HIV-1 TAR as anchoring site for optimized catalytic RNAs

Biological Chemistry

Volumn 384, Issue 3, 2003, Pages 343-350

  Puerta Fernández, Elena ^a   Barroso del Jesus, Alicia ^a   Romero López, Christina ^a   Berzal Herranz, Alfredo ^a  

^a INSTITUTO DE PARASITOLOGÍA Y BIOMEDICINA LÓPEZ NEYRA   (Spain)

Author keywords

Hammerhead ribozyme; Kissing complex; Ribozyme targeting

Indexed keywords

COMPLEMENTARY RNA; RIBOZYME;

BINDING SITE; COMPLEX FORMATION; CONTROLLED STUDY; ENZYME ACTIVE SITE; ENZYME BINDING; ENZYME SPECIFICITY; GENE CONSTRUCT; GENE DELETION; GENE SEQUENCE; GENE SILENCING; GENE TARGETING; HUMAN IMMUNODEFICIENCY VIRUS 1; MOLECULAR INTERACTION; MOLECULAR STABILITY; NONHUMAN; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN MOTIF; REVIEW; RNA CLEAVAGE; RNA HYBRIDIZATION; RNA STRUCTURE;

BASE SEQUENCE; BINDING SITES; CATALYTIC DOMAIN; ESCHERICHIA COLI; HIV LONG TERMINAL REPEAT; HIV-1; NUCLEIC ACID CONFORMATION; RNA, ANTISENSE; RNA, CATALYTIC; SEQUENCE DELETION; SUBSTRATE SPECIFICITY;

HUMAN IMMUNODEFICIENCY VIRUS; HUMAN IMMUNODEFICIENCY VIRUS 1; RNA VIRUSES;

EID: 0012785323     PISSN: 14316730     EISSN: None     Source Type: Journal    
DOI: 10.1515/BC.2003.040     Document Type: Review

References (32)

