Abstract
We report here the first photo-chemical control of a ribozyme reaction by the site-specific modification of the 2'-hydroxyl nucleophile in the hammerhead system with a caging functionality. Rapid laser photolysis of the O-(2-nitrobenzyl) caging group initiates an efficient and accurate hammerhead-catalyzed cleavage of substrate RNA under native conditions. RNAs in which reactive functionalities or recognition elements are caged in this manner will be useful tools to probe RNA reactivity and dynamics.
Full Text
The Full Text of this article is available as a PDF (115.2 KB).
Selected References
These references are in PubMed. This may not be the complete list of references from this article.
- Adams S. R., Tsien R. Y. Controlling cell chemistry with caged compounds. Annu Rev Physiol. 1993;55:755–784. doi: 10.1146/annurev.ph.55.030193.003543. [DOI] [PubMed] [Google Scholar]
- Allerson C. R., Verdine G. L. Synthesis and biochemical evaluation of RNA containing an intrahelical disulfide crosslink. Chem Biol. 1995 Oct;2(10):667–675. doi: 10.1016/1074-5521(95)90030-6. [DOI] [PubMed] [Google Scholar]
- Branch A. D., Robertson H. D. Efficient trans cleavage and a common structural motif for the ribozymes of the human hepatitis delta agent. Proc Natl Acad Sci U S A. 1991 Nov 15;88(22):10163–10167. doi: 10.1073/pnas.88.22.10163. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Brubaker M. J., Dyer D. H., Stoddard B., Koshland D. E., Jr Synthesis, kinetics, and structural studies of a photolabile caged isocitrate: a catalytic trigger for isocitrate dehydrogenase. Biochemistry. 1996 Mar 5;35(9):2854–2864. doi: 10.1021/bi951105v. [DOI] [PubMed] [Google Scholar]
- Capaldi D. C., Reese C. B. Use of the 1-(2-fluorophenyl)-4-methoxypiperidin-4-yl (Fpmp) and related protecting groups in oligoribonucleotide synthesis: stability of internucleotide linkages to aqueous acid. Nucleic Acids Res. 1994 Jun 25;22(12):2209–2216. doi: 10.1093/nar/22.12.2209. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Cate J. H., Gooding A. R., Podell E., Zhou K., Golden B. L., Kundrot C. E., Cech T. R., Doudna J. A. Crystal structure of a group I ribozyme domain: principles of RNA packing. Science. 1996 Sep 20;273(5282):1678–1685. doi: 10.1126/science.273.5282.1678. [DOI] [PubMed] [Google Scholar]
- Fedor M. J., Uhlenbeck O. C. Kinetics of intermolecular cleavage by hammerhead ribozymes. Biochemistry. 1992 Dec 8;31(48):12042–12054. doi: 10.1021/bi00163a012. [DOI] [PubMed] [Google Scholar]
- Guo H. C., Collins R. A. Efficient trans-cleavage of a stem-loop RNA substrate by a ribozyme derived from neurospora VS RNA. EMBO J. 1995 Jan 16;14(2):368–376. doi: 10.1002/j.1460-2075.1995.tb07011.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Konarska M. M., Grabowski P. J., Padgett R. A., Sharp P. A. Characterization of the branch site in lariat RNAs produced by splicing of mRNA precursors. Nature. 1985 Feb 14;313(6003):552–557. doi: 10.1038/313552a0. [DOI] [PubMed] [Google Scholar]
- MacMillan A. M., Query C. C., Allerson C. R., Chen S., Verdine G. L., Sharp P. A. Dynamic association of proteins with the pre-mRNA branch region. Genes Dev. 1994 Dec 15;8(24):3008–3020. doi: 10.1101/gad.8.24.3008. [DOI] [PubMed] [Google Scholar]
- McCray J. A., Trentham D. R. Properties and uses of photoreactive caged compounds. Annu Rev Biophys Biophys Chem. 1989;18:239–270. doi: 10.1146/annurev.bb.18.060189.001323. [DOI] [PubMed] [Google Scholar]
