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. 1998 Aug;4(8):875–889. doi: 10.1017/s1355838298980876

Hammerhead ribozyme kinetics.

T K Stage-Zimmermann 1, O C Uhlenbeck 1
PMCID: PMC1369666  PMID: 9701280

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Selected References

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  1. Almond G. H. Myositis Ossificans (Juvenile Progressive Type). Proc R Soc Med. 1915;8(CLIN):7–10. doi: 10.1177/003591571500800204. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Amiri K. M., Hagerman P. J. Global conformation of a self-cleaving hammerhead RNA. Biochemistry. 1994 Nov 15;33(45):13172–13177. doi: 10.1021/bi00249a003. [DOI] [PubMed] [Google Scholar]
  3. Bassi G. S., Murchie A. I., Lilley D. M. The ion-induced folding of the hammerhead ribozyme: core sequence changes that perturb folding into the active conformation. RNA. 1996 Aug;2(8):756–768. [PMC free article] [PubMed] [Google Scholar]
  4. Bassi G. S., Møllegaard N. E., Murchie A. I., von Kitzing E., Lilley D. M. Ionic interactions and the global conformations of the hammerhead ribozyme. Nat Struct Biol. 1995 Jan;2(1):45–55. doi: 10.1038/nsb0195-45. [DOI] [PubMed] [Google Scholar]
  5. Beebe J. A., Fierke C. A. A kinetic mechanism for cleavage of precursor tRNA(Asp) catalyzed by the RNA component of Bacillus subtilis ribonuclease P. Biochemistry. 1994 Aug 30;33(34):10294–10304. doi: 10.1021/bi00200a009. [DOI] [PubMed] [Google Scholar]
  6. Birikh K. R., Heaton P. A., Eckstein F. The structure, function and application of the hammerhead ribozyme. Eur J Biochem. 1997 Apr 1;245(1):1–16. doi: 10.1111/j.1432-1033.1997.t01-3-00001.x. [DOI] [PubMed] [Google Scholar]
  7. Bratty J., Chartrand P., Ferbeyre G., Cedergren R. The hammerhead RNA domain, a model ribozyme. Biochim Biophys Acta. 1993 Dec 14;1216(3):345–359. doi: 10.1016/0167-4781(93)90001-t. [DOI] [PubMed] [Google Scholar]
  8. Breaker R. R., Joyce G. F. A DNA enzyme that cleaves RNA. Chem Biol. 1994 Dec;1(4):223–229. doi: 10.1016/1074-5521(94)90014-0. [DOI] [PubMed] [Google Scholar]
  9. Breaker R. R., Joyce G. F. A DNA enzyme with Mg(2+)-dependent RNA phosphoesterase activity. Chem Biol. 1995 Oct;2(10):655–660. doi: 10.1016/1074-5521(95)90028-4. [DOI] [PubMed] [Google Scholar]
  10. Burgin A. B., Jr, Gonzalez C., Matulic-Adamic J., Karpeisky A. M., Usman N., McSwiggen J. A., Beigelman L. Chemically modified hammerhead ribozymes with improved catalytic rates. Biochemistry. 1996 Nov 12;35(45):14090–14097. doi: 10.1021/bi961264u. [DOI] [PubMed] [Google Scholar]
  11. Chartrand P., Harvey S. C., Ferbeyre G., Usman N., Cedergren R. An oligodeoxyribonucleotide that supports catalytic activity in the hammerhead ribozyme domain. Nucleic Acids Res. 1995 Oct 25;23(20):4092–4096. doi: 10.1093/nar/23.20.4092. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Chartrand P., Leclerc F., Cedergren R. Relating conformation, Mg2+ binding, and functional group modification in the hammerhead ribozyme. RNA. 1997 Jul;3(7):692–696. [PMC free article] [PubMed] [Google Scholar]
