Generation of a catalytic module on a self-folding RNA

RNA

Volumn 10, Issue 12, 2004, Pages 1900-1906

  Yoshioka, Wataru ^a   Ikawa, Yoshiya ^a   Jaeger, Luc ^b   Shiraishi, Hideaki ^a   Inoue, Tan ^a  

^a KYOTO UNIVERSITY   (Japan)

^b UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

Catalytic RNA; In vitro selection; Ligation

Indexed keywords

NUCLEOTIDE; RIBOZYME;

3' UNTRANSLATED REGION; 5' UNTRANSLATED REGION; ARTICLE; CRYSTAL STRUCTURE; ENZYME ACTIVE SITE; ENZYME MECHANISM; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; RNA ANALYSIS; TECHNIQUE;

ANIMALS; BASE SEQUENCE; CATALYTIC DOMAIN; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; MUTAGENESIS, SITE-DIRECTED; NUCLEIC ACID CONFORMATION; RNA; RNA, CATALYTIC; RNA, PROTOZOAN; TETRAHYMENA;

EID: 9344227328     PISSN: 13558382     EISSN: None     Source Type: Journal    
DOI: 10.1261/rna.7170304     Document Type: Article

References (24)

1. 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.
2. Bartel, D.P. and Szostak, J.W. 1993. Isolation of new ribozymes from a large pool of random sequences. Science 261: 1411-1418.
3. Cate, J.H., Gooding, A.R., Podell, E., Zhou, K., Golden, B.I., Kundrot, C.E., Cech, T.R., and Doudna, J.A. 1996. Crystal structure of a group I ribozyme domain: Principles of RNA packing. Science 273: 1678-1685.
4. 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.
5. Davis, J.H. and Szostak, J.W. 2002. Isolation of high-affinity GTP aptamers from partially structured RNA libraries. Proc. Natl. Acad. Sci. 99: 11616-11621.
6. Golden, B.L, Gooding, A.R., Podell, E.R., and Cech, T.R. 1998. A preorganized active site in the crystal structure of the Tetrahymena ribozyme. Science 282: 259-264.
7. Hamm, J. 1996. Characterization of antibody-binding RNAs selected from structurally constrained libraries. Nucleic Acids Res. 24: 2220-2227.
8. Ikawa, Y., Yoshioka, W., Ohki, Y., Shiraishi, H., and Inoue, T. 2001. Self-splicing of the Tetrahymena group I ribozyme without conserved base-triples. Genes Cells 6: 411-420.
9. 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.
10. Jaeger, L., Wright, M.C., and Joyce, G.F. 1999. A complex ligase ribozyme evolved in vitro from a group I ribozyme domain. Proc. Natl. Acad. Sci. 96: 14712-14717.
11. 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.
12. Juneau, K. and Cech, T.R. 1999. In vitro selection of RNAs with increased tertiary structure stability. RNA 5: 1119-1129.
13. Juneau, K., Podell, E., Harrington, D.J., and Cech, T.R. 2001. Structural basis of the enhanced stability of a mutant ribozyme domain and a detailed view of RNA-solvent interactions. Structure 9: 221-231.
14. Keith, G. 1995. Mobilities of modified ribonucleotides on two-dimensional cellulose thin-layer chromatography. Biochimie 77: 142-144.
15. Mathews, D.H., Sabina, J., Zuker, M., and Turner, D.H. 1999. Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure. J. Mol. Biol. 288: 911-940.
16. Murphy, F.L. and Cech, T.R. 1993. An independently folding domain of RNA tertiary structure within the Tetrahymena ribozyme. Biochemistry 32: 5291-5300.
17. Murphy, F.L., Wang, Y.H., Griffith, J.D., and Cech, T.R. 1994. Coaxially stacked RNA helices in the catalytic center of the Tetrahymena ribozyme. Science 265: 1709-1712.
18. Naito, Y., Shiraishi, H., and Inoue, T. 1998. P5abc of the Tetrahymena ribozyme consists of three functionally independent elements. RNA 4: 837-846.
19. Ohuchi, S.J., Ikawa, Y., Shiraishi, H., and Inoue, T. 2002. Modular engineering of a Group I intron ribozyme. Nucleic Acids Res. 30: 3473-3480.
20. Rohatgi, R., Bartel, O.P., and Szostak, J.W. 1996. Kinetic and mechanistic analysis of nonenzymatic, template-directed oligoribonucleotide ligation. J. Am. Chem. Soc. 118: 3332-3339.
21. Sabeti, P.C., Unrau, P.J., and Bartel, O.P. 1997. Accessing rare activities from random RNA sequences: The importance of the length of molecules in the starting pool. Chem. Biol. 4: 767-774.
22. Williams, K.P., Imahori, H., Fujimoto, D.N., and Inoue, T. 1994. Selection of novel forms of a functional domain within the Tetrahymena ribozyme. Nucleic Acids Res. 22: 2003-2009.
23. Young, B.T. and Silverman, S.K. 2002. The GAAA tetraloop-receptor interaction contributes differentially to folding thermodynamics and kinetics for the P4-P6 RNA domain. Biochemistry 41: 12271-12276.
24. Zuker, M. 2003. Mfold Web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res. 31: 3406-3415.