Dinucleotide Junction Cleavage Versatility of 8-17 Deoxyribozyme

Chemistry and Biology

Volumn 11, Issue 1, 2004, Pages 57-67

  Cruz, Rani P G ^a   Withers, Johanna B ^a   Li, Yingfu ^a  

^a MCMASTER UNIVERSITY   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 1142281951     PISSN: 10745521     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.chembiol.2003.12.012     Document Type: Article

References (50)

1. Tuerk C., Gold L. Systematic evolution of ligands by exponential enrichment. RNA ligands to bacteriophage T4 DNA polymerase Science. 249:1990;505-510.
2. Ellington A.D., Szostak J.W. In vitro selection of RNA molecules that bind specific ligands. Nature. 346:1990;818-822.
3. Sen D., Geyer C.R. DNA enzymes. Curr. Opin. Chem. Biol. 2:1998;680-687.
4. Li Y., Breaker R.R. Deoxyribozymes. New players in the ancient game of biocatalysis Curr. Opin. Struct. Biol. 9:1999;315-323.
5. Wilson D.S., Szostak J.W. In vitro selection of functional nucleic acids. Annu. Rev. Biochem. 68:1999;611-647.
6. Jaschke A. Artificial ribozymes and deoxyribozymes. Curr. Opin. Struct. Biol. 11:2001;321-326.
7. Emilsson G.M., Breaker R.R. Deoxyribozymes. new activities and new applications Cell. Mol. Life Sci. 59:2002;596-607.
8. Breaker R.R., Joyce G.F. A DNA enzyme that cleaves RNA. Chem. Biol. 1:1994;223-229.
9. Breaker R.R., Joyce G.F. A DNA enzyme with Mg(II)-dependent RNA phosphoesterase activity. Chem. Biol. 2:1995;655-660.
10. 2+ ion as a cofactor for a novel RNA-cleaving deoxyribozyme. Angew. Chem. Int. Ed. Engl. 35:1996;2809-2813.
11. Santoro S.W., Joyce G.F. A general-purpose RNA-cleaving DNA enzyme. Proc. Natl. Acad. Sci. USA. 94:1997;4262-4266.
12. Geyer C.R., Sen D. Evidence for the metal-cofactor independence of an RNA phosphodiester-cleaving DNA enzyme. Chem. Biol. 4:1997;579-593.
13. Li J., Zheng W., Kwon A.H., Lu Y. In vitro selection and characterization of a highly efficient Zn(II)-dependent RNA-cleaving deoxyribozyme. Nucleic Acids Res. 28:2000;481-488.
14. Feldman A.R., Sen D. A new and efficient DNA enzyme for the sequence-specific cleavage of RNA. J. Mol. Biol. 313:2001;283-294.
15. Mei S.H.J., Liu Z., Brennan J.D., Li Y. An efficient RNA-cleaving DNA enzyme that synchronizes catalysis with fluorescence signaling. J. Am. Chem. Soc. 125:2003;412-420.
16. Liu Z., Mei S.H.J., Brennan J.D., Li Y. Assemblage of signalling DNA enzymes with intriguing metal specificity and pH dependences. J. Am. Chem. Soc. 125:2003;7539-7545.
17. Khachigian L.M. DNAzymes. cutting a path to a new class of therapeutics Curr. Opin. Mol. Ther. 4:2002;119-121.
18. Santoro S.W., Joyce G.F. Mechanism and utility of an RNA-cleaving DNA enzyme. Biochemistry. 37:1998;13330-13342.
19. Cairns M.J., King A., Sun L.Q. Optimisation of the 10-23 DNAzyme-substrate pairing interactions enhanced RNA cleavage activity at purine-cytosine target sites. Nucleic Acids Res. 31:2003;2883-2889.
20. Li J., Lu Y. A highly sensitive and selective catalytic DNA biosensor for lead ions. J. Am. Chem. Soc. 122:2002;10466-10467.
21. Stojanovic M.N., Mitchell T.E., Stefanovic D. Deoxyribozyme-based logic gates. J. Am. Chem. Soc. 124:2002;3555-3561.
22. Soukup G.A., Breaker R.R. Engineering precision RNA molecular switches. Proc. Natl. Acad. Sci. USA. 96:1999;3584-3589.
23. Breaker R.R. Engineered allosteric ribozymes as biosensor components. Curr. Opin. Biotechnol. 13:2002;31-39.
24. Silverman S.K. Rube Goldberg goes (ribo)nuclear? Molecular switches and sensors made from RNA. RNA. 9:2003;377-383.
25. Wang W., Billen L.P., Li Y. Sequence diversity, metal specificity and catalytic proficiency of metal-dependent phosphorylating DNA enzymes. Chem. Biol. 9:2002;507-517.