  13. Chin K., Pyle A. M. Branch-point attack in group II introns is a highly reversible transesterification, providing a potential proofreading mechanism for 5'-splice site selection. RNA. 1995 Jun;1(4):391–406. [PMC free article] [PubMed] [Google Scholar]
  14. Chowrira B. M., Berzal-Herranz A., Burke J. M. Ionic requirements for RNA binding, cleavage, and ligation by the hairpin ribozyme. Biochemistry. 1993 Feb 2;32(4):1088–1095. doi: 10.1021/bi00055a014. [DOI] [PubMed] [Google Scholar]
  15. Christoffersen R. E., Marr J. J. Ribozymes as human therapeutic agents. J Med Chem. 1995 Jun 9;38(12):2023–2037. doi: 10.1021/jm00012a001. [DOI] [PubMed] [Google Scholar]
  16. Clouet-D'Orval B., Uhlenbeck O. C. Kinetic characterization of two I/II format hammerhead ribozymes. RNA. 1996 May;2(5):483–491. [PMC free article] [PubMed] [Google Scholar]
  17. Dahm S. C., Derrick W. B., Uhlenbeck O. C. Evidence for the role of solvated metal hydroxide in the hammerhead cleavage mechanism. Biochemistry. 1993 Dec 7;32(48):13040–13045. doi: 10.1021/bi00211a013. [DOI] [PubMed] [Google Scholar]
  18. Dahm S. C., Uhlenbeck O. C. Role of divalent metal ions in the hammerhead RNA cleavage reaction. Biochemistry. 1991 Oct 1;30(39):9464–9469. doi: 10.1021/bi00103a011. [DOI] [PubMed] [Google Scholar]
  19. Denman R. B. Cleavage of full-length beta APP mRNA by hammerhead ribozymes. Nucleic Acids Res. 1993 Aug 25;21(17):4119–4125. doi: 10.1093/nar/21.17.4119. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. Fedor M. J., Uhlenbeck O. C. Kinetics of intermolecular cleavage by hammerhead ribozymes. Biochemistry. 1992 Dec 8;31(48):12042–12054. doi: 10.1021/bi00163a012. [DOI] [PubMed] [Google Scholar]
  21. Fedor M. J., Uhlenbeck O. C. Substrate sequence effects on "hammerhead" RNA catalytic efficiency. Proc Natl Acad Sci U S A. 1990 Mar;87(5):1668–1672. doi: 10.1073/pnas.87.5.1668. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Feig A. L., Scott W. G., Uhlenbeck O. C. Inhibition of the hammerhead ribozyme cleavage reaction by site-specific binding of Tb. Science. 1998 Jan 2;279(5347):81–84. doi: 10.1126/science.279.5347.81. [DOI] [PubMed] [Google Scholar]
  23. Forster A. C., Symons R. H. Self-cleavage of plus and minus RNAs of a virusoid and a structural model for the active sites. Cell. 1987 Apr 24;49(2):211–220. doi: 10.1016/0092-8674(87)90562-9. [DOI] [PubMed] [Google Scholar]
  24. Forster A. C., Symons R. H. Self-cleavage of virusoid RNA is performed by the proposed 55-nucleotide active site. Cell. 1987 Jul 3;50(1):9–16. doi: 10.1016/0092-8674(87)90657-x. [DOI] [PubMed] [Google Scholar]
  25. Fu D. J., McLaughlin L. W. Importance of specific purine amino and hydroxyl groups for efficient cleavage by a hammerhead ribozyme. Proc Natl Acad Sci U S A. 1992 May 1;89(9):3985–3989. doi: 10.1073/pnas.89.9.3985. [DOI] [PMC free article] [PubMed] [Google Scholar]
  26. Fu D. J., Rajur S. B., McLaughlin L. W. Activity of the hammerhead ribozyme upon inversion of the stereocenters for the guanosine 2'-hydroxyls. Biochemistry. 1994 Nov 22;33(46):13903–13909. doi: 10.1021/bi00250a045. [DOI] [PubMed] [Google Scholar]
