The many faces of the hairpin ribozyme: Structural and functional variants of a small catalytic rna

IUBMB Life

Volumn 64, Issue 1, 2012, Pages 36-47

  Müller, Sabine ^a   Appel, Bettina ^a   Krellenberg, Tobias ^a   Petkovic, Sonja ^a  

^a UNIVERSITY OF GREIFSWALD   (Germany)

Author keywords

extended linker; oligonucleotides; phosphodiester linkage; ribozyme; Watson Crick base pair

Indexed keywords

RIBOZYME;

CATALYSIS; CRYSTALLIZATION; OXIDATION REDUCTION REACTION; REVIEW; RNA BINDING; RNA PROCESSING; RNA RECOMBINATION; RNA STRUCTURE; RNA TRANSCRIPTION;

BASE SEQUENCE; CATALYTIC DOMAIN; GENETIC ENGINEERING; HUMANS; MOLECULAR SEQUENCE DATA; MUTAGENESIS; NUCLEIC ACID CONFORMATION; RNA CLEAVAGE; RNA, CATALYTIC;

EID: 84855472299     PISSN: 15216543     EISSN: 15216551     Source Type: Journal    
DOI: 10.1002/iub.575     Document Type: Review

References (65)

1. Guo, P., (2010) The emerging field of RNA nanotechnology. Nat. Nanotechnol. 5, 833-842.
2. Weigand, J. E., and, Suess, B., (2009) Aptamers and riboswitches: perspectives in biotechnology. Appl. Microbiol. Biotechnol. 85, 229-236.
3. Link, K. H., and, Breaker, R. R., (2009) Engineering ligand-responsive gene-control elements: lessons learned from natural riboswitches. Gene Ther. 16, 1189-1201.
4. Schubert, S., and, Kurreck, J., (2004) Ribozyme- and deoxyribozyme- strategies for medical applications. Curr. Drug Targets 5, 667-681. (Pubitemid 39610363)
5. Shippy, R., Lockner, R., Farnsworth, M., and, Hampel, A., (1999) The hairpin ribozyme. Discovery, mechanism, and development for gene therapy. Mol. Biotechnol. 12, 117-129. (Pubitemid 29530087)
6. Ferré-D'Amaré, A. R., (2004) The hairpin ribozyme. Biopolymers 73, 71-78. (Pubitemid 38101471)
7. Feldstein, P.A., Buzayan, J.M., and, Bruening, G., (1989) Two sequences participating in the autolytic processing of satellite tobacco ringspot virus complementary RNA. Gene 82, 53-61. (Pubitemid 19248657)
8. Hampel, A., and, Tritz, R., (1989) RNA catalytic properties of the minimum (-)sTRSV sequence. Biochemistry 28, 4929-4933. (Pubitemid 19162737)
9. Fedor, M. J., (1999) Tertiary structure stabilization promotes hairpin ribozyme ligation. Biochemistry 38, 11040-11050.
10. Rupert, P. B., and, Ferré-D'Amaré, A. R., (2001) Crystal structure of a hairpin ribozyme-inhibitor complex with implications for catalysis. Nature 410, 780-786. (Pubitemid 32303769)
11. Walter, N. G., Hampel, K. J., Brown, K. M., and, Burke, J. M., (1998) Tertiary structure formation in the hairpin ribozyme monitored by fluorescence resonance energy transfer. EMBO J. 17, 2378-2391. (Pubitemid 28171922)
12. Spitale, R. C., Volpini, R., Heller, M. G., Krucinska, J., Cristalli, G., et al. (2009) Identification of an imino group indispensable for cleavage by a small ribozyme. J. Am. Chem. Soc. 131, 6093-6105.
13. Suydam, I.T., Levandoski, S. D., and, Strobel, S. A., (2010) Catalytic importance of a protonated adenosine in the hairpin ribozyme active site. Biochemistry 49, 3823-3732.
14. Feng, Y., Leavitt, M., Tritz, R., Duarte, E., Kang, D., et al. (2000) Inhibition of CCR5-dependent HIV-1 infection by hairpin ribozyme gene therapy against CC-chemokine receptor 5. Virology 276, 271-278.
