT, Sancar A. 2003. Recognition and repair of the cyclobutane thymine dimer, a major cause of skin cancers, by the human excision nuclease. Genes Dev. 17: 2539-2551.
41. Reardon JT, Sancar A. 2005. Nucleotide excision repair. Prog. Nucleic Acid Res. Mol. Biol. 79: 183-235.
42. Riedl T, Hanaoka F, Egly JM. 2003. The comings and goings of nucleotide excision repair factors on damaged DNA. EMBO J. 22: 5293-52303.
43. Safronov IV, Shcherbik NV, Khodyreva SN, Vlasov VA, Dobrikov MI, Shishkin GV, Lavrik OI. 1997. New photoreactive N(4)-substituted dCTP analogues:synthesis, photochemical characteristics, and substrate properties in HIV-1 reverse transcriptase catalyzed DNA synthesis. Bioorg. Khim. 23: 576-585.
44. Salas TR, Petruseva I, Lavrik O, Bourdoncle A, Mergny JL, Favre A, Saintome C. 2006. Human replication protein A unfolds telomeric G-quadruplexes. Nucleic Acids Res. 34: 4857-4865.
45. Sambrook J, Fritsch EF, Maniatis T. 1989. Molecular Cloning: A Laboratory manual, 2nd edn. Cold Spring Harbor Laboratory: Cold Spring Harbor, NY.
46. Scharer OD. 2003. Chemistry and biology of DNA repair. Angew. Chem. 42: 2946-2974.
47. Schweizer U, Hey T, Lipps G, Krauss G. 1999. Photocrosslinking locates a binding site for the large subunit of human replication protein A to the damaged strand of cisplatin-modified DNA. Nucleic Acids Res. 27: 3183-3189.
48. Smith CA, Taylor JS. 1993. Preparation and characterization of a set of deoxyoligonucleotide 49-mers containing site-specific cis-syn, trans-syn-l, (6-4), and Dewar photoproducts of thymidylyl (3′→5′)-thymidine. J. Biol. Chem. 268: 11143-11151.
49. Tapias A, Auriol J, Forget D, Enzlin JH, Scharer OD, Coin F, Coulombe B, Egly JM. 2004. Ordered conformational changes in damaged DNA induced by nucleotide excision repair factors. J. Biol. Chem. 279: 19074-19083.
50. Trego KS, Turchi JJ. 2006. Pre-steady-state binding of damaged DNA by XPC-hHR23B reveals a kinetic mechanism for damage discrimination. Biochemistry 45: 1961-1969.
51. Vasquez KM, Christensen J, Li L, Finch RA, Glazer PM. 2002. Human XPA and RPA DNA repair proteins participate in specific recognition of triplex-induced helical distortions. Proc. Natl. Acad. Sci. USA 99: 5848-5853.
52. Weisshart K, Pestryakov P, Smith RW, Hartmann H, Kremmer E, Lavrik O, Nasheuer HP. 2004. Coordinated regulation of replication protein A activities by its subunits p14 and p32. J. Biol. Chem. 279: 35368-35376.
53. Wold MS. 1997. Replication protein A: a heterotrimeric, single-stranded DNA-binding protein required for eukaryotic DNA metabolism. Annu. Rev. Biochem. 66: 61-92.
54. Wu M, Yan S, Patel DJ, Geacintov NE, Broyde S. 2002. Relating repair susceptibility of carcinogen-damaged DNA with structural distortion and thermodynamic stability. Nucleic Acids Res. 30: 3422-3432.
55. Wyka IM, Dhar K, Binz SK, Wold MS. 2003. Replication protein A interactions with DNA: differential binding of the core domains and analysis of the DNA interaction surface. Biochemistry 42: 12909-12918.