  27. Goodchild J. Enhancement of ribozyme catalytic activity by a contiguous oligodeoxynucleotide (facilitator) and by 2'-O-methylation. Nucleic Acids Res. 1992 Sep 11;20(17):4607–4612. doi: 10.1093/nar/20.17.4607. [DOI] [PMC free article] [PubMed] [Google Scholar]
  28. Grasby J. A., Jonathan P., Butler G., Gait M. J. The synthesis of oligoribonucleotides containing O6-methylguanosine: the role of conserved guanosine residues in hammerhead ribozyme cleavage. Nucleic Acids Res. 1993 Sep 25;21(19):4444–4450. doi: 10.1093/nar/21.19.4444. [DOI] [PMC free article] [PubMed] [Google Scholar]
  29. Guo H. C., Collins R. A. Efficient trans-cleavage of a stem-loop RNA substrate by a ribozyme derived from neurospora VS RNA. EMBO J. 1995 Jan 16;14(2):368–376. doi: 10.1002/j.1460-2075.1995.tb07011.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  30. Haseloff J., Gerlach W. L. Simple RNA enzymes with new and highly specific endoribonuclease activities. Nature. 1988 Aug 18;334(6183):585–591. doi: 10.1038/334585a0. [DOI] [PubMed] [Google Scholar]
  31. Hegg L. A., Fedor M. J. Kinetics and thermodynamics of intermolecular catalysis by hairpin ribozymes. Biochemistry. 1995 Dec 5;34(48):15813–15828. doi: 10.1021/bi00048a027. [DOI] [PubMed] [Google Scholar]
  32. Heidenreich O., Eckstein F. Hammerhead ribozyme-mediated cleavage of the long terminal repeat RNA of human immunodeficiency virus type 1. J Biol Chem. 1992 Jan 25;267(3):1904–1909. [PubMed] [Google Scholar]
  33. Hendrix C., Mahieu M., Anné J., Van Calenbergh S., Van Aerschot A., Content J., Herdewijn P. Catalytic activity and stability of hammerhead ribozymes containing 2'-acetamido-2'-deoxyribonucleosides. Biochem Biophys Res Commun. 1995 May 5;210(1):67–73. doi: 10.1006/bbrc.1995.1628. [DOI] [PubMed] [Google Scholar]
  34. Hendry P., McCall M. J. A comparison of the in vitro activity of DNA-armed and all-RNA hammerhead ribozymes. Nucleic Acids Res. 1995 Oct 11;23(19):3928–3936. doi: 10.1093/nar/23.19.3928. [DOI] [PMC free article] [PubMed] [Google Scholar]
  35. Hendry P., McCall M. J., Santiago F. S., Jennings P. A. A ribozyme with DNA in the hybridising arms displays enhanced cleavage ability. Nucleic Acids Res. 1992 Nov 11;20(21):5737–5741. doi: 10.1093/nar/20.21.5737. [DOI] [PMC free article] [PubMed] [Google Scholar]
  36. Hendry P., McCall M. J., Santiago F. S., Jennings P. A. In vitro activity of minimised hammerhead ribozymes. Nucleic Acids Res. 1995 Oct 11;23(19):3922–3927. doi: 10.1093/nar/23.19.3922. [DOI] [PMC free article] [PubMed] [Google Scholar]
  37. Hendry P., McCall M. Unexpected anisotropy in substrate cleavage rates by asymmetric hammerhead ribozymes. Nucleic Acids Res. 1996 Jul 15;24(14):2679–2684. doi: 10.1093/nar/24.14.2679. [DOI] [PMC free article] [PubMed] [Google Scholar]
  38. Herschlag D., Cech T. R. Catalysis of RNA cleavage by the Tetrahymena thermophila ribozyme. 1. Kinetic description of the reaction of an RNA substrate complementary to the active site. Biochemistry. 1990 Nov 6;29(44):10159–10171. doi: 10.1021/bi00496a003. [DOI] [PubMed] [Google Scholar]
