Abstract
The hairpin ribozyme is a member of a family of small RNA endonucleases, which includes hammerhead, human hepatitis delta virus, Neurospora VS, and the lead-dependent catalytic RNAs. All these catalytic RNAs reversibly cleave the phosphodiester bond of substrate RNA to generate 5′-hydroxyl and 2′,3′-cyclic phosphate termini. Whereas the reaction products from family members are similar, large structural and mechanistic differences exist. Structurally the hairpin ribozyme has two principal domains that interact to facilitate catalysis. The hairpin ribozyme uses a catalytic mechanism that does not require metals for cleavage or ligation of substrate RNA. In this regard it is presently unique among RNA catalysts. Targeting rules for cleavage of substrate have been determined and required bases for catalysis have been identified. The hairpin ribozyme has been developed and used for gene therapy and was the first ribozyme to be approved for human clinical trials.
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References
Hampel, A. (1998) The hairpin ribozyme: discovery, two-dimensional model and development for gene therapy, in Progress in Nucleic Acids Research and Molecular Biology, vol 58 (Moldave, K., ed.), Academic Press, San Diego, pp. 1–38.
Eckstein, F. and Lilley, D.M.J. (1996), Nucleic Acids and Molecular Biology: RNA Catalysis, vol 10, Springer-Verlag, Berlin.
Haseloff, J. and Gerlach, W. (1989) Sequences required for self-catalyzed cleavage of the satellite RNA of tobacco ringspot virus. Gene 82, 43–52.
De Young, M., Siwkowski, A., Lian, Y., and Hampel A. (1995) Catalytic properties derived from chicory yellow mottle virus and arabis mosaic virus satellite RNAs. Biochemistry 34, 15,785–15,791.
Gerlach, W. Buzayan, J., Schneider, I., and Bruening, G. (1986) Satellite tobacco ringspot virus RNA: biological activity of DNA clones and their in vitro transcripts. Virology 151, 172–185.
Hampel, A. and Tritz, R. (1989) RNA catalytic properties of the minimum (-)sTRSV sequence. Biochemistry 28, 4929–4933.
Hampel, A., Tritz, R., Hicks, M., and Cruz, P. (1990) Hairpin catalytic RNA model: evidence for helices and sequence requirement for substrate RNA. Nucleic Acids Acids Res. 18, 299–304.
Siwkowski, A., Shippy, R., and Hampel, A. (1997) Analysis of hairpin ribozyme base mutations in loops 2 and 4 and their effects on cis-cleavage in vitro. Biochemistry 36, 3930–3940.
Shippy, R., Siwkowski, A., and Hampel, A. (1997) Mutational analysis of loops1 and 5 of the hairpin ribozyme. Biochemistry 37, 564–570.
Komatsu, Y., Kanzaki, I., and Ohtsuka, E. (1996) Enhanced folding of hairpin ribozymes with replaced domains. Biochemistry 35, 9815–9820.
Feldstein, P. and Bruening, G. (1993) Catalytically active geometry in the reversible circularization of mini-monomer RNAs derived from the complementary strand of tobacco ringspot virus satellite RNA. Nucleic Acids Res. 21, 1991–1998.
Komatsu, Y., Koizumi M. Nakamura, H., and Ohtsuka, E. (1994) Loop-size variation to probe a bent structure of a hairpin ribozyme. J. Am. Chem. Soc. 116, 3692–3696.
Anderson, P., Monforte, J., Tritz, R., Nesbitt, S., Hearst, J., and Hampel, A. (1994) Mutagenesis of the hairpin ribozyme. Nucleic Acids Res. 22, 1096–1100.
Murchie, A., Thompson, J., Walter, F., and Lilley, D. (1998) Folding of the hairpin ribozyme in its natural conformation achieves close physical proximity of the loops. Molecular Cell 1, 873–881.
