Redesign of an artificial ligase ribozyme based on the analysis of its structural elements

RNA Biology

Volumn 2, Issue 4, 2005, Pages 137-142

  Ikawa, Yoshiya ^a   Matsumoto, Junko ^b   Horie, Souta ^b   Inoue, Tan ^b  

^a KYUSHU UNIVERSITY   (Japan)

^b KYOTO UNIVERSITY   (Japan)

Author keywords

In vitro selection; Ligase; Molecular design; Ribozyme; RNA; RNA folding

Indexed keywords

LIGASE; RIBOZYME; RNA POLYMERASE;

ARTICLE; CATALYSIS; ENZYME ACTIVITY; ENZYME ANALYSIS; ENZYME STRUCTURE; PROTEIN FOLDING; PROTEIN INTERACTION;

EID: 34548842520     PISSN: 15476286     EISSN: 15558584     Source Type: Journal    
DOI: 10.4161/rna.2.4.2302     Document Type: Article

References (31)

1. Ikawa Y, Tsuda K, Matsumura S, Inoue T. De novo synthesis and development of an RNA enzyme. Proc Natl Acad Sci USA 2004; 101:13750-5.
2. Yoshioka W, Ikawa Y, Jaeger L, Shiraishi H, Inoue T. Generation of a catalytic module on a self-folding RNA. RNA 2004; 10:1900-6.
3. Ikawa Y, Fukada K, Watanabe S, Shiraishi H, Inoue T. Design, construction, and analysis of a novel class of self-folding RNA. Structure 2002; 10:527-34.
4. Costa M, Michel F. Frequent use of the same tertiary motif by self-folding RNAs. EMBO J 1995; 15:1276-85.
5. Michel F, Westhof E. Modeling of the three-dimensional architecture of group I catalytic introns based on comparative sequence analysis. J Mol Biol 1990; 216:585-610.
6. Zarrinkar PP, Williamson JR. The kinetic folding pathway of the Tetrahymena ribozyme reveals possible similarities between RNA and protein folding. Nat Struct Biol 1996; 3:432-8.
7. Milligan JF, Groebe DR, Witherell GW, Uhlenbeck OC. Oligoribonucleotide synthesis using T7 RNA polymerase and synthetic DNA templates. Nucleic Acids Res 1987; 15:8783-98.
8. Byrappa S, Gavin DK, Gupta KC. A highly efficient procedure for site-specific mutagenesis of full-length plasmids using vent DNA polymerase. Genome Res 1995; 5:404-7.
9. Murphy FL, Wang YH, Griffith JD, Cech TR. Coaxially stacked RNA helices in the catalytic center of the Tetrahymena ribozyme. Science 1997; 265:1709-12.
10. Ikawa Y, Shiraishi H, Inoue T. A small structural element, Pc-J5/5a, plays dual roles in a group IC1 intron RNA. Biochem Biophys Res Commun 2000; 274:259-65.
11. Matsumura S, Ikawa Y, Inoue T. Biochemical characterization of the kink-turn RNA motif. Nucleic Acids Res 2003; 31:5544-51.
12. Ikawa Y, Naito D, Aono N, Shiraishi H, Inoue T. A conserved motif in group IC3 introns is a new class of GNRA receptor. Nucleic Acids Res 1999; 27:1859-65.
13. Cate JH, Hanna RL, Doudna JA. A magnesium ion core at the heart of a ribozyme domain. Nat Struct Biol 1997; 4:553-8.
14. Jaeger L, Leontis N. Tecto-RNA: One-dimensional self-assembly through tertiary interactions. Angew Chem Int Ed 2000; 39:2521-4.
15. Bartel DP, Szostak JW. Isolation of new ribozymes from a large pool of random sequences. Science 1993; 261:1411-8.
16. Ekland EH, Szostak JW, Bartel DP. Structurally complex and highly active RNA ligases derived from random RNA sequences. Science 1995; 269:364-70.
17. Ekland EH, Bartel DP. The secondary structure and sequence optimization of an RNA ligase ribozyme. Nucleic Acids Res 1995; 23:3231-8.
18. Jaeger L, Wright MC, Joyce GF. A complex ligase ribozyme evolved in vitro from a group I ribozyme domain. Proc Natl Acad Sci USA 1999; 96:14712-7.
19. Robertson MP, Ellington AD. In vitro selection of an allosteric ribozyme that transduces analytes to amplicons. Nat Biotechnol 1999; 17:62-6.
20. Robertson MP, Hesselberth JR, Ellington AD. Optimization and optimality of a short ribozyme ligase that joins non Watson-Crick base pairings. RNA 2001; 7:513-23.
21. Rogers J, Joyce GF. A ribozyme that lacks cytidine. Nature 1999; 402:323-5.
22. Rogers J, Joyce GF. The effect of cytidine on the structure and function of an RNA ligase ribozyme. RNA 2001; 7:395-404.
23. McGinness KE, Joyce GF. In search of an RNA replicase ribozyme. Chem Biol 2003; 10:5-14.
24. Ekland EH, Bartel DP. RNA-catalysed RNA polymerization using nucleoside triphosphates. Nature 1996; 382:373-6.
25. Johnston WK, Unrau PJ, Lawrence MS, Glasner ME, Bartel DP. RNA-catalyzed RNA polymerization: Accurate and general RNA-templated primer extension. Science 2001; 292:1319-25.
26. McGinness KE, Wright MC, Joyce GF. Continuous in vitro evolution of a ribozyme that catalyzes three successive nucleotidyl addition reactions. Chem Biol 2002; 9:585-96.
27. McGinness KE, Joyce GF. RNA-catalyzed RNA ligation on an external RNA template. Chem Biol 2002; 9:297-307.
28. Lawrence MS, Bartel DP. New ligase-derived RNA polymerase ribozymes. RNA 2005; 11:1173-80.
29. Kertsburg A, Soukup GA. A versatile communication module for controlling RNA folding and catalysis. Nucleic Acids Res 2002; 30:4599-606.
30. Breaker RR. Engineered allosteric ribozymes as biosensor components. Curr Opin Biotechnol 2002; 13:31-9.
31. Hesselberth JR, Robertson MP, Knudsen SM, Ellington AD. Simultaneous detection of diverse analytes with an aptazyme ligase array. Anal Biochem 2003; 312:106-12.