26. Wang Y., Silverman S.K. Deoxyribozymes that synthesize branched and lariat RNA. J. Am. Chem. Soc. 125:2003;6880-6881.
27. Li Y., Breaker R.R. Kinetics of RNA degradation by specific base catalysis of transesterification involving the 2′-hydroxyl group. J. Am. Chem. Soc. 121:1999;5364-5372.
28. Faulhammer D., Famulok M. Characterization and divalent metal-ion dependence of in vitro selected deoxyribozymes which cleave DNA/RNA chimeric oligonucleotides. J. Mol. Biol. 269:1997;188-202.
29. 2+ ions. Evidence for the identity of 8-17 with the catalytic domain of the Mg5 deoxyribozyme. J. Biol. Chem. 275:2000;11693-11697.
30. Brown A.K., Li J., Pavot C.M., Lu Y. A lead-dependent DNAzyme with a two-step mechanism. Biochemistry. 42:2003;7152-7161.
31. Lehman N. Assessing the likelihood of recurrence during RNA evolution in vitro. Artif. Life. in press:2004.
32. Pabon-Pena L.M., Zhang Y., Epstein L.M. Newt satellite 2 transcripts self-cleave by using an extended hammerhead structure. Mol. Cell. Biol. 11:1991;6109-6115.
33. Zhang Y., Epstein L.M. Cloning and characterization of extended hammerheads from a diverse set of caudate amphibians. Gene. 172:1996;183-190.
34. Ferbeyre G., Smith J.M., Cedergren R. Schistosome satellite DNA encodes active hammerhead ribozymes. Mol. Cell. Biol. 18:1998;3880-3888.
35. Rojas A.A., Vazquez-Tello A., Ferbeyre G., Venanzetti F., Bachmann L., Paquin B., Sbordoni V., Cedergren R. Hammerhead-mediated processing of satellite pDo500 family transcripts from Dolichopoda cave crickets. Nucleic Acids Res. 28:2000;4037-4043.
36. Tang J., Breaker R.R. Structural diversity of self-cleaving ribozymes. Proc. Natl. Acad. Sci. USA. 97:2000;5784-5789.
37. Salehi-Ashtiani K., Szostak J.W. In vitro evolution suggests multiple origins for the hammerhead ribozyme. Nature. 414:2001;82-84.
38. 2+ concentration. Nucleic Acids Res. 27:1999;2400-2407.
39. Liu J., Lu Y. FRET study of a trifluorophore-labeled DNAzyme. J. Am. Chem. Soc. 124:2002;15208-15216.
40. Bloomfield V.A., Crothers D.M., Tinoco I. Jr. Nucleic Acids - Structures, Properties and Functions. 1996;University Science Books, Sausalito, CA.
41. Nowakowski J., Shim P.J., Prasad G.S., Stout C.D., Joyce G.F. Crystal structure of an 82-nucleotide RNA-DNA complex formed by the 10-23 DNA enzyme. Nat. Struct. Biol. 6:1999;151-156.
42. Robertson M.P., Ellington A.D. In vitro selection of an allosteric ribozyme that transduces analytes to amplicons. Nat. Biotechnol. 17:1999;62-66.
43. Koizumi M., Soukup G.A., Kerr J.N., Breaker R.R. Allosteric selection of ribozymes that respond to the second messengers cGMP and cAMP. Nat. Struct. Biol. 6:1999;1062-1071.
44. Seetharaman S., Zivarts M., Sudarsan N., Breaker R.R. Immobilized RNA switches for the analysis of complex chemical and biological mixtures. Nat. Biotechnol. 19:2001;336-341.
45. Robertson M.P., Ellington A.D. In vitro selection of nucleoprotein enzymes. Nat. Biotechnol. 19:2001;650-655.
46. Piganeau N., Thuillier V., Famulok M. In vitro selection of allosteric ribozymes. theory and experimental validation J. Mol. Biol. 312:2001;1177-1190.
47. Hartig J.S., Najafi-Shoushtari S.H., Grune I., Yan A., Ellington A.D., Famulok M. Protein-dependent ribozymes report molecular interactions in real time. Nat. Biotechnol. 20:2002;717-722.
48. Levy M., Ellington A.D. ATP-dependent allosteric DNA enzymes. Chem. Biol. 9:2002;417-426.
49. Vaish N.K., Dong F., Andrews L., Schweppe R.E., Ahn N.G., Blatt L., Seiwert S.D. Monitoring post-translational modification of proteins with allosteric ribozymes. Nat. Biotechnol. 20:2002;810-815.
50. Vaish N.K., Jadhav V.R., Kossen K., Pasko C., Andrews L.E., McSwiggen J.A., Polisky B., Seiwert S.D. Zeptomole detection of a viral nucleic acid using a target-activated ribozyme. RNA. 9:2003;1058-1072.