15. Drude, I., Strahl, A., Galla, D., Müller, O., and, Müller, S., (2011) Design of hairpin ribozyme variants with improved activity for poorly processed substrates. FEBS J. 278, 622-633.
16. Pérez-Ruiz, M., Barosso-delJesus, A., and, Berzal-Herranz, A., (1999) Specificity of the hairpin ribozyme. J. Biol. Chem. 274, 29376-29380.
17. Sargueil, B., Pecchia, D. B., and, Burke, J.M., (1995) An improved version of the hairpin ribozyme functions as a ribonucleoprotein complex. Biochemistry 34, 7739-7748.
18. Murchie, A. I. H., Thomson, J. B., Walter, F., and, Lilley, D. M. J., (1998) Folding of the hairpin ribozyme in its natural conformation achieves close physical proximity of the loops. Mol. Cell 1, 873-881. (Pubitemid 128379071)
19. Walter, N. G., Burke, J. M., and, Millar, D. P., (1999) Stability of hairpin ribozyme tertiary structure is governed by the interdomain junction. Nat. Struct. Biol. 6, 544-549. (Pubitemid 29252833)
20. Walter, N. G., Chan, P. A., Hampel, K. J., Millar, D. P., and, Burke, J. M., (2001) A base change in the catalytic core of the hairpin ribozyme perturbs function but not domain docking. Biochemistry 40, 2580-2587. (Pubitemid 32171733)
21. Welz, R., Schmidt, C., and, Müller, S., (2001) Spermine supports hairpin ribozyme variants to differing extents. Biochem. Biophys. Res. Commmun. 283, 648-654. (Pubitemid 32917939)
22. Komatsu, Y., Shirai, M., Yamashita, S., and, Ohtsuka, E., (1997) Construction of hairpin ribozymes with a three-way junction. Bioorg. Med. Chem. 5, 1063-1069. (Pubitemid 27264832)
23. Esteban, J. A., Walter, N. G., Kotzorek, G., Heckman, J. E., and, Burke, J. M., (1998) Structural basis for heterogeneous kinetics: reengineering the hairpin ribozyme. Proc. Natl. Acad. Sci. USA 95, 6091-6096. (Pubitemid 28248969)
24. Komatsu, Y., Kanzaki, I., Shirai, M., and, Ohtsuka, E., (1997) A new type of hairpin ribozyme consisting of three domains. Biochemistry 36, 9935-9940. (Pubitemid 27364706)
25. Earnshaw, D. J., and, Gait, M. J., (1998) Hairpin ribozyme cleavage catalyzed by aminoglycoside antibiotics and the polyamine spermine in the absence of metal ions. Nucleic Acids Res. 26, 5551-5561. (Pubitemid 28554721)
26. Stolze, K., Holmes, S. C., Earnshaw, D. J., Singh, M., Stetsenko, D., et al. (2001) Novel spermine-amino acid conjugates and basic tripeptides enhance cleavage of the hairpin ribozyme at low magnesium ion concentration. Bioorg. Med. Chem. Lett. 11, 3007-3010. (Pubitemid 33063617)
27. Marsh, A. J., Williams, D. M., and, Grasby, J. A., (2004) The synthesis and properties of oligoribonucleotide-spermine conjugates. Org. Biomol. Chem. 2, 2103-2112.
28. Feldstein, P. A., 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. (Pubitemid 23178920)
29. 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.
30. Butcher, S. E., and, Burke, J. M., (1994) Structure-mapping of the hairpin ribozyme. Magnesium-dependent folding and evidence for tertiary interactions within the ribozyme-substrate complex. J. Mol. Biol. 244, 52-56.
31. Butcher, S. E., Heckman, J. E., and, Burke, J. M., (1995) Reconstitution of hairpin ribozyme activity following separation of functional domains. J. Biol. Chem. 270, 29648-29651. (Pubitemid 26001624)
