An RNA ligase-mediated method for the efficient creation of large, synthetic RNAs

RNA

Volumn 12, Issue 11, 2006, Pages 2014-2019

  Stark, Martha R ^a   Pleiss, Jeffrey A ^b   Deras, Michael ^c   Scaringe, Stephen A ^c   Rader, Stephen D ^a  

^a UNIVERSITY OF NORTHERN BRITISH COLUMBIA   (Canada)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c Dharmacon Inc   (United States)

Author keywords

Ligation; RNA; Splint; T4 RNA ligase; YOL047c

Indexed keywords

FLUORESCENT DYE; OLIGORIBONUCLEOTIDE; RNA; RNA LIGASE;

ARTICLE; IN VITRO STUDY; PRIORITY JOURNAL; PROTEIN FUNCTION; RNA SPLICING; RNA STRUCTURE; RNA TRANSCRIPTION;

GENETIC TECHNIQUES; MOLECULAR BIOLOGY; OLIGORIBONUCLEOTIDES; RNA; RNA LIGASE (ATP);

EID: 33751118289     PISSN: 13558382     EISSN: 14699001     Source Type: Journal    
DOI: 10.1261/rna.93506     Document Type: Article

References (22)

1. Amitsur, M., Levitz, R., and Kaufmann, G. 1987. Bacteriophage T4 anticodon nuclease, polynucleotide kinase and RNA ligase reprocess the host lysine tRNA. EMBO J. 6: 2499-2503.
2. Bain, J.D. and Switzer, C. 1992. Regioselective ligation of oligoribonucleotides using DNA splints. Nucleic Acids Res. 20: 4372.
3. Chavatte, L., Frolova, L., Kisselev, L., and Favre, A. 2001. The polypeptide chain release factor eRF1 specifically contacts the s(4)UGA stop codon located in the A site of eukaryotic ribosomes. Eur. J. Biochem. 268: 2896-2904.
4. England, T.E., Bruce, A.G., and Uhlenbeck, O.C. 1980. Specific labeling of 3′ termini of RNA with T4 RNA ligase. Methods Enzymol. 65: 65-74.
5. Golden, B.L., Gooding, A.R., Podell, E.R., and Cech, T.R. 1996. X-ray crystallography of large RNAs: Heavy-atom derivatives by RNA engineering. RNA 2: 1295-1305.
6. Gumport, R.I. and Uhlenbeck, O.C. 1981. T4 RNA ligase as a nucleic acid synthesis and modification reagent. Gene Amplif. Anal. 2: 313-345.
7. Hartsel, S.A., Kitchen, D.E., Scaringe, S.A., and Marshall, W.S. 2004. RNA oligonucleotide synthesis via 5′-silyl-2′-orthoester chemistry. Methods Mol. Biol. 288: 33-50.
8. Heilek, G.M., Marusak, R., Meares, C.F., and Noller, H.F. 1995. Directed hydroxyl radical probing of 16S rRNA using Fe(II) tethered to ribosomal protein S4. Proc. Natl. Acad. Sci. 92: 1113-1116.
9. Kurschat, W.C., Muller, J., Wombacher, R., and Helm, M. 2005. Optimizing splinted ligation of highly structured small RNAs. RNA 11: 1909-1914.
10. 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.
11. McGregor, A., Rao, M.V., Duckworth, G., Stockley, P.G., and Connolly, B.A. 1996. Preparation of oligoribonucleotides containing 4-thiouridine using Fpmp chemistry. Photo-crosslinking to RNA binding proteins using 350 nm irradiation. Nucleic Acids Res. 24: 3173-3180.
12. Moore, M.J. and Query, C.C. 2000. Joining of RNAs by splinted ligation. Methods Enzymol. 317: 109-123.
13. Moore, M.J. and Sharp, P.A. 1992. Site-specific modification of pre-mRNA: The 2′-hydroxyl groups at the splice sites. Science 256: 992-997.
14. Pleiss, J.A., Derrick, M.L., and Uhlenbeck, O.C. 1998. T7 RNA polymerase produces 5′ end heterogeneity during in vitro transcription from certain templates. RNA 4: 1313-1317.
15. Romaniuk, P.J. and Uhlenbeck, O.C. 1983. Joining of RNA molecules with RNA ligase. Methods Enzymol. 100: 52-59.
16. Scaringe, S.A. 2001. RNA oligonucleotide synthesis via 5′-silyl-2′-orthoester chemistry. Methods 23: 206-217.
17. Spingola, M., Grate, L., Haussler, D., and Ares Jr., M. 1999. Genomewide bioinformatic and molecular analysis of introns in Saccharomyces cerevisiae. RNA 5: 221-234.
18. Teigelkamp, S., Newman, A.J., and Beggs, J.D. 1995. Extensive interactions of PRP8 protein with the 5′ and 3′ splice sites during splicing suggest a role in stabilization of exon alignment by U5 snRNA. EMBO J. 14: 2602-2612.
19. Wittenberg, W.L. and Uhlenbeck, O.C. 1985. Specific replacement of functional groups of uridine-33 in yeast phenylalanine transfer ribonucleic acid. Biochemistry 24: 2705-2712.
20. Wyatt, J.R., Sontheimer, E.J., and Steitz, J.A. 1992. Site-specific crosslinking of mammalian U5 snRNP to the 5′ splice site before the first step of pre-mRNA splicing. Genes & Dev. 6: 2542-2553.
21. Xia, T., SantaLucia Jr., J., Burkard, M.E., Kierzek, R., Schroeder, S.J., Jiao, X., Cox, C., and Turner, D.H. 1998. Thermodynamic parameters for an expanded nearest-neighbor model for formation of RNA duplexes with Watson-Crick base pairs. Biochemistry 37: 14719-14735.
22. Zuker, M. 2003. Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res. 31: 3406-3415.