Efficient RNA ligation by reverse-joined hairpin ribozymes and engineering of twin ribozymes consisting of conventional and reverse-joined hairpin ribozyme units

FEBS Journal

Volumn 272, Issue 17, 2005, Pages 4464-4474

  Ivanov, Sergei A ^a   Vauléon, St́phanie ^a   Müller, Sabine ^a  

^a RUHR UNIVERSITY BOCHUM   (Germany)

Author keywords

Rational design; RNA catalysis; RNA ligation; Sequence alteration; Twin ribozyme

Indexed keywords

NUCLEOTIDE DERIVATIVE; RIBOZYME; RNA;

ARTICLE; DELETION MUTANT; ENZYME DEGRADATION; ENZYME ENGINEERING; ENZYME MECHANISM; ENZYME SUBSTRATE; ENZYME SUBUNIT; GENE INSERTION; GENE MUTATION; PRIORITY JOURNAL; RNA SEQUENCE; RNA STRUCTURE;

BASE SEQUENCE; BINDING SITES; DRUG DESIGN; GENETIC ENGINEERING; KINETICS; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; NUCLEIC ACID CONFORMATION; RNA; RNA, CATALYTIC; THERMODYNAMICS;

EID: 24644465157     PISSN: 1742464X     EISSN: None     Source Type: Journal    
DOI: 10.1111/j.1742-4658.2005.04865.x     Document Type: Article

References (39)