  39. Herschlag D., Cech T. R. Catalysis of RNA cleavage by the Tetrahymena thermophila ribozyme. 2. Kinetic description of the reaction of an RNA substrate that forms a mismatch at the active site. Biochemistry. 1990 Nov 6;29(44):10172–10180. doi: 10.1021/bi00496a004. [DOI] [PubMed] [Google Scholar]
  40. Herschlag D. Implications of ribozyme kinetics for targeting the cleavage of specific RNA molecules in vivo: more isn't always better. Proc Natl Acad Sci U S A. 1991 Aug 15;88(16):6921–6925. doi: 10.1073/pnas.88.16.6921. [DOI] [PMC free article] [PubMed] [Google Scholar]
  41. Herschlag D., Khosla M., Tsuchihashi Z., Karpel R. L. An RNA chaperone activity of non-specific RNA binding proteins in hammerhead ribozyme catalysis. EMBO J. 1994 Jun 15;13(12):2913–2924. doi: 10.1002/j.1460-2075.1994.tb06586.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  42. Herschlag D. RNA chaperones and the RNA folding problem. J Biol Chem. 1995 Sep 8;270(36):20871–20874. doi: 10.1074/jbc.270.36.20871. [DOI] [PubMed] [Google Scholar]
  43. Hertel K. J., Herschlag D., Uhlenbeck O. C. A kinetic and thermodynamic framework for the hammerhead ribozyme reaction. Biochemistry. 1994 Mar 22;33(11):3374–3385. doi: 10.1021/bi00177a031. [DOI] [PubMed] [Google Scholar]
  44. Hertel K. J., Herschlag D., Uhlenbeck O. C. Specificity of hammerhead ribozyme cleavage. EMBO J. 1996 Jul 15;15(14):3751–3757. [PMC free article] [PubMed] [Google Scholar]
  45. Hertel K. J., Pardi A., Uhlenbeck O. C., Koizumi M., Ohtsuka E., Uesugi S., Cedergren R., Eckstein F., Gerlach W. L., Hodgson R. Numbering system for the hammerhead. Nucleic Acids Res. 1992 Jun 25;20(12):3252–3252. doi: 10.1093/nar/20.12.3252. [DOI] [PMC free article] [PubMed] [Google Scholar]
  46. Hertel K. J., Peracchi A., Uhlenbeck O. C., Herschlag D. Use of intrinsic binding energy for catalysis by an RNA enzyme. Proc Natl Acad Sci U S A. 1997 Aug 5;94(16):8497–8502. doi: 10.1073/pnas.94.16.8497. [DOI] [PMC free article] [PubMed] [Google Scholar]
  47. Hertel K. J., Uhlenbeck O. C. The internal equilibrium of the hammerhead ribozyme reaction. Biochemistry. 1995 Feb 7;34(5):1744–1749. doi: 10.1021/bi00005a031. [DOI] [PubMed] [Google Scholar]
  48. Heus H. A., Uhlenbeck O. C., Pardi A. Sequence-dependent structural variations of hammerhead RNA enzymes. Nucleic Acids Res. 1990 Mar 11;18(5):1103–1108. doi: 10.1093/nar/18.5.1103. [DOI] [PMC free article] [PubMed] [Google Scholar]
  49. Hodgson R. A., Shirley N. J., Symons R. H. Probing the hammerhead ribozyme structure with ribonucleases. Nucleic Acids Res. 1994 May 11;22(9):1620–1625. doi: 10.1093/nar/22.9.1620. [DOI] [PMC free article] [PubMed] [Google Scholar]
  50. Holm P. S., Dietel M., Krupp G. Similar cleavage efficiencies of an oligoribonucleotide substrate and an mdr1 mRNA segment by a hammerhead ribozyme. Gene. 1995 Dec 29;167(1-2):221–225. doi: 10.1016/0378-1119(95)00709-1. [DOI] [PubMed] [Google Scholar]
  51. Homann M., Tabler M., Tzortzakaki S., Sczakiel G. Extension of helix II of an HIV-1-directed hammerhead ribozyme with long antisense flanks does not alter kinetic parameters in vitro but causes loss of the inhibitory potential in living cells. Nucleic Acids Res. 1994 Sep 25;22(19):3951–3957. doi: 10.1093/nar/22.19.3951. [DOI] [PMC free article] [PubMed] [Google Scholar]