- McKay D. B. Structure and function of the hammerhead ribozyme: an unfinished story. RNA. 1996 May;2(5):395–403. [PMC free article] [PubMed] [Google Scholar]
- Milligan J. F., Uhlenbeck O. C. Synthesis of small RNAs using T7 RNA polymerase. Methods Enzymol. 1989;180:51–62. doi: 10.1016/0076-6879(89)80091-6. [DOI] [PubMed] [Google Scholar]
- Moore M. J., Sharp P. A. Site-specific modification of pre-mRNA: the 2'-hydroxyl groups at the splice sites. Science. 1992 May 15;256(5059):992–997. doi: 10.1126/science.1589782. [DOI] [PubMed] [Google Scholar]
- Murray J. B., Terwey D. P., Maloney L., Karpeisky A., Usman N., Beigelman L., Scott W. G. The structural basis of hammerhead ribozyme self-cleavage. Cell. 1998 Mar 6;92(5):665–673. doi: 10.1016/s0092-8674(00)81134-4. [DOI] [PubMed] [Google Scholar]
- Peebles C. L., Perlman P. S., Mecklenburg K. L., Petrillo M. L., Tabor J. H., Jarrell K. A., Cheng H. L. A self-splicing RNA excises an intron lariat. Cell. 1986 Jan 31;44(2):213–223. doi: 10.1016/0092-8674(86)90755-5. [DOI] [PubMed] [Google Scholar]
- Pley H. W., Flaherty K. M., McKay D. B. Three-dimensional structure of a hammerhead ribozyme. Nature. 1994 Nov 3;372(6501):68–74. doi: 10.1038/372068a0. [DOI] [PubMed] [Google Scholar]
- Pyle A. M., Green J. B. RNA folding. Curr Opin Struct Biol. 1995 Jun;5(3):303–310. doi: 10.1016/0959-440x(95)80091-3. [DOI] [PubMed] [Google Scholar]
- Query C. C., Moore M. J., Sharp P. A. Branch nucleophile selection in pre-mRNA splicing: evidence for the bulged duplex model. Genes Dev. 1994 Mar 1;8(5):587–597. doi: 10.1101/gad.8.5.587. [DOI] [PubMed] [Google Scholar]
- Schlichting I., Almo S. C., Rapp G., Wilson K., Petratos K., Lentfer A., Wittinghofer A., Kabsch W., Pai E. F., Petsko G. A. Time-resolved X-ray crystallographic study of the conformational change in Ha-Ras p21 protein on GTP hydrolysis. Nature. 1990 May 24;345(6273):309–315. doi: 10.1038/345309a0. [DOI] [PubMed] [Google Scholar]
- Scott W. G., Finch J. T., Klug A. The crystal structure of an all-RNA hammerhead ribozyme: a proposed mechanism for RNA catalytic cleavage. Cell. 1995 Jun 30;81(7):991–1002. doi: 10.1016/s0092-8674(05)80004-2. [DOI] [PubMed] [Google Scholar]
- Scott W. G., Murray J. B., Arnold J. R., Stoddard B. L., Klug A. Capturing the structure of a catalytic RNA intermediate: the hammerhead ribozyme. Science. 1996 Dec 20;274(5295):2065–2069. doi: 10.1126/science.274.5295.2065. [DOI] [PubMed] [Google Scholar]
- Sigurdsson S. T., Tuschl T., Eckstein F. Probing RNA tertiary structure: interhelical crosslinking of the hammerhead ribozyme. RNA. 1995 Aug;1(6):575–583. [PMC free article] [PubMed] [Google Scholar]
- Symons R. H. Small catalytic RNAs. Annu Rev Biochem. 1992;61:641–671. doi: 10.1146/annurev.bi.61.070192.003233. [DOI] [PubMed] [Google Scholar]
- Uhlenbeck O. C. A small catalytic oligoribonucleotide. Nature. 1987 Aug 13;328(6131):596–600. doi: 10.1038/328596a0. [DOI] [PubMed] [Google Scholar]
- Williams D. M., Pieken W. A., Eckstein F. Function of specific 2'-hydroxyl groups of guanosines in a hammerhead ribozyme probed by 2' modifications. Proc Natl Acad Sci U S A. 1992 Feb 1;89(3):918–921. doi: 10.1073/pnas.89.3.918. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Zarrinkar P. P., Williamson J. R. Kinetic intermediates in RNA folding. Science. 1994 Aug 12;265(5174):918–924. doi: 10.1126/science.8052848. [DOI] [PubMed] [Google Scholar]