Buzayan, J., Hampel, A., and Bruening, G. (1986) Nucleotide sequence and newly formed phosphodiester bond of spontaneously ligated satellite tobacco ringspot virus RNA. Nucleic Acids Res. 14, 9729–9743.
van Tol, H., Buzayan, J., Feldstein, P. Eckstein, F., and Bruening, G. (1990) Two autolytic processing reactions of a satellite RNA proceed with inversion of configuration. Nucleic Acids. Res. 18, 1971–1975.
Buzayan, J., Gerlach, W., and Bruening, G. (1986) Non-enzymatic cleavage and ligation of RNAs complementary to a plant virus satellite RNA. Nature 323, 349–353.
Feldstein, P., Buzayan, J., and Bruening, G. (1989) Two sequences participating in the autolytic processing of satellite tobacco ringspot virus complementary RNA. Gene 82, 53–61.
Hampel, A. and Siwkowski, A. (1998) Biochemistry of the hairpin ribozyme, in Ribozymes in the Gene Therapy of Cancer, R. G., (Scanlon, K. and Kashani-Sabet, M., ed.) Landes, Austin, pp. 15–22.
Hegg, L. and Fedor, M. (1995) Kinetics and thermodynamics of intermolecular catalysis by hairpin ribozymes. Biochemistry 34, 15,813–15,828.
Schmidt, S., Beigelman, L., Karpeisky, A., Usman, N. Sorensen, U., and Gait, M. (1996) Base and sugar requirements for RNA cleavage of essential nucleoside residues in internal loop B of the hairpin ribozyme: implications for secondary structure. Nucleic Acids Res. 24, 573–581.
Komatsu, Y., Kanzaki, I., Koizumi, M., and Ohtsuka, E. (1995) Modification of primary structures of hairpin ribozymes for probing active conformations. J. Mol. Biol. 252, 296–304.
Walter, N. and Burke, J. (1998) The hairpin ribozyme: structure, assembly and catalysis. Current Opinion in Chemical Biology 2, 24–30.
Berzal-Herranz, A., Joseph, B., and Burke, J. (1992) In vitro selection of active hairpin ribozymes by sequential RNA-catalyzed cleavage and ligation reactions. Genes and Development 6, 129–134.
Buzayan, J., Feldstein, P., Bruening, G., and Eckstein, F. (1988) RNA mediated formation of a phoshporothioate diester bond. Biochem. Biophys. Res. Com. 156, 340–347.
Chowrira, B. and Burke, J. (1991) Binding and cleavage of nucleic acids by the hairpin ribozyme. Biochemistry 30, 8518–8522.
Hampel, A. and Cowen, J. (1997) A unique mechanism for RNA ctalysis: the role of metal cofactors in hairpin ribozyme cleavage. Chemistry and Biology 4, 513–517.
Nesbitt, S., Hegg, L., and Fedor, M. (1997) An unusual pH-independent and metal ion independent mechanism for hairpin ribozyme catalysis. Chemistry and Biology 4, 619–630.
Young, K., Gill, F., and Grasby, J. (1997) Metal ions play a passive role in the hairpin ribozyme catalysed reaction. Nucleic Acids Res. 25, 3760–3766.
Walter, F., Alastair, I., Murchie, H., Thomson, J., and Lilley, D. (1998) Structure and activity of hairpin ribozyme in its natural junction conformation: effect of metal ions. Biochemistry 37, 14,195–14,203.
Earnshaw, D. and Gait, M. (1998) Hairpin ribozyme cleavage catalyzed by aminoglycoside antibiotics and the polyamine spermine in the absence of metal ions. Nucleic Acids Res. 26, 5551–5561.
Cowan, J. (1993) Metallobiochemistry of RNA: cobalt hexaammine as a probe for magnesium binding sites. Journal of Inorganic Biochemistry 49, 171–175.
Cowan, J. (1995) Biological chemistry of magnesium ion with physiological metabolites, nucleic acids, and drug molecules. in The Biological Chemistry of Magnesium, (Cowen, J. ed.) VCH publishers, Inc., New York, pp. 185–209.
Laing, L., Gluick, T., and Draper, D. (1994) Stabilization of RNA structure by Mg ions: Specific and non-specific effects. J. Mol. Biol. 237, 577–587.