  52. Hormes R., Homann M., Oelze I., Marschall P., Tabler M., Eckstein F., Sczakiel G. The subcellular localization and length of hammerhead ribozymes determine efficacy in human cells. Nucleic Acids Res. 1997 Feb 15;25(4):769–775. doi: 10.1093/nar/25.4.769. [DOI] [PMC free article] [PubMed] [Google Scholar]
  53. Hutchins C. J., Rathjen P. D., Forster A. C., Symons R. H. Self-cleavage of plus and minus RNA transcripts of avocado sunblotch viroid. Nucleic Acids Res. 1986 May 12;14(9):3627–3640. doi: 10.1093/nar/14.9.3627. [DOI] [PMC free article] [PubMed] [Google Scholar]
  54. Jankowsky E., Schwenzer B. Oligonucleotide facilitators may inhibit or activate a hammerhead ribozyme. Nucleic Acids Res. 1996 Feb 1;24(3):423–429. doi: 10.1093/nar/24.3.423. [DOI] [PMC free article] [PubMed] [Google Scholar]
  55. Jankowsky E., Strunk G., Schwenzer B. Peptide nucleic acid (PNA) is capable of enhancing hammerhead ribozyme activity with long but not with short RNA substrates. Nucleic Acids Res. 1997 Jul 15;25(14):2690–2693. doi: 10.1093/nar/25.14.2690. [DOI] [PMC free article] [PubMed] [Google Scholar]
  56. Jeffries A. C., Symons R. H. A catalytic 13-mer ribozyme. Nucleic Acids Res. 1989 Feb 25;17(4):1371–1377. doi: 10.1093/nar/17.4.1371. [DOI] [PMC free article] [PubMed] [Google Scholar]
  57. Kawakami J., Yuda K., Suh Y. A., Kumar P. K., Nishikawa F., Maeda H., Taira K., Ohtsuka E., Nishikawa S. Constructing an efficient trans-acting genomic HDV ribozyme. FEBS Lett. 1996 Sep 30;394(2):132–136. doi: 10.1016/0014-5793(96)00941-6. [DOI] [PubMed] [Google Scholar]
  58. Koizumi M., Hayase Y., Iwai S., Kamiya H., Inoue H., Ohtsuka E. Design of RNA enzymes distinguishing a single base mutation in RNA. Nucleic Acids Res. 1989 Sep 12;17(17):7059–7071. doi: 10.1093/nar/17.17.7059. [DOI] [PMC free article] [PubMed] [Google Scholar]
  59. Koizumi M., Iwai S., Ohtsuka E. Cleavage of specific sites of RNA by designed ribozymes. FEBS Lett. 1988 Nov 7;239(2):285–288. doi: 10.1016/0014-5793(88)80935-9. [DOI] [PubMed] [Google Scholar]
  60. Koizumi M., Ohtsuka E. Effects of phosphorothioate and 2-amino groups in hammerhead ribozymes on cleavage rates and Mg2+ binding. Biochemistry. 1991 May 28;30(21):5145–5150. doi: 10.1021/bi00235a005. [DOI] [PubMed] [Google Scholar]
  61. Long D. M., LaRiviere F. J., Uhlenbeck O. C. Divalent metal ions and the internal equilibrium of the hammerhead ribozyme. Biochemistry. 1995 Nov 7;34(44):14435–14440. doi: 10.1021/bi00044a021. [DOI] [PubMed] [Google Scholar]
  62. Long D. M., Uhlenbeck O. C. Kinetic characterization of intramolecular and intermolecular hammerhead RNAs with stem II deletions. Proc Natl Acad Sci U S A. 1994 Jul 19;91(15):6977–6981. doi: 10.1073/pnas.91.15.6977. [DOI] [PMC free article] [PubMed] [Google Scholar]
  63. Long D. M., Uhlenbeck O. C. Self-cleaving catalytic RNA. FASEB J. 1993 Jan;7(1):25–30. doi: 10.1096/fasebj.7.1.8422971. [DOI] [PubMed] [Google Scholar]
