The ARiBo tag: A reliable tool for affinity purification of RNAs under native conditions

Nucleic Acids Research

Volumn 39, Issue 3, 2011, Pages

  Di Tomasso, Genevive ^a   Lampron, Philipe ^a   Dagenais, Pierre ^a   Omichinski, James G ^a   Legault, Pascale ^a  

^a UNIVERSITÉ DE MONTRÉAL   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

GLUCOSAMINE 6 PHOSPHATE; GLUTATHIONE; GLUTATHIONE TRANSFERASE; HYBRID PROTEIN; MICRORNA; PEPTIDE; PHOSPHORUS DERIVATIVE; RIBOZYME; SEPHAROSE; UNCLASSIFIED DRUG;

AFFINITY BATCH PURIFICATION; ARTICLE; BACTERIOPHAGE LAMBDA; BOXB GENE; CONTROLLED STUDY; GENE; GENE INTERACTION; GLMS GENE; INTERMETHOD COMPARISON; PRIORITY JOURNAL; PROTEIN CLEAVAGE; PROTEIN DENATURATION; PROTEIN INTERACTION; RELIABILITY; RIBOSWITCH; RNA PURIFICATION; RNA SYNTHESIS;

BACTERIOPHAGE LAMBDA; BASE SEQUENCE; GENETIC TECHNIQUES; INDICATORS AND REAGENTS; RNA; RNA, CATALYTIC; RNA, VIRAL;

ENTEROBACTERIA PHAGE LAMBDA;

EID: 79951574779     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkq1084     Document Type: Article

References (31)