Siwkowski, A., Humphrey, M., DeYoung, M., and Hampel, A. (1998) Screening for important base identities in the hairpin ribozyme by in vitro selection for cleavage. Biotechniques 24, 278–284.
Saenger, W. (1984) Principles of Nucleic Acid Structure (Cantor, D. ed.), Springer-Verlag, New York, pp. 341–349.
Chowrira, B. M., Berzal-Herranz, A., and Burke, J. (1991) Novel guanosine requirement for catalysis by the hairpin ribozyme. Nature 354, 320–322.
Grasby, J., Mersmann, K., Singh, M., and Gait, M. (1995) Purine functional groups in essential residues of the hairpin ribozyme required for catalytic cleavage of RNA. Biochemistry 34, 4068–4076.
Thomson, J. and Lilley, D. (1999) The influence of junction conformation on RNA cleavage by the hairpin ribozyme in its natural junction form. RNA 5, 180–187.
Welch, P., Barber, J., and Wong-Staal, F. (1998) Expression of ribozymes in gene transfer systems to modulate target RNA levels. Current Opinion in Biotechnology. 9, 486–496.
Wong-Staal, F. (1994) Testing the promise of gene therapy. HIV-Advances in Research and Therapy 4, 3–8.
Welch, P., Hampel, A., Barber, J., Wong-Staal, F., and Yu, M. (1996) Inhibition of HIV replication by the hairpin ribozyme, in Catalytic RNA, vol. 10, (Eckstein, F. and Lilley, D. ed.) Springer-Verlag, Berlin, pp. 315–327.
Gervaix, A., Li, X., Kraus, G., and Wong-Staal, F. (1997) Multigene antiviral vectors inhibit diverse human immunodeficiency virus type 1 clades. Journal of Virology 71, 3048–3053
Gervaix, A., Schwarz, L., Law, P. Ho, A., Looney, D., Lane, T., and Wong-Staal, F. (1997) Gene therapy targeting peripheral blood CD34+ hematopoietic stem cells of HIV-infected individuals. Human Gene Therapy 8, 2229–2238.
Koizumi, M., Ozawa, Y., Nishigaki, Y., Kaneko, M., Oka, S., Kimura, S., Iwamoto, A., Komatsu, Y., and Ohtsuka, E. (1998) Design and anti-HIV-1 activity of hammerhead and hairpin ribozymes containing a stable loop. Nucleosides and Nucleotides 17, 207–218.
Li, X., Gervaix, A., Kang, D., Law, P., Spector, S., Ho, A., and Wong-Staal, F. (1998) Gene therapy targeting cord blood-derived CD34+ cells from HIV-exposed infants: preclinical studies. Gene Therapy 5, 233–239.
Ojwang, J., Hampel, A., Looney, D., and Wong-Staal, F. (1992) Inhibition of human immunodeficiency virus type 1 expression by a hairpin ribozyme. Proc. Nat. Acad. Sci. USA 89, 10,802–10,806.
Rosenzweig, M., Marks, D., Hempel, D., Heusch, M., Kraus, G., Wong-Staal, F., and Johnson, R. (1997) Intracellular immunization of rhesus CD34+hematopoietic progenitor cells with a hairpin ribozyme protects T cells and macrophages from simian immunodeficiency virus infection. Blood. 90, 4822–4831.
Yamada, O., Yu, M., Yee, J., Kraus, G., Looney, D., and F. Wong-Staal (1994) Intracellular immunization of human T-cells with a hairpin riibozyme against human immunodeficiecy virus type 1. Gene Therapy, 1, 38–45.
Yu, M., Ojwang, J., Yamada, O., Hampel, A., Rapapport, J., Looney, D., and Wong-Staal, F. (1993) A hairpin ribozyme inhibits expression of diverse strains of human immunodeficiency virus type 1. Proc. Nat. Acad. Sci. USA 90, 6340–6344.