  64. McCall M. J., Hendry P., Jennings P. A. Minimal sequence requirements for ribozyme activity. Proc Natl Acad Sci U S A. 1992 Jul 1;89(13):5710–5714. doi: 10.1073/pnas.89.13.5710. [DOI] [PMC free article] [PubMed] [Google Scholar]
  65. McKay D. B. Structure and function of the hammerhead ribozyme: an unfinished story. RNA. 1996 May;2(5):395–403. [PMC free article] [PubMed] [Google Scholar]
  66. Menger M., Tuschl T., Eckstein F., Porschke D. Mg(2+)-dependent conformational changes in the hammerhead ribozyme. Biochemistry. 1996 Nov 26;35(47):14710–14716. doi: 10.1021/bi960440w. [DOI] [PubMed] [Google Scholar]
  67. Nelson J. W., Tinoco I., Jr Comparison of the kinetics of ribooligonucleotide, deoxyribooligonucleotide, and hybrid oligonucleotide double-strand formation by temperature-jump kinetics. Biochemistry. 1982 Oct 12;21(21):5289–5295. doi: 10.1021/bi00264a026. [DOI] [PubMed] [Google Scholar]
  68. Paolella G., Sproat B. S., Lamond A. I. Nuclease resistant ribozymes with high catalytic activity. EMBO J. 1992 May;11(5):1913–1919. doi: 10.1002/j.1460-2075.1992.tb05244.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  69. Peracchi A., Beigelman L., Scott E. C., Uhlenbeck O. C., Herschlag D. Involvement of a specific metal ion in the transition of the hammerhead ribozyme to its catalytic conformation. J Biol Chem. 1997 Oct 24;272(43):26822–26826. doi: 10.1074/jbc.272.43.26822. [DOI] [PubMed] [Google Scholar]
  70. Peracchi A., Beigelman L., Usman N., Herschlag D. Rescue of abasic hammerhead ribozymes by exogenous addition of specific bases. Proc Natl Acad Sci U S A. 1996 Oct 15;93(21):11522–11527. doi: 10.1073/pnas.93.21.11522. [DOI] [PMC free article] [PubMed] [Google Scholar]
  71. Perkins T. A., Wolf D. E., Goodchild J. Fluorescence resonance energy transfer analysis of ribozyme kinetics reveals the mode of action of a facilitator oligonucleotide. Biochemistry. 1996 Dec 17;35(50):16370–16377. doi: 10.1021/bi961234r. [DOI] [PubMed] [Google Scholar]
  72. Perreault J. P., Labuda D., Usman N., Yang J. H., Cedergren R. Relationship between 2'-hydroxyls and magnesium binding in the hammerhead RNA domain: a model for ribozyme catalysis. Biochemistry. 1991 Apr 23;30(16):4020–4025. doi: 10.1021/bi00230a029. [DOI] [PubMed] [Google Scholar]
  73. Pley H. W., Flaherty K. M., McKay D. B. Three-dimensional structure of a hammerhead ribozyme. Nature. 1994 Nov 3;372(6501):68–74. doi: 10.1038/372068a0. [DOI] [PubMed] [Google Scholar]
  74. Pyle A. M., Green J. B. Building a kinetic framework for group II intron ribozyme activity: quantitation of interdomain binding and reaction rate. Biochemistry. 1994 Mar 8;33(9):2716–2725. doi: 10.1021/bi00175a047. [DOI] [PubMed] [Google Scholar]
  75. Pörschke D., Eigen M. Co-operative non-enzymic base recognition. 3. Kinetics of the helix-coil transition of the oligoribouridylic--oligoriboadenylic acid system and of oligoriboadenylic acid alone at acidic pH. J Mol Biol. 1971 Dec 14;62(2):361–381. doi: 10.1016/0022-2836(71)90433-5. [DOI] [PubMed] [Google Scholar]
