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Proceedings of the National Academy of Sciences of the United States of America logoLink to Proceedings of the National Academy of Sciences of the United States of America
. 1994 Apr 12;91(8):3373–3377. doi: 10.1073/pnas.91.8.3373

Kinetics of an RNA conformational switch.

K A LeCuyer 1, D M Crothers 1
PMCID: PMC43579  PMID: 8159754

Abstract

The spliced leader RNA from Leptomonas collosoma has two competing secondary structures of nearly equal free energy. Short, complementary oligonucleotides can drive the structure from one form of the other. We report stopped-flow rapid-mixing and temperature-jump measurements of the kinetics of the structural switch. At high concentrations of oligonucleotide, the rate of binding becomes limited by the rate of the structural switch, which occurs on a time scale of a fraction of a second. The low activation energy observed for the process implies a branch migration type of mechanism in which portions of the two competing helices transiently coexist.

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Selected References

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  1. Agabian N. Trans splicing of nuclear pre-mRNAs. Cell. 1990 Jun 29;61(7):1157–1160. doi: 10.1016/0092-8674(90)90674-4. [DOI] [PubMed] [Google Scholar]
  2. Babitzke P., Yanofsky C. Reconstitution of Bacillus subtilis trp attenuation in vitro with TRAP, the trp RNA-binding attenuation protein. Proc Natl Acad Sci U S A. 1993 Jan 1;90(1):133–137. doi: 10.1073/pnas.90.1.133. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Bevilacqua P. C., Kierzek R., Johnson K. A., Turner D. H. Dynamics of ribozyme binding of substrate revealed by fluorescence-detected stopped-flow methods. Science. 1992 Nov 20;258(5086):1355–1358. doi: 10.1126/science.1455230. [DOI] [PubMed] [Google Scholar]
  4. Cole P. E., Crothers D. M. Conformational changes of transfer ribonucleic acid. Relaxation kinetics of the early melting transition of methionine transfer ribonucleic acid (Escherichia coli). Biochemistry. 1972 Nov 7;11(23):4368–4374. doi: 10.1021/bi00773a025. [DOI] [PubMed] [Google Scholar]
  5. Craig M. E., Crothers D. M., Doty P. Relaxation kinetics of dimer formation by self complementary oligonucleotides. J Mol Biol. 1971 Dec 14;62(2):383–401. doi: 10.1016/0022-2836(71)90434-7. [DOI] [PubMed] [Google Scholar]
  6. Fayat G., Mayaux J. F., Sacerdot C., Fromant M., Springer M., Grunberg-Manago M., Blanquet S. Escherichia coli phenylalanyl-tRNA synthetase operon region. Evidence for an attenuation mechanism. Identification of the gene for the ribosomal protein L20. J Mol Biol. 1983 Dec 15;171(3):239–261. doi: 10.1016/0022-2836(83)90092-x. [DOI] [PubMed] [Google Scholar]
  7. LeCuyer K. A., Crothers D. M. The Leptomonas collosoma spliced leader RNA can switch between two alternate structural forms. Biochemistry. 1993 May 25;32(20):5301–5311. doi: 10.1021/bi00071a004. [DOI] [PubMed] [Google Scholar]
  8. Madhani H. D., Guthrie C. A novel base-pairing interaction between U2 and U6 snRNAs suggests a mechanism for the catalytic activation of the spliceosome. Cell. 1992 Nov 27;71(5):803–817. doi: 10.1016/0092-8674(92)90556-r. [DOI] [PubMed] [Google Scholar]
  9. Milligan J. F., Groebe D. R., Witherell G. W., Uhlenbeck O. C. Oligoribonucleotide synthesis using T7 RNA polymerase and synthetic DNA templates. Nucleic Acids Res. 1987 Nov 11;15(21):8783–8798. doi: 10.1093/nar/15.21.8783. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Murphy W. J., Watkins K. P., Agabian N. Identification of a novel Y branch structure as an intermediate in trypanosome mRNA processing: evidence for trans splicing. Cell. 1986 Nov 21;47(4):517–525. doi: 10.1016/0092-8674(86)90616-1. [DOI] [PubMed] [Google Scholar]
  11. Perry K., Agabian N. mRNA processing in the Trypanosomatidae. Experientia. 1991 Feb 15;47(2):118–128. doi: 10.1007/BF01945412. [DOI] [PubMed] [Google Scholar]
  12. Putzer H., Gendron N., Grunberg-Manago M. Co-ordinate expression of the two threonyl-tRNA synthetase genes in Bacillus subtilis: control by transcriptional antitermination involving a conserved regulatory sequence. EMBO J. 1992 Aug;11(8):3117–3127. doi: 10.1002/j.1460-2075.1992.tb05384.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Pörschke D., Eigen M. Co-operative non-enzymic base recognition. 3. Kinetics of the helix-coil transition of the oligoribouridylic--oligoriboadenylic acid system and of oligoriboadenylic acid alone at acidic pH. J Mol Biol. 1971 Dec 14;62(2):361–381. doi: 10.1016/0022-2836(71)90433-5. [DOI] [PubMed] [Google Scholar]
  14. Ross P. D., Sturtevant J. M. THE KINETICS OF DOUBLE HELIX FORMATION FROM POLYRIBOADENYLIC ACID AND POLYRIBOURIDYLIC ACID. Proc Natl Acad Sci U S A. 1960 Oct;46(10):1360–1365. doi: 10.1073/pnas.46.10.1360. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Steitz J. A. Splicing takes a holliday. Science. 1992 Aug 14;257(5072):888–889. doi: 10.1126/science.1386941. [DOI] [PubMed] [Google Scholar]
  16. Sutton R. E., Boothroyd J. C. Evidence for trans splicing in trypanosomes. Cell. 1986 Nov 21;47(4):527–535. doi: 10.1016/0092-8674(86)90617-3. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Ullu E., Tschudi C. Permeable trypanosome cells as a model system for transcription and trans-splicing. Nucleic Acids Res. 1990 Jun 11;18(11):3319–3326. doi: 10.1093/nar/18.11.3319. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Wool I. G., Glück A., Endo Y. Ribotoxin recognition of ribosomal RNA and a proposal for the mechanism of translocation. Trends Biochem Sci. 1992 Jul;17(7):266–269. doi: 10.1016/0968-0004(92)90407-z. [DOI] [PubMed] [Google Scholar]

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