1. Milligan, J.F., Groebe, D.R., Witherell, G.W. and Uhlenbeck, O.C. (1987) Oligoribonucleotide synthesis using T7 RNA polymerase and synthetic DNA templates. Nucleic Acids Res., 15, 8783-8798.
2. Wyatt, J.R., Chastain, M. and Puglisi, J.D. (1991) Synthesis and purification of large amounts of RNA oligonucleotides. Biotechniques, 11, 764-769.
3. Legault, P. (1995) Ph.D. Structural studies of ribozymes by heteronuclear NMR spectroscopy. Thesis. University of Colorado at Boulder Boulder.
4. Doudna, J.A. (1997) Preparation of homogeneous ribozyme RNA for crystallization. Methods Mol. Biol., 74, 365-370.
5. Uhlenbeck, O.C. (1995) Keeping RNA happy. RNA, 1, 4-6.
6. Lukavsky, P.J. and Puglisi, J.D. (2004) Large-scale preparation and purification of polyacrylamide-free RNA oligonucleotides. RNA, 10, 889-893. (Pubitemid 38529751)
7. Shields, T.P., Mollova, E., Ste Marie, L., Hansen, M.R. and Pardi, A. (1999) High-performance liquid chromatography purification of homogenous-length RNA produced by trans cleavage with a hammerhead ribozyme. RNA, 5, 1259-1267. (Pubitemid 29422767)
8. Kim, I., McKenna, S.A., Puglisi, E.V. and Puglisi, J.D. (2007) Rapid purification of RNAs using fast performance liquid chromatography (FPLC). RNA, 13, 289-294. (Pubitemid 46147903)
9. McKenna, S.A., Kim, I., Puglisi, E.V., Lindhout, D.A., Aitken, C.E., Marshall, R.A. and Puglisi, J.D. (2007) Purification and characterization of transcribed RNAs using gel filtration chromatography. Nature Protocols, 2, 3270-3277.
10. Keel, A.Y., Easton, L.E., Lukavsky, P.J. and Kieft, J.S. (2009) Methods in Enzymology, Vol. 469: Biophysical, Chemical, and Functional Probes of Rna Structure, Interactions and Folding, Pt B, Vol. 469. Academic Press, London, UK, pp. 3-25.
11. Easton, L.E., Shibata, Y. and Lukavsky, P.J. (2010) Rapid, nondenaturing RNA purification using weak anion-exchange fast performance liquid chromatography. RNA, 16, 647-653.
12. Cheong, H.K., Hwang, E., Lee, C., Choi, B.S. and Cheong, C. (2004) Rapid preparation of RNA samples for NMR spectroscopy and X-ray crystallography. Nucleic Acids Res., 32, e84.
13. Kieft, J.S. and Batey, R.T. (2004) A general method for rapid and nondenaturing purification of RNAs. RNA, 10, 988-995. (Pubitemid 38669771)
14. Batey, R.T. and Kieft, J.S. (2007) Improved native affinity purification of RNA. RNA, 13, 1384-1389. (Pubitemid 47080482)
15. Boese, B.J., Corbino, K. and Breaker, R.R. (2008) In vitro selection and characterization of cellulose-binding RNA aptamers using isothermal amplification. Nucleos. Nucleot. Nuc., 27, 949-966.
16. Vicens, Q., Gooding, A.R., Duarte, L.F. and Batey, R.T. (2009) Preparation of group I introns for biochemical studies and crystallization assays by native affinity purification. Plos One, 4, 1-14.
17. Pereira, M.J., Behera, V. and Walter, N.G. (2010) Nondenaturing purification of co-transcriptionally folded RNA avoids common folding heterogeneity. Plos One, 5, 1-7.
18. Mogridge, J., Legault, P., Li, J., Van Oene, M.D., Kay, L.E. and Greenblatt, J. (1998) Independent ligand-induced folding of the RNA-binding domain and two functionally distinct antitermination regions in the phage lambda N protein. Mol. Cell, 1, 265-275. (Pubitemid 128378667)
19. Austin, R.J., Xia, T., Ren, J., Takahashi, T.T. and Roberts, R.W. (2002) Designed arginine-rich RNA-binding peptides with picomolar affinity. J. Am. Chem. Soc., 124, 10966-10967. (Pubitemid 35025642)
20. Rastogi, T. and Collins, R.A. (1998) Smaller, faster ribozymes reveal the catalytic core of Neurospora VS RNA. J. Mol. Biol., 277, 215-224. (Pubitemid 28174963)
21. Delfosse, V., Bouchard, P., Bonneau, E., Dagenais, P., Lemay, J.F., Lafontaine, D.A. and Legault, P. (2010) Riboswitch structure: an internal residue mimicking the purine ligand. Nucleic Acids Res., 38, 2057-2068.
22. Legault, P., Li, J., Mogridge, J., Kay, L.E. and Greenblatt, J. (1998) NMR structure of the bacteriophage lambda N peptide/boxB RNA complex: recognition of a GNRA fold by an arginine-rich motif. Cell, 93, 289-299. (Pubitemid 28180861)
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. (Pubitemid 38418792)
24. 0 non-core region of the glmS ribozyme enhances self-cleavage activity. RNA, 11, 1788-1794. (Pubitemid 41720028)
25. Cochrane, J.C., Lipchock, S.V. and Strobel, S.A. (2007) Structural investigation of the GlmS ribozyme bound to its catalytic cofactor. Chem. Biol., 14, 97-105. (Pubitemid 46124067)
26. McCarthy, T.J., Plog, M.A., Floy, S.A., Jansen, J.A., Soukup, J.K. and Soukup, G.A. (2005) Ligand requirements for glmS ribozyme self-cleavage. Chem. Biol., 12, 1221-1226. (Pubitemid 41628257)
27. Roth, A., Nahvi, A., Lee, M., Jona, I. and Breaker, R.R. (2006) Characteristics of the glmS ribozyme suggest only structural roles for divalent metal ions. RNA, 12, 607-619.
28. Barrick, J.E., Corbino, K.A., Winkler, W.C., Nahvi, A., Mandal, M., Collins, J., Lee, M., Roth, A., Sudarsan, N., Jona, I. et al. (2004) New RNA motifs suggest an expanded scope for riboswitches in bacterial genetic control. Proc. Natl Acad. Sci. USA, 101, 6421-6426. (Pubitemid 38585989)
29. 15N labelled RNAs for heteronuclear multidimensional NMR studies. Nucleic Acids Res., 20, 4507-4513.
30. Batey, R.T., Inada, M., Kujawinski, E., Puglisi, J.D. and Williamson, J.R. (1992) Preparation of isotopically labeled ribonucleotides for multidimensional NMR spectroscopy of RNA. Nucleic Acids Res., 20, 4515-4523.
31. 0-groups using a mutant T7 RNA polymerase (RNAP). Nucleic Acids Res., 27, 1561-1563. (Pubitemid 29206303)