1. Kurreck J (2003) Antisense technologies. Improvement through novel chemical modifications. Eur J Biochem 270, 1628-1644.
2. Scanlon KJ (2004) Anti-genes: siRNA, ribozymes and antisense. Curr Pharm Biotechnol 5, 415-420.
3. Long MB, Jones JP 3rd, Sullenger BA & Byun J (2003) Ribozyme-mediated revision of RNA and DNA. J Clin Invest 112, 312-318.
4. Puerta-Fernandez E, Romero-Lopez C, Barosso-del-Jesus A & Berzal-Herranz A (2003) Ribozymes: recent advances in the development of RNA tools. FEMS Microbiol Rev 27, 75-97.
5. Rimmele M (2003) Nucleic acid aptamers as tools and drugs: recent developments. Chembiochem 4, 963-971.
6. Alisky JM & Davidson BL (2004) Towards therapy using RNA interference. Am J Pharmacogenom 4, 45-51.
7. Berkhout A (2004) RNA interference as an antiviral approach: targeting HIV-1. Curr Opin Mol Ther 6, 141-145.
8. Burgstaller P, Jenne A & Blind M (2002) Aptamers and aptazymes: accelerating small molecule drug discovery. Curr Opin Drug Discov Devel 5, 690-700.
9. Famulok M & Verma S (2002) In vivo-applied functional RNAs as tools in proteomics and genomics research. Trends Biotechnol 20, 462-466.
10. Silverman SK (2003) Rube Goldberg goes (ribo) nuclear? Molecular switches and sensors made from RNA. RNA 9, 377-383.
11. Mandal M & Breaker RR (2004) Gene regulation by riboswitches. Nat Rev Mol Cell Biol 5, 451-463.
12. Mandal M, Lee M, Barrick JE, Weinberg Z, Emilsson GM, Ruzo WL & Breaker RR (2004) A glycine-dependent riboswitch that uses cooperative binding to control expression. Science 306, 275-279.
13. Brantl S (2004) Bacterial gene regulation: from transcription attenuation to riboswitches and ribozymes. Trends Microbiol 12, 473-475.
14. Chowdhury S, Ragaz C, Kreuger E & Narberhaus F (2003) Temperature-controlled structural alterations of an RNA thermometer. J Biol Chem 278, 47915-47921.
15. Schmidt C, Welz R & Müller S (2000) RNA double cleavage by a hairpin-derived twin ribozyme. Nucleic Acids Res 28, 886-894.
16. Welz R, Bossmann K, Klug C, Schmidt C, Fritz H-J & Müller S (2003) Site-directed alteration of RNA sequence mediated by a small engineered twin ribozyme. Angew Chem Int Ed 42, 2424-2427.
17. Müller S (2003) Engineered ribozymes as molecular tools for site-specific alteration of RNA sequence. Chembiochem 4, 991-997.
18. Vauléon S, Ivanov SA, Gwiazda S & Müller S (2005) Site-specific fluorescent and affinity labeling of RNA using a small engineered ribozyme. Chembiochem in press.
19. Feldstein A, Buzayan JM & Bruening G (1989) Two sequences participating in the autolytic processing of satellite tobacco ringspot virus complementary RNA. Gene 82, 53-61.
20. Hampel A & Tritz R (1989) RNA catalytic properties of the minimum (-) sTRSV sequence. Biochemistry 28, 4929-4933.
21. Rupert PB, Massey AP, Sigurdsson ST & Ferré-D'Amaré AR (2002) Transition state stabilization by a catalytic RNA. Science 298, 1421-1424.
22. Zhuang X, Kim H, Pereira MJ, Babcock HP, Walter NG & Chu S (2002) Correlating structural dynamics and function in single ribozyme molecules. Science 296, 1473-1476.
23. Nahas MK, Wilson TJ, Hohng S, Jarvie K, Lilley DMJ & Ha T (2004) Observation of internal cleavage and ligation reactions of a ribozyme. Nat Struct Mol Biol 11, 1107-1113.
24. Nesbitt SM, Erlacher HA & Fedor MJ (1999) The internal equilibrium of the hairpin ribozyme: temperature, ion and pH effects. J Mol Biol 286, 1009-1024.
25. Fedor MJ (1999) Tertiary structure stabilization promotes hairpin ribozyme ligation. Biochemistry 38, 11040-11050.
26. Fedor MJ (2000) Structure and function of the hairpin ribozyme. J Mol Biol 297, 269-291.
27. Welz R, Schmidt C & Müller S (2001) Spermine supports catalysis of hairpin ribozyme variants to differing extents. Biochem Biophys Res Commun 283, 648-654.
28. Ivanov SA, Volkov EM, Oretskaya TS & Müller S (2004) Chemical synthesis of an artificially branched hairpin ribozyme variant with RNA cleavage activity. Tetrahedron 60, 9273-9281.
29. Komatsu Y, Kanzaki I, Koizumi M & Ohtsuka E (1995) Modification of primary structures of hairpin ribozymes for probing active conformations. J Mol Biol 252, 296-304.
30. Komatsu Y, Kanzaki I & Ohtsuka E (1996) Enhanced folding of hairpin ribozymes with replaced domains. Biochemistry 35, 9815-9820.
31. Rupert PB & Ferré-D'Amaré AR (2001) Crystal structure of a hairpin ribozyme-inhibitor complex with implications for catalysis. Nature 410, 780-786.
32. Müller S, Welz R, Ivanov S & Bossmann K (2004) Twin ribozymes. In Highlights in Bioorganic Chemistry: Methods and Application (Schmuck C & Wennemers H, eds), pp. 404-419. Wiley-VCH, Weinheim.
33. Drude I (2005) Design und Synthese von Twinribozymen zur Reparatur von Insertions - und Punktmutationen. Diploma thesis, Ruhr-Universität Bochum, Fakultät Chemie, Germany.
34. Esteban JA, Walter NG, Kotzorek G, Heckman JE & Burke JM (1998) Structural basis for heterogenic kinetics: reengineering the hairpin ribozyme. Proc Natl Acad Sci USA 95, 6091-6096.
35. Murchie AIH, Thomson JB, Walter F & Lilley DMJ (1998) Folding of the hairpin ribozyme in its natural conformation achieves close physical proximity of the loops. Mol Cell 1, 873-881.
36. Kirk BW, Feinsod M, Favis R, Kliman RM & Barany F (2002) Single nucleotide polymorphism seeking long term association with complex disease. Nucleic Acids Res 30, 3295-3311.
37. Lechner D, Lathrop GM & Gut IG (2002) Large-scale genotyping by mass spectrometry: experience, advances and obstacles. Curr Opin Chem Biol 6, 31-38.
38. Sauer S, Gelfand DH, Boussicault F, Bauer K, Reichert F & Gut IG (2002) Facile method for automated genotyping of single nucleotide polymorphisms by mass spectrometry. Nucleic Acids Res 30, 22.
39. Perez-Ruiz M, Barroso-delJesus A & Berzal-Herranz A (1999) Specificity of the hairpin ribozyme. Sequence requirements surrounding the cleavage site. J Biol Chem 274, 29376-29380.