Ribozyme motif structure mapped using random recombination and selection

RNA

Volumn 11, Issue 4, 2005, Pages 404-411

  Wang, Qing S ^a   Unrau, Peter J ^a  

^a SIMON FRASER UNIVERSITY   (Canada)

Author keywords

Random recombination; RNA motif isolation; Systematic deletion

Indexed keywords

DNA; PYRIMIDINE NUCLEOTIDE; RIBOZYME; SYNTHETASE;

ARTICLE; CATALYSIS; EVOLUTION; GENE CONSTRUCT; GENE DELETION; GENE TRANSLOCATION; GENETIC RECOMBINATION; GENETIC SELECTION; GENOME ANALYSIS; ISOLATION PROCEDURE; MOLECULE; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PROTEIN FUNCTION; STRUCTURE ANALYSIS;

BASE SEQUENCE; DEOXYRIBONUCLEASE I; DNA LIGASES; DNA-DIRECTED DNA POLYMERASE; GENE LIBRARY; MOLECULAR SEQUENCE DATA; NUCLEIC ACID CONFORMATION; NUCLEOTIDE MAPPING; PHOSPHORIC MONOESTER HYDROLASES; PYRIMIDINE NUCLEOTIDES; RECOMBINATION, GENETIC; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; RNA, CATALYTIC; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA; SEQUENCE DELETION; THIOURACIL;

EID: 15444362048     PISSN: 13558382     EISSN: None     Source Type: Journal    
DOI: 10.1261/rna.7238705     Document Type: Article

References (25)

1. Bittker, J.A., Le, B.V., and Liu, D.R. 2002. Nucleic acid evolution and minimization by nonhomologous random recombination. Nat. Biotechnol. 20: 1024-1029.
2. Bittker, J.A., Le, B.V., Liu, J.M., and Liu, D.R. 2004. Directed evolution of protein enzymes using nonhomologous random recombination. Proc. Natl. Acad. Sci. 101: 7011-7016.
3. Campbell, V.W. and Jackson, DA. 1980. The effect of divalent cations on the mode of action of DNase I. The initial reaction products produced from covalently closed circular DNA. J. Biol. Chem. 255: 3726-3735.
4. Chapple, K.E., Bartel, D.P., and Unrau, P.J. 2003. Combinatorial minimization and secondary structure determination of a nucleotide synthase ribozyme. RNA 9: 1208-1220.
5. Ekland, E.H., Szostak, J.W., and Bartel, D.P. 1995. Structurally complex and highly-active RNA ligases derived from random RNA sequences. Science 269: 364-370.
6. Igloi, G.L. 1988. Interaction of transfer-RNAs and of phosphorothioate- substituted nucleic-acids with an organomercurial - Probing the chemical environment of thiolated residues by affinity electrophoresis. Biochemistry 27: 3842-3849.
7. Illangasekare, M., Kovalchuke, O., and Yarus, M. 1997. Essential structures of a self-aminoacylating RNA. J. Mol. Biol. 274: 519-529.
8. Khvorova, A., Lescoute, A., Westhof, E., and Jayasena, S.D. 2003. Sequence elements outside the hammerhead ribozyme catalytic core enable intracellular activity. Nat. Struct. Biol. 10: 708-712.
9. Knight, R. and Yarus, M. 2003. Finding specific RNA motifs: Function in a zeptomole world? RNA 9: 218-230.
10. Krasilnikov, A.S., Xiao, Y., Pan, T., and Mondragon, A. 2004. Basis for structural diversity in homologous RNAs. Science 306: 104-107.
11. Lau, W.L., Cadieux, K.E.C., and Unrau, P.J. 2004. Isolation of fast purine nucleotide synthase ribozymes. J. Am. Chem. Soc. 126: 15686-15693.
12. Mandal, M. and Breaker, R. 2004. An mRNA structure that differentially controls gene expression by binding guanine or adenine. Biophys. J. 86: 32A.
13. Melgar, E. and Goldthwait, D.A. 1968. Deoxyribonucleic acid nucleases. II. The effects of metals on the mechanism of action of deoxyribonuclease I. J. Biol. Chem. 243: 4409-4416.
14. Rivas, E. and Eddy, S.R. 1999. A dynamic programming algorithm for RNA structure prediction including pseudoknots. J. Mol. Biol. 285: 2053-2068.
15. Sabeti, P.C., Unrau, P.J., and Bartel, D.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.
16. Szewczak, A.A. and Moore, P.B. 1995. The sarcin/ricin loop, a modular RNA. J. Mol. Biol. 247: 81-98.
17. Uhlenbeck, O.C. 2003. Less isn't always more. RNA 9: 1415-1417.
18. Unrau, P.J. and Bartel, D.P. 1998. RNA-catalysed nucleotide synthesis. Nature 395: 260-263.
19. _. 2003. An oxocarbenium-ion intermediate of a ribozyme reaction indicated by kinetic isotope effects. Proc. Natl. Acad. Sci. 100: 15393-15397.
20. Westhof, E. and Massire, C. 2004. Evolution of RNA architecture. Science 306: 62-63.
21. Williams, K.P. and Bartel, D.P. 1996. Phylogenetic analysis of tmRNA secondary structure. RNA 2: 1306-1310.
22. Williams, K.P., Martindale, K.A., and Bartel, D.P. 1999. Resuming translation on tmRNA: A unique mode of determining a reading frame. EMBO J. 18: 5423-5433.
23. Winkler, W.C., Nahvi, A., Roth, A., Collins, J.A., and Breaker, R.R. 2004. Control of gene expression by a natural metabolite-responsive ribozyme. Nature 428: 281-286.
24. Yusupov, M.M., Yusupova, G.Z., Baucom, A., Lieberman, K., Earnest, T.N., Cate, J.H.D., and Noller, H.F. 2001. Crystal structure of the ribosome at 5.5 Å resolution. Science 292: 883-896.
25. Zaher, H.S. and Unrau, P.J. 2005. Nucleic acid library construction using synthetic DNA constructs. In Oligonucleotide synthesis methods and applications (ed. P. Herdewijn), pp. 359-378. Humana Press, Totowa, NJ.