Electron Hole Flow Patterns through the RNA-Cleaving 8-17 Deoxyribozyme Yield Unusual Information about Its Structure and Folding

Chemistry and Biology

Volumn 14, Issue 1, 2007, Pages 41-51

  Leung, Edward K Y ^a   Sen, Dipankar ^a  

^a SIMON FRASER UNIVERSITY   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

CYTOSINE; DEOXYRIBOZYME; RNA; SOLVENT;

ARTICLE; CHEMISTRY; CONFORMATION; ELECTRON; ENZYME ACTIVE SITE; METABOLISM;

CATALYTIC DOMAIN; CYTOSINE; DNA, CATALYTIC; ELECTRONS; NUCLEIC ACID CONFORMATION; RNA; SOLVENTS;

EID: 33846308160     PISSN: 10745521     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.chembiol.2006.11.006     Document Type: Article

References (46)

1. Giese B. Long-distance electron transfer through DNA. Annu. Rev. Biochem. 71 (2002) 51-70
2. Schuster G.B. Long range charge transfer in DNA: transient structural distortions control the distance dependence. Acc. Chem. Res. 33 (2000) 253-260
3. Núñez M.E., Hall D.B., and Barton J.K. Long-range oxidative damage to DNA: effects of distance and sequence. Chem. Biol. 6 (1999) 85-97
4. Henderson P.T., Jones D., Hampikian G., Kan Y., and Schuster G.B. Long-distance charge transport in duplex DNA: the phonon-assisted polaron-like hopping mechansim. Proc. Natl. Acad. Sci. USA 96 (1999) 8353-8358
5. Joy A., and Schuster G.B. Long-range radical cation migration in DNA: investigation of the mechanism. Chem. Commun. (2005) 2778-2784
6. Meggers E., Michel-Beyerle M.E., and Giese B. Sequence dependent long range hole transport in DNA. J. Am. Chem. Soc. 120 (1998) 12950-12955
7. Ratner M. Electronic motion in DNA. Nature 397 (1999) 480-481
8. Jortner J., Bixon M., Langenbacher T., and Michel-Beyerle M.E. Charge transfer and transport in DNA. Proc. Natl. Acad. Sci. USA 95 (1998) 12759-12765
9. Burrows C.J., and Muller J.G. Oxidative nucleobase modifications leading to strand scission. Chem. Rev. 98 (1998) 1109-1151
10. Fahlman R.P., and Sen D. DNA conformational switches as sensitive electronic sensors of analytes. J. Am. Chem. Soc. 124 (2002) 4610-4616
11. Odom D.T., Dill E.A., and Barton J.K. Charge transport through DNA four-way junctions. Nucleic Acids Res. 29 (2001) 2026-2033
12. Fahlman R.P., Sharma R.D., and Sen D. The charge conduction properties of DNA holliday junctions depend critically on the identity of the tethered photooxidant. J. Am. Chem. Soc. 124 (2002) 12477-12485
13. Santhosh U., and Schuster G.B. Long-distance radical cation reactions in DNA three-way junctions: inter-arm interaction and migration through the junction. Nucleic Acids Res. 31 (2003) 5692-5699
14. Bhattacharya P.K., and Barton J.K. Influence of intervening mismatches on long-range guanine oxidation in DNA duplexes. J. Am. Chem. Soc. 123 (2001) 8649-8656
15. Hall D.B., and Barton J.K. Sensitivity of DNA-mediated electron transfer to the intervening stack: a probe for the integrity of the DNA base stack. J. Am. Chem. Soc. 123 (2001) 5045-5046
16. Sankar C.G., and Sen D. DNA helix-stack switching as the basis for the design of versatile deoxyribosensors. J. Mol. Biol. 340 (2004) 459-467
17. Robertson S.A., Harada K., Frankel A.D., and Wemmer D.E. Structure determination and binding kinetics of a DNA aptamer-argininamide complex. Biochemistry 39 (2000) 946-954
18. Doudna J.A., and Cech T.R. The chemical repertoire of natural ribozymes. Nature 418 (2002) 222-228
19. Winkler W.C., Nahvi A., Roth A., Collins J.A., and Breaker R.R. Control of gene expression by a natural metabolite-responsive ribozyme. Nature 428 (2004) 281-286
20. 2+ ion as a cofactor for a novel RNA-cleaving deoxyribozyme. Angew. Chem. Int. Ed. Engl. 35 (1996) 2837-2841
21. Santoro S.W., and Joyce G.F. A general purpose RNA-cleaving DNA enzyme. Proc. Natl. Acad. Sci. USA 94 (1997) 4262-4266
22. Feldman A.R., and Sen D. A new and efficient DNA enzyme for the sequence-specific cleavage of RNA. J. Mol. Biol. 313 (2001) 283-294
