Towards Elucidation of the Mechanism of UV1C, a Deoxyribozyme with Photolyase Activity

Journal of Molecular Biology

Volumn 365, Issue 5, 2007, Pages 1326-1336

  Chinnapen, Daniel J F ^a   Sen, Dipankar ^a  

^a SIMON FRASER UNIVERSITY   (Canada)

Author keywords

DNAzyme; photolyase; ribozyme; thymine dimers

Indexed keywords

DEOXYRIBODIPYRIMIDINE PHOTOLYASE; DEOXYRIBONUCLEOTIDE; DEOXYRIBOZYME; DIMER; GUANINE; INOSINE; PROTEIN UV1C; THYMINE; UNCLASSIFIED DRUG;

ARTICLE; CROSS LINKING; ENZYME ACTIVITY; ENZYME ANALYSIS; ENZYME LOCALIZATION; ENZYME MECHANISM; ENZYME STRUCTURE; ENZYME SUBSTRATE COMPLEX; IN VITRO STUDY; PHOTOCHEMISTRY; PRIORITY JOURNAL; PROTEIN DNA INTERACTION; PROTEIN FOLDING;

BACTERIA (MICROORGANISMS);

EID: 33846023648     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2006.10.062     Document Type: Article

References (30)

1. Friedberg E.C., Walker G.C., and Siede W. DNA Repair and Mutagenesis (1995), ASM Press, Washington, DC
2. Vink A.A., and Roza L. Biological consequences of cyclobutane pyrimidine dimers. J. Photochem. Photobiol. B 65 (2001) 101-104
3. Sancar A. Structure and function of DNA photolyase and cryptochrome blue-light photoreceptors. Chem. Rev. 103 (2003) 2203-2237
4. Komori H., Masui R., Kuramitsu S., Yokoyama S., Shibata T., Inoue Y., and Miki K. Crystal structure of thermostable DNA photolyase: pyrimidine-dimer recognition mechanism. Proc. Natl Acad. Sci. USA 98 (2001) 13560-13565
5. Mees A., Klar T., Gnau P., Hennecke U., Eker A.P., Carell T., and Essen L.O. Crystal structure of a photolyase bound to a CPD-like DNA lesion after in situ repair. Science 306 (2004) 1789-1793
6. Tamada T., Kitadokoro K., Higuchi Y., Inaka K., Yasui A., de Ruiter P.E., et al. Crystal structure of DNA photolyase from Anacystis nidulans. Nature Struct. Biol. 4 (1997) 887-891
7. Chinnapen D.J., and Sen D. A deoxyribozyme that harnesses light to repair thymine dimers in DNA. Proc. Natl Acad. Sci. USA 101 (2004) 65-69
8. Shafer R.H., and Smirnov I. Biological aspects of DNA/RNA quadruplexes. Biopolymers 56 (2000) 209-227
9. Mergny J.L., Phan A.T., and Lacroix L. Following G-quartet formation by UV-spectroscopy. FEBS Letters 435 (1998) 74-78
10. Kao Y.T., Saxena C., Wang L., Sancar A., and Zhong D. Direct observation of thymine dimer repair in DNA by photolyase. Proc. Natl Acad. Sci. USA 102 (2005) 16128-16132
11. Breeger S., Hennecke U., and Carell T. Excess electron-transfer-based repair of a cis-syn thymine dimer in DNA is not sequence dependent. J. Am. Chem. Soc. 126 (2004) 1302-1303
12. Ogata R., and Gilbert W. Contacts between the lac repressor and the thymines in the lac operator. Proc. Natl Acad. Sci. USA 74 (1977) 4973-4976
13. Willis M.C., Hicke B.J., Uhlenbeck O.C., Cech T.R., and Koch T.H. Photocrosslinking of 5-iodouracil-substituted RNA and DNA to proteins. Science 262 (1993) 1255-1257
14. Henderson E., Hardin C.C., Walk S.K., Tinoco Jr. I., and Blackburn E.H. Telomeric DNA oligonucleotides form novel intramolecular structures containing guanine-guanine base pairs. Cell 51 (1987) 899-908
15. Sen D., and Gilbert W. Formation of parallel four-stranded complexes by guanine-rich motifs in DNA and its implications for meiosis. Nature 334 (1988) 364-366
16. Sen D., and Gilbert W. A sodium-potassium switch in the formation of four-stranded G4-DNA. Nature 344 (1990) 410-414
17. Williamson J.R., Raghuraman M.K., and Cech T.R. Monovalent cation-induced structure of telomeric DNA: the G-quartet model. Cell 59 (1989) 871-880
18. Kavarnos G.J. Fundamentals of Photoinduced Electron Transfer (1993), VCH Publishers, New York, NY
19. Rehm D., and Weller A. Kinetics of fluorescence quenching by electron and H-atom transfer. J. Isr. Chem. 8 (1970) 259-271
20. Steenken S., and Jovanovic S.V. How easily oxidizable is DNA? One-electron reduction potentials of adenosine and guanosine radicals. J. Am. Chem. Soc. 119 (1997) 617-618
21. Seidel C.A.M., Schulz A., and Sauer M.H.M. Nucleobase-specific quenching of fluorescent dyes. 1. Nucleobase one-electron redox potentials and their correlation with static dynamic quenching efficiencies. J. Phys. Chem. 100 (1996) 5541-5553
22. Dandliker P.J., Nunez M.E., and Barton J.K. Oxidative charge transfer to repair thymine dimers and damage guanine bases in DNA assemblies containing tethered metallointercalators. Biochemistry 37 (1998) 6491-6502
23. Ito T., and Rokita S.E. Criteria for efficient transport of excess electrons in DNA. Angew. Chem. Int. Ed. Engl. 43 (2004) 1839-1842
24. Scannell M.P., Fenick D.J., Yeh S.R., and Falvey D.E. Model studies of DNA photorepair: reduction potentials of thymine and cytosine cyclobutane dimers measured by fluorescence quenching. J. Am. Chem. Soc. 119 (1997) 1971-1977
25. Kawai K., Fujitsuka M., and Majima T. Selective guanine oxidation by UVB-irradiation in telomeric DNA. Chem. Commun. (2005) 1476-1477
26. Stefl R., Spackova N., Berger I., Koca J., and Sponer J. Molecular dynamics of DNA quadruplex molecules containing inosine, 6-thioguanine and 6-thiopurine. Biophys. J. 80 (2001) 455-468
27. Smith F.W., Schultze P., and Feigon J. Solution structures of unimolecular quadruplexes formed by oligonucleotides containing Oxytricha telomere repeats. Structure 3 (1995) 997-1008
28. Sponer J., Leszczynski J., and Hobza P. Structures and energies of hydrogen-bonded DNA base pairs. A nonempirical study with inclusion of electron correlation. J. Phys. Chem. 100 (1996) 1965-1974
29. Hush N.S., and Cheung A.S. Ionization potentials and donor properties of nucleic acid bases and related compounds. Chem. Phys. Letters 34 (1975) 11-13
30. Kim S.T., and Sancar A. Effect of base, pentose, and phosphodiester backbone structures on binding and repair of pyrimidine dimers by Escherichia coli DNA photolyase. Biochemistry 30 (1991) 8623-8630