  76. Rossi J. J. Controlled, targeted, intracellular expression of ribozymes: progress and problems. Trends Biotechnol. 1995 Aug;13(8):301–306. doi: 10.1016/S0167-7799(00)88969-6. [DOI] [PubMed] [Google Scholar]
  77. Ruffner D. E., Dahm S. C., Uhlenbeck O. C. Studies on the hammerhead RNA self-cleaving domain. Gene. 1989 Oct 15;82(1):31–41. doi: 10.1016/0378-1119(89)90027-9. [DOI] [PubMed] [Google Scholar]
  78. Scott W. G., Finch J. T., Klug A. The crystal structure of an all-RNA hammerhead ribozyme: a proposed mechanism for RNA catalytic cleavage. Cell. 1995 Jun 30;81(7):991–1002. doi: 10.1016/s0092-8674(05)80004-2. [DOI] [PubMed] [Google Scholar]
  79. Scott W. G., Murray J. B., Arnold J. R., Stoddard B. L., Klug A. Capturing the structure of a catalytic RNA intermediate: the hammerhead ribozyme. Science. 1996 Dec 20;274(5295):2065–2069. doi: 10.1126/science.274.5295.2065. [DOI] [PubMed] [Google Scholar]
  80. Serra M. J., Turner D. H. Predicting thermodynamic properties of RNA. Methods Enzymol. 1995;259:242–261. doi: 10.1016/0076-6879(95)59047-1. [DOI] [PubMed] [Google Scholar]
  81. Shimayama T., Nishikawa F., Nishikawa S., Taira K. Nuclease-resistant chimeric ribozymes containing deoxyribonucleotides and phosphorothioate linkages. Nucleic Acids Res. 1993 Jun 11;21(11):2605–2611. doi: 10.1093/nar/21.11.2605. [DOI] [PMC free article] [PubMed] [Google Scholar]
  82. Shimayama T., Nishikawa S., Taira K. Generality of the NUX rule: kinetic analysis of the results of systematic mutations in the trinucleotide at the cleavage site of hammerhead ribozymes. Biochemistry. 1995 Mar 21;34(11):3649–3654. doi: 10.1021/bi00011a020. [DOI] [PubMed] [Google Scholar]
  83. Sigurdsson S. T., Tuschl T., Eckstein F. Probing RNA tertiary structure: interhelical crosslinking of the hammerhead ribozyme. RNA. 1995 Aug;1(6):575–583. [PMC free article] [PubMed] [Google Scholar]
  84. Slim G., Gait M. J. Configurationally defined phosphorothioate-containing oligoribonucleotides in the study of the mechanism of cleavage of hammerhead ribozymes. Nucleic Acids Res. 1991 Mar 25;19(6):1183–1188. doi: 10.1093/nar/19.6.1183. [DOI] [PMC free article] [PubMed] [Google Scholar]
  85. Slim G., Gait M. J. The role of the exocyclic amino groups of conserved purines in hammerhead ribozyme cleavage. Biochem Biophys Res Commun. 1992 Mar 16;183(2):605–609. doi: 10.1016/0006-291x(92)90525-p. [DOI] [PubMed] [Google Scholar]
  86. Symons R. H. Self-cleavage of RNA in the replication of small pathogens of plants and animals. Trends Biochem Sci. 1989 Nov;14(11):445–450. doi: 10.1016/0968-0004(89)90103-5. [DOI] [PubMed] [Google Scholar]
  87. Takagi Y., Taira K. Temperature-dependent change in the rate-determining step in a reaction catalyzed by a hammerhead ribozyme. FEBS Lett. 1995 Mar 20;361(2-3):273–276. doi: 10.1016/0014-5793(95)00192-c. [DOI] [PubMed] [Google Scholar]
  88. Taylor N. R., Kaplan B. E., Swiderski P., Li H., Rossi J. J. Chimeric DNA-RNA hammerhead ribozymes have enhanced in vitro catalytic efficiency and increased stability in vivo. Nucleic Acids Res. 1992 Sep 11;20(17):4559–4565. doi: 10.1093/nar/20.17.4559. [DOI] [PMC free article] [PubMed] [Google Scholar]