32. Shin, C., Choi, J. N., Song, S. I., Song, J. T., et al. (1996) The loop B domain is physically separable from the loop A domain in the hairpin ribozyme. Nucleic Acids Res. 24, 2685-2689. (Pubitemid 26239734)
33. Vlassov, A. V., Johnston, B. H., Landweber, L. F., and, Kazakov, S. A., (2004) Ligation activity of fragmented ribozymes in frozen solution: implications for the RNA world. Nucleic Acids Res. 32, 2966-2974. (Pubitemid 38885962)
34. 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.
35. Schmidt, C., Welz, R., and, Müller, S., (2000) RNA double cleavage by a hairpin-derived twin ribozyme. Nucleic Acids Res. 28, 886-894. (Pubitemid 30085313)
36. Ivanov, S. A., Vauléon, S., and, Müller, S., (2005) Efficient RNA ligation by reverse-joined hairpin ribozymes and engineering of twin ribozymes consisting of conventional and reverse-joined hairpin ribozyme units. FEBS J. 272, 4464-4474. (Pubitemid 41284419)
37. Ivanov, S. A., Volkov, E. M., Oretskaya, T. S., and, Müller, S., (2004) Chemical synthesis of an artificially branched hairpin ribozyme variant with RNA cleavage activity. Tetrahedron 60, 9273-9281. (Pubitemid 39201203)
38. Welz, R., Bossmann, K., Klug, C., Schmidt, C., Fritz, H.-J., et al. (2003), Site-directed alteration of RNA sequence mediated by an engineered twin ribozyme. Angew Chem. Int. Ed. 42, 2424-2427. (Pubitemid 36735559)
39. Vauléon, S., Ivanov, S. A., Gwiazda, S., and, Müller S,. (2005) Site-specific fluorescent and affinity labeling of RNA mediated by an engineered twin ribozyme. ChemBioChem 6, 2158-2162.
40. Drude, I., Vauléon, S., and, Müller, S., (2007) Twin ribozyme mediated removal of nucleotides from an internal RNA site. Biochem. Biophys. Res. Commun. 363, 24-29. (Pubitemid 47430090)
41. Nesbitt, S. M., Erlacher, H. A., and, Fedor, M. J., (1999) The internal equilibrium of the hairpin ribozyme: temperature, ion and pH effects. J. Mol. Biol. 286, 1009-1024. (Pubitemid 29116672)
42. Korinek, V., Barker, N., Morin, P. J., van Wichen, D., de Weger, R., etal. (1997) Constitutive transcriptional activation by -catenin-Tcf complex in APC-/-colon carcinoma. Science 275, 1784-1787. (Pubitemid 27136714)
43. Morin, P. J., Sparks, A. B., Korinek, V., Barker, N., Clevers, H., et al. (1997) Activation of β-catenin-Tcf signalling in colon cancer by mutations in β-catenin or APC. Science 275, 1787-1790. (Pubitemid 27136715)
44. Drude, I., Bahlke, D., Strahl, A., Müller, O., and, Müller, S., manuscript in preparation.
45. Link, K. H., and, Breaker, R. R., (2009) Engineering ligand-responsive gene-control elements: lessons learned from natural riboswitches. Gene Ther. 16, 1189-1291.
46. Silverman, S. K., (2003) Rube Goldberg goes (ribo)nuclear? Molecular switches and sensors made from RNA. RNA 9, 377-384.
47. Komatsu, Y, Nobuoka, K., Karino-Abe, N., Matsuda, A., and, Ohtsuka, E., (2002) In vitro selection of hairpin ribozymes activated with short oligonucleotides. Biochemistry 41, 9090-9098. (Pubitemid 34787266)
48. Vauléon, S., and, Müller, S., (2003) External regulation of hairpin ribozyme activity by an oligonucleotide effector. ChemBioChem 4, 220-224. (Pubitemid 36347798)