23. Peracchi A. DNA catalysis: potential, limitations, open questions. ChemBioChem 6 (2005) 1316-1322
24. Silverman S.K. In vitro selection, characterization, and application of deoxyribozymes that cleave RNA. Nucleic Acids Res. 33 (2005) 6151-6163
25. Egli M. Nucleic acid crystallography: current progress. Curr. Opin. Chem. Biol. 8 (2004) 580-591
26. Liu J., and Lu Y. FRET study of a trifluorophore-labeled DNAzyme. J. Am. Chem. Soc. 124 (2002) 15208-15216
27. Cruz R.P.G., Withers J.B., and Li Y. Dinucleotide junction cleavage versatility of 8-17 deoxyribozyme. Chem. Biol. 11 (2004) 57-67
28. Silverman S.K. Breaking up is easy to do (if you're a DNA enzyme that cleaves RNA). Chem. Biol. 11 (2004) 7-8
29. Peracchi A., Bonaccio M., and Clerici M. A mutational analysis of the 8-17 deoxyribozyme core. J. Mol. Biol. 352 (2005) 783-794
30. Peracchi A. Preferential activation of the 8-17 deoxyribozyme by Ca(2+) ions. Evidence for the identity of 8-17 with the catalytic domain of the Mg5 deoxyribozyme. J. Biol. Chem. 275 (2000) 11693-11697
31. Brown A.K., Li J., Pavot C.M.B., and Lu Y. A lead-dependent DNAzyme with a two-step mechanism. Biochemistry 42 (2003) 7152-7161
32. Li J., Zheng W., Kwon A.H., and Lu Y. In vitro selection and characterization of a highly efficient Zn(II)-dependent RNA-cleaving deoxyribozyme. Nucleic Acids Res. 28 (2000) 481-488
33. Bonaccio M., Credali A., and Peracchi A. Kinetic and thermodynamic characterization of the RNA-cleaving 8-17 deoxyribozyme. Nucleic Acids Res. 32 (2004) 916-925
34. Armitage B., Yu C., Devadoss C., and Schuster G.B. Cationic anthraquinone derivatives as catalytic DNA photonucleases-mechanisms for DNA damage and quinone recycling. J. Am. Chem. Soc. 116 (1994) 9847-9859
35. Dohno C., Ogawa A., Nakatani K., and Saito I. Hole trapping at N6-cyclopropyldeoxyadenosine suggests a direct contribution of adenine bases to hole transport through DNA. J. Am. Chem. Soc. 125 (2003) 10154-10155
36. Shao F., O'Neill M.A., and Barton J.K. Long-range oxidative damage to cytosines in duplex DNA. Proc. Natl. Acad. Sci. USA 101 (2004) 17914-17919
37. Cadet J., Berger M., Douki T., and Ravanat J.-L. Oxidative damage to DNA: formation, measurement, and biological significance. Rev. Physiol. Biochem. Pharmacol. 131 (1997) 1-87
38. Cadet J., Ravanat J.-L., Buchko G.W., Yeo H.C., and Ames B.N. Singlet oxygen DNA damage: chromatographic and mass spectrometric analysis of damage products. Methods Enzymol. 234 (1994) 79-88
39. Cadet J., Douki T., Pouget J.-P., and Ravanat J.-L. Singlet oxygen DNA damage products: formation and measurement. Methods Enzymol. 319 (2000) 143-153
40. Cadet J., Ravanat J.-L., Martinez G.R., Medeiros M.H.G., and Di Mascio P. Singlet oxygen oxidation of isolated and cellular DNA: product formation and mechanistic insights. Photochem. Photobiol. 82 (2006) 1219-1225
41. Perrotta A.T., Shih I., and Been M.D. Imidazole rescue of a cytosine mutation in a self-cleaving ribozyme. Science 286 (1999) 123-126
42. Nakano S., Chadalavada D.M., and Bevilacqua P.C. General acid-base catalysis in the mechanism of an HDV ribozyme. Science 287 (2000) 1493-1497
43. Fiala E.S., Conaway C.C., Biles W.T., and Johnson B. Enhanced mutagenicity of 2-nitropropane nitronate with respect to 2-nitropropane-possible involvement of free radical species. Mutat. Res. 179 (1987) 15-22
44. Anwar W.A., Au W.W., Legator M.S., and Ramanujam V.M. Effect of dimethyl sulfoxide on the genotoxicity and metabolism of benzene in vivo. Carcinogenesis 10 (1989) 441-445
45. Odom D.T., and Barton J.K. Long-range oxidative damage in DNA/RNA duplexes. Biochemistry 40 (2001) 8727-8737
46. O'Neill M.A., and Barton J.K. 2-Aminopurine: a probe of structural dynamics and charge transfer in DNA and DNA:RNA hybrids. J. Am. Chem. Soc. 124 (2002) 13053-13066