Selection of a novel class of RNA-RNA interaction motifs based on the ligase ribozyme with defined modular architecture

Nucleic Acids Research

Volumn 36, Issue 11, 2008, Pages 3600-3607

  Ohuchi, S P Shoji P ^a   Ikawa, Yoshiya ^b,c   Nakamura, Yoshikazu ^a,c  

^a UNIVERSITY OF TOKYO   (Japan)

^b KYUSHU UNIVERSITY   (Japan)

^c JAPAN SCIENCE AND TECHNOLOGY AGENCY   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

ADENINE; GUANINE; RIBOZYME; RNA; RNA LIGASE;

ARTICLE; CHEMICAL ANALYSIS; ENZYME ACTIVITY; ENZYME STRUCTURE; IN VITRO SELECTION; IN VITRO STUDY; PRIORITY JOURNAL; PROTEIN FUNCTION; PROTEIN MOTIF; RNA ISOLATION; RNA RNA HYBRIDIZATION; RNA SEQUENCE; RNA STRUCTURE;

BASE SEQUENCE; BINDING SITES; GENETIC ENGINEERING; MOLECULAR SEQUENCE DATA; NUCLEIC ACID CONFORMATION; RNA LIGASE (ATP); RNA, CATALYTIC;

EID: 46349089384     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkn206     Document Type: Article

References (30)

1. Gesteland,R.F., Cech,T.R. and Atkins, J.F. (eds) (2006) The RNA World 3rd edn. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
2. Batey,R.T. (2006) Structures of regulatory elements in mRNAs. Curr. Opin. Struct. Biol., 16, 299-306.
3. Mattick,J.S. and Makunin,I.V. (2006) Non-coding RNA. Hum. Mol. Genet. 15, R17-R29.
4. Sosnick,T. R., and Pan,T. (2003) RNA folding: Models and perspectives. Curr. Opin. Struct. Biol., 13, 309-316.
5. Onoa,B. and Tinoco, J. Jr. (2004) RNA folding and unfolding. Curr. Opin. Struct. Biol., 14, 374-379.
6. Bokinsky,G. and Zhuang,X. (2005) Single-molecule RNA folding. Acc. Chem. Res., 38, 566-573.
7. Furtig,B., Buck,J., Manoharan,V., Bermel,W., Jaschke,A., Wenter,P., Pitsch,S. and Schwalbe,H. (2007) Time-resolved NMR studies of RNA folding. Biopolymers, 86, 360-383.
8. van der Horst,G., Christian,A. and Inoue,T. (1991) Reconstitution of a group I intron self-splicing reaction with an activator RNA. Proc. Natl Acad. Sci. USA, 88, 184-188.
9. Murphy,F.L. and Cech,T.R. (1993) An independently folding domain of RNA tertiary structure within the Tetrahymena ribozyme. Biochemistry, 25, 5291-5300.
10. Murphy,F.L. and Cech,T.R. (1994) GAAA tetraloop and conserved bulge stabilize tertiary structure of a group 1 intron domain. J. Mol. Biol., 236; 49-63.
11. Naito,Y., Shiraishi,H. and Inoue,T. (1998) P5abc of the Tetrahymena ribozyme consists of three functionally independent elements. RNA 4, 837-846.
12. Johnson,T.H., Tijerina,P., Chadee,A.B., Herschlag,D. and Russell,R. (2005) Structural specificity conferred by a group I RNA peripheral element. Proc. Natl Acad. Sci. USA, 102, 10176-10181.
13. Ikawa,Y., Fukada,K., Watanabe,S., Shiraishi,H. and Inoue,T. (2002) Design, construction, and analysis of a novel class of self-folding RNA. Structure, 10, 527-534.
14. Ikawa,Y., Tsuda,K., Matsumura,S. and Inoue,T. (2004) De novo synthesis and development of an RNA enzyme. Proc. Natl Acad. Sci. USA 101, 13750-13755.
15. Ikawa,Y., Matsumoto,J., Horie,S. and Inoue,T. (2005) Redesign of an artificial figase ribozyme based on the analysis of its structural elements. RNA Biol., 2, 137-142.
16. 2+-induced cleavage of RNA. In Hartmann,R.K., Bindereif,A., Schön,A. and Westhof,E. (eds), Handbook of RNA Biochemistry, Vol. 1. Wiley-VCH, Weinheim, Germany, pp. 214-228.
17. Toulme,J.J., Darfeuille,F., Kolb,G., Chabas,S, and Staedel,C. (2003) Modulating viral gene expression by aptamers to RNA structures. Biol. Cell, 95, 229-238.
18. Costa,M. and Michel,F. (1997) Rules for RNA recognition of GNRA tetraloops deduced by in vitro selection: Comparison with in vivo evolution. EMBO J., 16, 3289-3302.
19. Lescoute,A., Leontis,N.B., Massire,C. and Westhof,E. (2005) Recurrent structural RNA motifs, isostericity matrices and sequence alignments. Nucleic Acids Res., 33, 2395-2409.
20. Rohatgi,R., Bartel,D.P. and Szostak,J.W. (1996) Kinetic and mechanistic analysis of nonenzymatic, template-directed oligoribonucleotide ligation. J. Am. Chem. Soc., 118, 3332-3339.
21. Jaeger,L. and Leontis,N.B. (2000) Tecto-RNA: One-dimensional self-assembly through tertiary interactions. Angew. Chem. Int. Ed. Engl., 39, 2521-2524.
22. Jaeger L., Westhof,E. and Leontis,N.B. (2001) TectoRNA: Modular assembly units for the construction of RNA nano-objects. Nucleic Acids Res. 29, 455-463.
23. Ikawa,Y., Naito,D., Aono,N., Shiraishi,H. and Inoue,T. (1999) A conserved motif in group IC3 introns is a new class of GNRA receptor. Nucleic Acids Res., 27, 1859-1865.
24. Ikawa,Y., Nohmi,K., Atsumi,S., Shiraishi,H. and Inoue,T. (1999) A comparative study on two GNRA-tetraloop receptors: 11-nt and IC3 motifs. J. Biochem., 130, 251-255.
25. Atsumi,S., Ikawa,Y., Shiraishi,H. and Inoue,T. (2001) Design and development of a catalytic ribonucleoprotein. EMBO J., 20, 5453-5460.
26. Atsumi,S., Ikawa,Y., Shiraishi,H. and Inoue,T. (2003) Selections for constituting new RNA-protein interactions in catalytic RNP. Nucleic Acids Res., 31, 661-669.
27. Saksmerprome,V., Roychowdhury-Saha,M., Jayasena,S., Khvorova,A. and Burke,D.H. (2004) Artificial tertiary motifs stabilize trans cleaving hammerhead ribozymes under conditions of submillimolar divalent ions and high temperatures. RNA, 10, 1916-1924.
28. Juneau,K. and Cech,T.R. (1999) In vitro selection of RNAs with increased tertiary structure stability. RNA, 5, 1119-1129.
29. Jaeger,L. and Chworos,A. (2006) The architectonics of programmable RNA and DNA nanostructures. Curr. Opin. Struct. Biol., 16, 531-543.
30. Geary,C., Baudrey,S. and Jaeger,L. (2007) Comprehensive features of natural and in vitro selected GNRA tetraloop-binding receptors, Nucleic Acids Res., 36, 1138-1152.