49. Najafi-Shoushtari, S. H., Mayer, G., and, Famulok, M., (2004) Sensing complex regulatory networks by conformationally controlled hairpin ribozymes. Nucleic Acids Res. 32, 3212-3219. (Pubitemid 39023011)
50. Najafi-Shoushtari, S. H., and, Famulok, M., (2005) Competitive regulation of modular allosteric aptazymes by a small molecule and oligonucleotide effector. RNA 11, 1514-1520. (Pubitemid 41396921)
51. Najafi-Shoushtari, S. H., and, Famulok, M., (2007) DNA aptamer-mediated regulation of the hairpin ribozyme by human alpha-thrombin. Blood Cells Mol. Dis. 38, 19-24. (Pubitemid 44960867)
52. Strohbach, D., Novak, N., and, Müller S,. (2006) Redox-active riboswitching: allosteric regulation of ribozyme activity by ligand shape control. Angew Chem. Int. Ed. 45, 2127-2129. (Pubitemid 44105194)
53. Strohbach, D., Turku, F., Schuhmann, W., and, Müller, S., (2008) Electrochemically induced modulation of the catalytic activity of a reversible redoxsensitive riboswitch. Electroanalysis 20, 935-940.
54. Fan, P., Suri, A. K., Fiala, R., Live, D., and, Patel, D. J., (1996) Molecular recognition in the FMN-RNA aptamer complex. J. Mol. Biol. 258, 480-500. (Pubitemid 26145895)
55. Krellenberg, T., and, Müller, S., manuscript in preparation.
56. Hall, B., Hesselberth, J. R., and, Ellington, A. D., (2007) Computational selection of nucleic acid biosensors via a slip structure model. Biosensor. Bioelectron. 22, 1939-1947. (Pubitemid 46349630)
57. Meli, M., Vergne, J., and, Maurel, M. C., (2003) In vitro selection of adenine-dependent hairpin ribozymes. J. Biol. Chem. 278, 9835-9842. (Pubitemid 36800486)
58. Li, Y. L., Torchet, C., Vergne, J., and, Maurel, M. C., (2007) A cis and trans adenine-dependent hairpin ribozyme against Tpl-2 target. Biochimie 89, 1257-1263. (Pubitemid 47498689)
59. Li Y. L., Maurel, M. C., Ebel, C., Vergne, J., Pipich, V., et al. (2008) Self-association of adenine-dependent hairpin ribozymes. Eur. Biophys. J. 37, 173-182.
60. Li, Y. L., Vergne, J., Torchet, C., and, Maurel, M. C., (2009) In vitro selection of adenine-dependent ribozyme against Tpl2/Cot oncogene. FEBS J. 276, 303-314.
61. Ztouti, M., Kaddour, H., Miralles, F., Simian, C., Vergne, J., et al. (2009) Adenine, a hairpin ribozyme cofactor - high-pressure and competition studies. FEBS J. 276, 2574-2588.
62. Buck, J., Li, Y. L., Richter, C., Vergne, J., Maurel, M. C., et al. (2009) NMR spectroscopic characterization of the adenine-dependent hairpin ribozyme. ChembioChem. 10, 2100-2110.
63. Salter, J., Krucinska, J., Alam, S., Grum-Tokars, V., and, Wedekind, J. E., (2006) Water in the active site of an all-RNA hairpin ribozyme and effects of Gua8 base variants on the geometry of phosphoryl transfer. Biochemistry 45, 686-700. (Pubitemid 43122234)
64. Pieper, S., Vauléon, S., and, Müller S,. (2007) RNA self-processing towards changed topology and sequence oligomerization. Biol. Chem. 388, 743-746. (Pubitemid 46934161)
65. Diegelman, A. M., and, Kool, E. T., (1998) Generation of circular RNAs and trans-cleaving catalytic RNAs by rolling transcription of circular DNA oligonucleotides encoding hairpin ribozymes. Nucleic Acids Res. 26, 235-241.