Abstract
The hammerhead ribozyme was first identified as a motif that could catalyze sequence-specific self-cleavage of satellite RNAs of certain plant viruses (Buzayan et al. 1986; Hutchins et al. 1986; Prody et al. 1986). The consensus sequence required for bond cleavage consists of a “core” of nucleotides at the juncture of three base-paired stems (Fig. la; Forster and Symons 1987; Ruffner et al. 1990). Although the hammerhead ribozyme was originally characterized for its single-turnover activity in large RNA molecules, it has been demonstrated that short, synthetic oligoribonucleotides in which the consensus core is maintained but any or all of the stems are left openended can catalyze multiple-turnover cleavage in trans (Uhlenbeck 1987; Haseloff and Gerlach 1988). Thus, the hammerhead motif can act as a classical enzyme.
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References
Bratty J, Chartrand P, Ferbeyre G, Cedergren R (1993) The hammerhead RNA domain, a model ribozyme. Biochim Biophys Acta 1216: 345–359
Buzayan JM, Gerlach WL, Bruening G (1986) Nonenzymatic cleavage and ligation of RNAs complementary to a plant virus satellite RNA. Nature 323: 349–353
Buzayan JM, Hampel A, Bruening G (1986) Nucleotide sequence and newly formed phosphodiester bond of spontaneously ligated satellite tobacco ringspot virus RNA. Nucl Acids Res 14: 9729–9743
Dahm SC, Uhlenbeck OC (1990) Characterization of deoxy-and ribo-containing oligonucleotide substrates in the hammerhead self-cleavage reaction. Biochimie 72: 819–823
Dahm SC, Uhlenbeck OC (1991) Role of divalent metal ions in the hammerhead RNA cleavage reaction. Biochemistry 30: 9464–9469
Forster AC, Symons RH (1987) Self-cleavage of virusoid RNA is performed by the proposed 55-nucleotide active site. Cell 50: 9–16
Haseloff J, Gerlach WL (1988) Simple RNA enzymes with new and highly specific endoribonuclease activities. Nature 334: 585–591
Hertel KJ, Uhlenbeck OC (1995) The internal equilibrium of the hammerhead ribozyme reaction. Biochemistry 34: 1744–1749
Hertel KJ, Pardi A, Uhlenbeck OC, Koizumi M, Ohtsuka E, Uesugi S, Cedergren R, Eckstein F, Gerlach WL, Hodgson R (1992) Numbering system for the hammerhead. Nucl Acids Res 20: 32–52
Hertel KJ, Herschlag D, Uhlenbeck OC (1994) A kinetic and thermodynamic framework for the hammerhead ribozyme reaction. Biochemistry 33: 3374–3385
Hutchins CJ, Rathjen PD, Forster AC, Symons RH (1986) Self-cleavage of plus and minus RNA transcripts of avocado sunblotch viroid. Nucl Acids Res 14: 3627–3640
Koizumi M, Ohtsuka E (1991) Effects of phosphorothioate and 2-amino groups in hammerhead ribozymes on cleavage rates and Mg2+ binding. Biochemistry 30: 5145–5150
Kraulis P (1991) MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures. J Appl Cryst 24: 946–950
Massire C, Gaspin C, Westhof E (1994) DRAWNA: a program for drawing schematic views of nucleic acids. J Mol Graph 12: 201–206
Milligan JF, Groebe DR, Witherell GW, Uhlenbeck OC (1987) Oligoribonucleotide synthesis using 17 RNA polymerase and synthetic DNA templates. Nucl Acids Res 15: 8783–8798
Pley HW, Lindes DS, DeLuca FC, McKay DB (1993) Crystals of a hammerhead ribozyme. J Biol Chem 268: 19656–19658
Pley HW, Flaherty KM, McKay DB (1994) Three-dimensional structure of a hammerhead ribozyme. Nature 372: 68–74
Prody GA, Bakos JT, Buzayan JM, Schneider IR, Bruening G (1986) Autolytic processing of dimeric plant virus satellite RNA. Science 231: 1577–1580
Quigley GJ, Rich A (1976) Structural domains of transfer RNA molecules. Science 194: 796–806
Ruffner DE, Stormo GD, Uhlenbeck OC (1990) Sequence requirements of the hammerhead RNA self-cleavage reaction. Biochemistry 29: 10695–10702
SantaLucia JJ, Turner DH (1993) Structure of (rGGCGAGCC)2 in solution from NMR and restrained molecular dynamics. Biochemistry 32: 12612–12623
Scott WG, Finch JT, Klug A (1995) The crystal structure of an all-RNA hammerhead ribozyme: a proposed mechanism for RNA catalytic cleavage. Cell 81: 991–1002
Sheldon CC, Symons RH (1989) Mutagenesis analysis of a self-cleaving RNA. Nucl Acids Res 17: 5679–5685
Sigurdsson ST, Tuschl T, Eckstein F (1995) Probing RNA tertiary structure: inter-helical cross-linking of the hammerhead ribozyme. RNA 1: 575–583
Slim G, Gait MJ (1991) Configurationally defined phosphorothioate-containing oligoribonucleotides in the study of the mechanism of cleavage of hammerhead ribozymes. Nucl Acids Res 19: 1183–1188
Uhlenbeck OC (1987) A small catalytic oligoribonucleotide. Nature 328: 596–600
Van Tol H, Buzayan JM, Feldstein PA, Eckstein F, Bruening G (1990) Two autolytic processing reactions of a satellite RNA proceed with inversion of configuration. Nucl Acids Res 18: 1971–1975
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© 1996 Springer-Verlag Berlin Heidelberg
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McKay, D.B. (1996). Three-Dimensional Structure of the Hammerhead Ribozyme. In: Eckstein, F., Lilley, D.M.J. (eds) Catalytic RNA. Nucleic Acids and Molecular Biology, vol 10. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-61202-2_9
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DOI: https://doi.org/10.1007/978-3-642-61202-2_9
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