Yu, M., E. Poeschla, Yamada, O., Degrandis, P., Leavitt, M., Heusch, M., Yees, J., Wong-Staal, F., and Hampel, A. (1995) In vitro and in vivo characterization of a second functional haipin ribozyme against HIV-1. Virology 206, 381–386.
Alvarez-Salas, L., Cullinan, M., Siwkowski, A., Hampel, A., and DiPaolo, J. (1998) Inhibition of HPV-16 E6/E7 immortalization of normal keratinocytes by hairpin ribozymes. Proc. Nat. Acad. Sci. US 95, 1189–1194.
Welch, P., Tritz, R., Yei, S., Leavitt, M., Yu, M., and Barber, J. (1996) A potential therapeutic application of hairpin ribozymes: in vitro and in vivo studies of gene therapy for hepatitis C virus infection. Gene Therapy 3, 994–1001.
Welch, P., Tritz, R., Yei, S., Barber, J., and Yu, M. (1997) Intracellular application of hairpin ribozyme genes against hepatitis B virus. Gene Therapy 4, 736–743.
Drenser, K., Timmers, A., Hauswirth, W. and Lewin, A. (1998) Ribozyme-targeted destruction, of RNA associated with autosomal-dominant retinitis pigmentosa. Invest Ophthalmol Vis Sci 39, 681–689.
Lewin, A., Drenser, K., Hauswirth, W., Nishikawa, S., Yasumura, D., Flannery, J., and La Vail, M. (1998) Ribozyme rescue of photoreceptor cells in a transgenic rat model of autosomal dominant retinitis pigmentosa. Nature Medicine 4, 967–971.
Denman, R., Smedman, M., Ju, W., Rubenstein, R., Potempska, A., and Miller, D. (1994) Ribozyme mediated degradation of b-amyloid peptide precursor mRNA in COS-7 cells. Nucleic Acids Res. 22, 2375–2382.
Snyder, D., Wu, Y., McMahon, R., Yu, L., Rossi, J., and Forman, S. (1997) Ribozyme-mediated inhibition of Philadelphia chromosome-positive acute lymphoblastic leukemia cell line expressing the p190 bcr-abl oncogene. Biol. Blood Marrow Transplant 3, 179–186.
Cepero, E., Hnatyszyn, H., Kraus, G., and Lichtenheld, M. (1998) Potent inhibition of CTLA-4 expression by an anti-CTLA-4 ribozyme. Biochem. Biophys. Res. Com. 247, 838–843
Joseph, S., Berzal-Herranz, A., Chowrira, B., and Burke, J. (1993) Substrate selection rules for the hairpin ribozyme determined by in vitro selection, mutation, and analysis of mismatched substrates. Genes and Development 7, 130–138.
DeYoung, M.B., Siwkowski, A., and Hampel, A. (1997) Computer Analysis of the conservation and uniqueness of ribozyme-targeted HIV sequences. in Methods in Molecular Biology: Ribozyme Protocols, (Turner, P. ed.), Humana Press, Totawa, NJ, pp. 27–36.
Hampel, A., DeYoung, M., Galasinski, S., and Siwkowski, A. (1997) Design of the hairpin ribozyme for targeting specific RNA sequences. in Methods in Molecular Biology: Ribozyme Protocols, (Turner, P. ed.), Humana Press, Totawa, NJ, pp. 171–177.
Cheong, C., Varani, G., and Tinoco, I. (1990) Solution structure of an unusually stable RNA hairpin, 5′ GGAC(UUCG)GUCC. Nature, 346, 680–682.
Lian, Ying, DeYoung, M., Siwkowski, A., Hampel, A., and Rappaport, J. (1999) The sCYMV1 ribozyme: targeting rules and cleavage of heterologous RNA. Gene Therapy, 6, 1114–1119.
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Shippy, R., Lockner, R., Farnsworth, M. et al. The hairpin ribozyme. Mol Biotechnol 12, 117–129 (1999). https://doi.org/10.1385/MB:12:1:117
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DOI: https://doi.org/10.1385/MB:12:1:117