In vitro selection of self-cleaving DNAs

Chemistry and Biology

Volumn 3, Issue 12, 1996, Pages 1039-1046

  Carmi, Nir ^a   Shultz, Lisa A ^a   Breaker, Ronald R ^a  

^a YALE UNIVERSITY   (United States)

Author keywords

catalytic DNA; deoxyribozyme; DNA enzyme; in vitro selection; self cleaving DNA

Indexed keywords

EID: 0030482173     PISSN: 10745521     EISSN: None     Source Type: Journal    
DOI: 10.1016/S1074-5521(96)90170-2     Document Type: Article

References (30)

1. Cech, T.R. (1990). Self-splicing of group I introns. Annu. Rev. Biochem. 59, 543-568.
2. Symons, R.H. (1992). Small catalytic RNAs. Annu. Rev. Biochem. 61, 641-671.
3. Altman, S., Kirsebom, L. & Talbot, S. (1995). Recent studies of RNase P. In: tRNA: Structure, Biosynthesis, and Function. (Söll D. & RajBhandary, U. eds.), pp. 67-78, American Society for Microbiology, Washington, DC, USA.
4. Michel, F. & Ferat, J.-L (1995). Structure and activities of group II introns. Annu. Rev. Biochem. 64, 435-461.
5. 2+-dependent RNA phosphoesterase activity. Chemistry & Biology 2, 655-660.
6. Guthrie, J.P. (1977). Hydration and dehydration of phosphoric acid derivatives: free energies of formation of the pentacoordinate intermediates for phosphate ester hydrolysis and of monomeric metaphosphate. J. Am. Chem. Soc. 99, 3991-4001.
7. von Ahsen, U. & Schroeder, R.S. (1993). RNA as a catalyst: natural and designed ribozymes. BioEssays 15, 299-307.
8. Breaker, R. R. & Joyce, G. F. (1994). Inventing and improving ribozyme function: rational design versus iterative selection methods. Trends Biotechnol. 12, 268-275.
9. Breaker, R.R. (1996). Are engineered proteins getting competition from RNA? Curr. Opin. Biotechnol. 7, 442-448.
10. Breaker, R.R. & Joyce, G.F. (1994). A DNA enzyme that cleaves RNA. Chemistry & Biology 1, 223-229.
11. Cuenoud, B. & Szostak, J.W. (1995). A DNA metalloenzyme with DNA ligase activity. Nature 375, 611-614.
12. Li, Y. & Sen, D. (1996). A catalytic DNA for porphyrin metallation. Nat. Struct. Biol. 3, 743-747.
13. Lindahl, T. (1993). Instability and decay of the primary structure of DNA. Nature 362, 709-715.
14. Sigman, D.S. & Chen, C.B. (1990). Chemical nucleases: new reagents in molecular biology. Annu. Rev. Biochem. 59, 207-236.
15. Sigman, D.S., Mazumder, A. & Perrin, D.M. (1993). Chemical nucleases. Chem. Rev. 93, 2295-2316.
16. Hermann, T. & Heumann, H. (1995). Determination of nucleotide distances in RNA by means of a copper phenanthroline-generated hydroxyl radical cleavage pattern. RNA 1, 1009-1017.
17. Joshi, R.R., Likhite, S.M., Kumar, R.K. & Ganesh, K.N. (1994). DNA cleavage by Cu(II)-desferal: identification of C1′-hydroxylation as the initial event for DNA damage. Biochim. Biophys. Acta 1199, 285-292.
18. Berzal-Harranz, A., Joseph, A. & Burke, J.A. (1992). In vitro selection of active hairpin ribozymes by sequential RNA-catalyzed cleavage and ligation reactions. Genes Dev. 6, 129-134.
19. Woese, C.R. & Pace, N.R. (1993). Probing RNA structure, function, and history by comparative analysis. In The RNA World, (R.R. Gesteland & J.F. Atkins, eds.), pp 91-117, Cold Spring Harbor Laboratory Press, USA.
20. Williamson, J. R. (1994). G-quartet structures in telomeric DNA. Annu. Rev. Biophys. Biomol. Struct. 23, 703-730.
21. Bock, L.C., Griffin, L.C., Latham, J.A., Vermaas, E.H. & Toole, J.J. (1992). Selection of single-stranded DNA molecules that bind and inhibit human thrombin. Nature 355, 564-566.
22. Wyatt, J.R., et al., & Ecker, D.J. (1994). Combinatorially selected guanosine-quartet structure is a potent inhibitor of human immunodeficiency virus envelope-mediated cell fusion. Proc. Natl, Acad. Sci. USA 91, 1356-1360.
23. Lin, Y., Padmapriya, A., Morden, K.M. & Jayasena, S.D. (1995). Peptide conjugation to an in vitro-selected DNA ligand improves enzyme inhibition. Proc. Natl. Acad. Sci. USA 92, 11044-11048.
24. Huizenga, D.E. & Szostak, J.W. (1995). A DNA aptamer that binds adenosine and ATP. Biochemistry 34, 656-665.
25. Kazakov, S.A., Astashkina, T.G., Mamaev, S.V. & Vlassov, V.V. (1988). Site-specific cleavage of single-stranded DNAs at unique sites by a copper-dependent redox reaction. Nature 335, 186-188.
26. Strobel, S.A. & Dervan, P.B. (1991) Site-specific cleavage of a yeast chromosome by oligonucleotide-directed triplex formation. Nature 350, 172-174.
27. Herschlag, D. & Cech, T.R. (1990). DNA cleavage catalysed by the ribozyme from Tetrahymena. Nature 344, 405-409.
28. Robertson, D.L. & Joyce, G.F. (1990). Selection in vitro of an RNA enzyme that specifically cleaves single-stranded DNA. Nature 344, 467-468.
29. Perreault, J.-P. & Altman, S. (1992). Important 2′-hydroxyl groups in model substrates for M1 RNA, the catalytic RNA subunit of RNase P from Escherichia coli. J. Mol. Biol. 226, 399-409.
30. Christoffersen, R.E. & Marr, J.J. (1995). Ribozymes as human therapeutic agents. J. Med. Chem. 38, 2023-2037.