1. Barroso-delJesus, A. and Berzal-Herranz, A. (2001). Selection of targets and the most efficient hairpin ribozymes for inactivation of mRNAs using a self-cleaving RNA library. EMBO Rep. 2, 1112-1118.
2. Bertani, G. (1951). Studies on lysogenesis. I. The mode of phage liberation by lysogenic Escherichia coli. J. Bacteriol. 62, 293-300.
3. Bramlage, B., Luzi, E. and Eckstein, F. (2000). HIV-1 LTR as a target for synthetic ribozyme-mediated inhibition of gene expression: site selection and inhibition in cell culture. Nucleic Acids Res. 28, 4059-4067.
4. Campbell, T.B. and Cech, T.R. (1995). Identification of ribozymes within a ribozyme library that efficiently cleave a long substrate RNA. RNA 1, 598-609.
5. Ducongé, F. and Toulmé, J.J. (1999). In vitro selection identifies key determinants for loop-loop interactions: RNA aptamers selective for the TAR RNA element of HIV-1. RNA 5, 1605-1614.
6. Eckstein, F. and Lilley, D.M.J. (1996). Catalytic RNA. Nucleic Acids and Molecular Biology, Vol 10 (Berlin, Germany: Springer-Verlag).
7. Eguchi, Y., Itoh, T. and Tomizawa, J. (1991). Antisense RNA. Annu. Rev. Biochem. 60, 631-652.
8. Esteban, J.A., Banerjee, A.R. and Burke, J.M. (1997). Kinetic mechanism of the hairpin ribozyme. Identification and characterization of two non-exchangeable conformations. J. Biol. Chem. 272, 13629-13639.
9. Franch, T. and Gerdes, K. (2000). U-turns and regulatory RNAs. Curr. Opin. Microbiol. 3, 159-164.
10. Franch, T., Petersen, M., Wagner, E.G., Jacobsen, J.P. and Gerdes, K. (1999). Antisense RNA regulation in prokaryotes: rapid RNA/RNA interaction facilitated by a general U-turn loop structure. J. Mol. Biol. 294, 1115-1125.
11. Hananhan, D. (1985). Techniques for transformation of E. coli. In: DNA Cloning: A Practical Approach, Vol. 1, D.M. Glover, ed. (Oxford, UK: IRL Press), pp. 109-135.
12. Haseloff, J. and Gerlach, W.L. (1988). Simple RNA enzymes with new and highly specific endoribonuclease activities. Nature 334, 585-591.
13. Hazan, U., Thomas, D., Alcami, J., Bachelerie, F., Israel, N., Yssel, H., Virelizier, J.L. and Arenzana-Seisdedos, F. (1990). Stimulation of a human T-cell clone with anti-CD3 or tumor necrosis factor induces NF-κB translocation but not human immunodeficiency virus 1 enhancer-dependent transcription. Proc. Natl. Acad. Sci. USA 87, 7861-7865.
14. Inokuchi, Y., Yuyama, N., Hirashima, A., Nishikawa, S., Ohkawa, J. and Taira, K. (1994). A hammerhead ribozyme inhibits the proliferation of an RNA coliphage SP in Escherichia coli. J. Biol. Chem. 269, 11361-11366.
15. Jaeger, J.A., Turner, D.H. and Zuker, M. (1989). Improved predictions of secondary structures for RNA. Proc. Natl. Acad. Sci. USA 86, 7706-7710.
16. Kato, Y., Kuwabara, T., Warashina, M., Toda, H. and Taira, K. (2001). Relationships between the activities in vitro and in vivo of various kinds of ribozyme and their intracellular localization in mammalian cells. J. Biol. Chem. 276, 15378-15385.
17. Kawasaki, H. and Taira, K. (2002). Identification of genes by hybrid ribozymes that couple cleavage activity with the unwinding activity of an endogenous RNA helicase. EMBO Rep. 3, 443-450.
18. Kolb, F.A., Engdahl, H.M., Slagter-Jager, J.G., Ehresmann, B., Ehresmann, C., Westhof, E., Wagner, E.G. and Romby, P. (2000). Progression of a loop-loop complex to a four-way junction is crucial for the activity of a regulatory antisense RNA. EMBO J. 19, 5905-5915.
19. Lieber, A. and Strauss, M. (1995). Selection of efficient cleavage sites in target RNAs by using a ribozyme expression library. Mol. Cell Biol. 15, 540-551.
20. Lodmell, J.S., Ehresmann, C., Ehresmann, B. and Marquet, R. (2000). Convergence of natural and artificial evolution on an RNA loop-loop interaction: the HIV-1 dimerization initiation site. RNA 6, 1267-1276.
21. Ojwang, J.O., Hampel, A., Looney, D.J., Wong-Staal, F. and Rappaport, J. (1992). Inhibition of human immunodeficiency virus type 1 expression by a hairpin ribozyme. Proc. Natl. Acad. Sci. USA 89, 10802-10806.
22. Patzel, V. and Sczakiel, G. (1998). Theoretical design of antisense RNA structures substantially improves annealing kinetics and efficacy in human cells. Nature Biotechnol. 16, 64-68.
23. Pérez-Ruiz, M., Barroso-DelJesus, A. and Berzal-Herranz, A. (1999a). Specificity of the hairpin ribozyme. Sequence requirements surrounding the cleavage site. J. Biol. Chem. 274, 29376-29380.
24. Pérez-Ruiz, M., Sievers, D., Garcia-Lopez, P.A. and Berzal-Herranz, A. (1999b). The antisense sequence of the HIV-1 TAR stem-loop structure covalently linked to the hairpin ribozyme enhances its catalytic activity against two artificial substrates. Antisense Nucleic Acid Drug Dev. 9, 33-42.
25. Persson, C., Wagner, E.G. and Nordstrom, K. (1988). Control of replication of plasmid R1: kinetics of in vitro interaction between the antisense RNA, CopA, and its target, CopT. EMBO J. 7, 3279-3288.
26. Puerta-Fernández, E., Barroso-DelJesus, A. and Berzal-Herranz, A. (2002). Anchoring hairpin ribozymes to long target RNAs by loop-loop RNA interactions. Antisense Nucleic Acid Drug Dev. 12, 1-9.
27. Rossi, J.J. (1999). Ribozymes, genomics and therapeutics. Chem. Biol. 6, R33-37.
28. Ruffner, D.E., Stormo, G.D. and Uhlenbeck, O.C. (1990). Sequence requirements of the hammerhead RNA self-cleavage reaction. Biochemistry 29, 10695-10702.
29. Symons, R.H. (1992). Small catalytic RNAs. Annu. Rev. Biochem. 61, 641-671.
30. Uhlenbeck, O.C. (1987). A small catalytic oligoribonucleotide. Nature 328, 596-600.
31. Wagner, E.G. and Simons, R.W. (1994). Antisense RNA control in bacteria, phages, and plasmids. Annu. Rev. Microbiol. 48, 713-742.
32. Yu, Q., Pecchia, D.B., Kingsley, S.L., Heckman, J.E. and Burke, J.M. (1998). Cleavage of highly structured viral RNA molecules by combinatorial libraries of hairpin ribozymes. The most effective ribozymes are not predicted by substrate selection rules. J. Biol. Chem. 273, 23524-23533.