  89. Tsuchihashi Z., Khosla M., Herschlag D. Protein enhancement of hammerhead ribozyme catalysis. Science. 1993 Oct 1;262(5130):99–102. doi: 10.1126/science.7692597. [DOI] [PubMed] [Google Scholar]
  90. Turner D. H., Sugimoto N., Freier S. M. RNA structure prediction. Annu Rev Biophys Biophys Chem. 1988;17:167–192. doi: 10.1146/annurev.bb.17.060188.001123. [DOI] [PubMed] [Google Scholar]
  91. Tuschl T., Gohlke C., Jovin T. M., Westhof E., Eckstein F. A three-dimensional model for the hammerhead ribozyme based on fluorescence measurements. Science. 1994 Nov 4;266(5186):785–789. doi: 10.1126/science.7973630. [DOI] [PubMed] [Google Scholar]
  92. Tuschl T., Thomson J. B., Eckstein F. RNA cleavage by small catalytic RNAs. Curr Opin Struct Biol. 1995 Jun;5(3):296–302. doi: 10.1016/0959-440x(95)80090-5. [DOI] [PubMed] [Google Scholar]
  93. Uhlenbeck O. C. A small catalytic oligoribonucleotide. Nature. 1987 Aug 13;328(6131):596–600. doi: 10.1038/328596a0. [DOI] [PubMed] [Google Scholar]
  94. Usman N., Beigelman L., McSwiggen J. A. Hammerhead ribozyme engineering. Curr Opin Struct Biol. 1996 Aug;6(4):527–533. doi: 10.1016/s0959-440x(96)80119-9. [DOI] [PubMed] [Google Scholar]
  95. Wang L., Ruffner D. E. An ultraviolet crosslink in the hammerhead ribozyme dependent on 2-thiocytidine or 4-thiouridine substitution. Nucleic Acids Res. 1997 Nov 1;25(21):4355–4361. doi: 10.1093/nar/25.21.4355. [DOI] [PMC free article] [PubMed] [Google Scholar]
  96. Werner M., Uhlenbeck O. C. The effect of base mismatches in the substrate recognition helices of hammerhead ribozymes on binding and catalysis. Nucleic Acids Res. 1995 Jun 25;23(12):2092–2096. doi: 10.1093/nar/23.12.2092. [DOI] [PMC free article] [PubMed] [Google Scholar]
  97. Williams A. P., Longfellow C. E., Freier S. M., Kierzek R., Turner D. H. Laser temperature-jump, spectroscopic, and thermodynamic study of salt effects on duplex formation by dGCATGC. Biochemistry. 1989 May 16;28(10):4283–4291. doi: 10.1021/bi00436a025. [DOI] [PubMed] [Google Scholar]
  98. Williams D. M., Pieken W. A., Eckstein F. Function of specific 2'-hydroxyl groups of guanosines in a hammerhead ribozyme probed by 2' modifications. Proc Natl Acad Sci U S A. 1992 Feb 1;89(3):918–921. doi: 10.1073/pnas.89.3.918. [DOI] [PMC free article] [PubMed] [Google Scholar]
  99. Woisard A., Fourrey J. L., Favre A. Multiple folded conformations of a hammerhead ribozyme domain under cleavage conditions. J Mol Biol. 1994 Jun 10;239(3):366–370. doi: 10.1006/jmbi.1994.1378. [DOI] [PubMed] [Google Scholar]
  100. Yang J. H., Perreault J. P., Labuda D., Usman N., Cedergren R. Mixed DNA/RNA polymers are cleaved by the hammerhead ribozyme. Biochemistry. 1990 Dec 25;29(51):11156–11160. doi: 10.1021/bi00503a002. [DOI] [PubMed] [Google Scholar]
  101. Yang J. H., Usman N., Chartrand P., Cedergren R. Minimum ribonucleotide requirement for catalysis by the RNA hammerhead domain. Biochemistry. 1992 Jun 2;31(21):5005–5009. doi: 10.1021/bi00136a013. [DOI] [PubMed] [Google Scholar]

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