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. 2000 Jun;6(6):790–794. doi: 10.1017/s1355838200000522

Maximizing RNA folding rates: a balancing act.

D Thirumalai 1, S A Woodson 1
PMCID: PMC1369958  PMID: 10864039

Abstract

Large ribozymes typically require very long times to refold into their active conformation in vitro, because the RNA is easily trapped in metastable misfolded structures. Theoretical models show that the probability of misfolding is reduced when local and long-range interactions in the RNA are balanced. Using the folding kinetics of the Tetrahymena ribozyme as an example, we propose that folding rates are maximized when the free energies of forming independent domains are similar to each other. A prediction is that the folding pathway of the ribozyme can be reversed by inverting the relative stability of the tertiary domains. This result suggests strategies for optimizing ribozyme sequences for therapeutics and structural studies.

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Selected References

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  1. Banerjee A. R., Jaeger J. A., Turner D. H. Thermal unfolding of a group I ribozyme: the low-temperature transition is primarily disruption of tertiary structure. Biochemistry. 1993 Jan 12;32(1):153–163. doi: 10.1021/bi00052a021. [DOI] [PubMed] [Google Scholar]
  2. Brion P., Westhof E. Hierarchy and dynamics of RNA folding. Annu Rev Biophys Biomol Struct. 1997;26:113–137. doi: 10.1146/annurev.biophys.26.1.113. [DOI] [PubMed] [Google Scholar]
  3. Buchmueller K. L., Webb A. E., Richardson D. A., Weeks K. M. A collapsed non-native RNA folding state. Nat Struct Biol. 2000 May;7(5):362–366. doi: 10.1038/75125. [DOI] [PubMed] [Google Scholar]
  4. Caprara M. G., Mohr G., Lambowitz A. M. A tyrosyl-tRNA synthetase protein induces tertiary folding of the group I intron catalytic core. J Mol Biol. 1996 Apr 5;257(3):512–531. doi: 10.1006/jmbi.1996.0182. [DOI] [PubMed] [Google Scholar]
  5. 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]
  6. Cech T. R., Damberger S. H., Gutell R. R. Representation of the secondary and tertiary structure of group I introns. Nat Struct Biol. 1994 May;1(5):273–280. doi: 10.1038/nsb0594-273. [DOI] [PubMed] [Google Scholar]
  7. Celander D. W., Cech T. R. Visualizing the higher order folding of a catalytic RNA molecule. Science. 1991 Jan 25;251(4992):401–407. doi: 10.1126/science.1989074. [DOI] [PubMed] [Google Scholar]
  8. Dill K. A., Chan H. S. From Levinthal to pathways to funnels. Nat Struct Biol. 1997 Jan;4(1):10–19. doi: 10.1038/nsb0197-10. [DOI] [PubMed] [Google Scholar]
  9. Doherty E. A., Doudna J. A. The P4-P6 domain directs higher order folding of the Tetrahymena ribozyme core. Biochemistry. 1997 Mar 18;36(11):3159–3169. doi: 10.1021/bi962428+. [DOI] [PubMed] [Google Scholar]
  10. Fang X. W., Pan T., Sosnick T. R. Mg2+-dependent folding of a large ribozyme without kinetic traps. Nat Struct Biol. 1999 Dec;6(12):1091–1095. doi: 10.1038/70016. [DOI] [PubMed] [Google Scholar]
  11. Fresco J. R., Adams A., Ascione R., Henley D., Lindahl T. Tertiary structure in transfer ribonucleic acids. Cold Spring Harb Symp Quant Biol. 1966;31:527–537. doi: 10.1101/sqb.1966.031.01.068. [DOI] [PubMed] [Google Scholar]
  12. Gluick T. C., Draper D. E. Thermodynamics of folding a pseudoknotted mRNA fragment. J Mol Biol. 1994 Aug 12;241(2):246–262. doi: 10.1006/jmbi.1994.1493. [DOI] [PubMed] [Google Scholar]
  13. Herschlag D. RNA chaperones and the RNA folding problem. J Biol Chem. 1995 Sep 8;270(36):20871–20874. doi: 10.1074/jbc.270.36.20871. [DOI] [PubMed] [Google Scholar]
  14. Kim S. H., Cech T. R. Three-dimensional model of the active site of the self-splicing rRNA precursor of Tetrahymena. Proc Natl Acad Sci U S A. 1987 Dec;84(24):8788–8792. doi: 10.1073/pnas.84.24.8788. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Loria A., Pan T. Domain structure of the ribozyme from eubacterial ribonuclease P. RNA. 1996 Jun;2(6):551–563. [PMC free article] [PubMed] [Google Scholar]
  16. Michel F., Westhof E. Modelling of the three-dimensional architecture of group I catalytic introns based on comparative sequence analysis. J Mol Biol. 1990 Dec 5;216(3):585–610. doi: 10.1016/0022-2836(90)90386-Z. [DOI] [PubMed] [Google Scholar]
  17. Mohr G., Zhang A., Gianelos J. A., Belfort M., Lambowitz A. M. The neurospora CYT-18 protein suppresses defects in the phage T4 td intron by stabilizing the catalytically active structure of the intron core. Cell. 1992 May 1;69(3):483–494. doi: 10.1016/0092-8674(92)90449-m. [DOI] [PubMed] [Google Scholar]
  18. Murphy F. L., Cech T. R. An independently folding domain of RNA tertiary structure within the Tetrahymena ribozyme. Biochemistry. 1993 May 25;32(20):5291–5300. doi: 10.1021/bi00071a003. [DOI] [PubMed] [Google Scholar]
  19. Pan J., Deras M. L., Woodson S. A. Fast folding of a ribozyme by stabilizing core interactions: evidence for multiple folding pathways in RNA. J Mol Biol. 2000 Feb 11;296(1):133–144. doi: 10.1006/jmbi.1999.3439. [DOI] [PubMed] [Google Scholar]
  20. Pan J., Thirumalai D., Woodson S. A. Folding of RNA involves parallel pathways. J Mol Biol. 1997 Oct 17;273(1):7–13. doi: 10.1006/jmbi.1997.1311. [DOI] [PubMed] [Google Scholar]
  21. Pan J., Thirumalai D., Woodson S. A. Magnesium-dependent folding of self-splicing RNA: exploring the link between cooperativity, thermodynamics, and kinetics. Proc Natl Acad Sci U S A. 1999 May 25;96(11):6149–6154. doi: 10.1073/pnas.96.11.6149. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Pan J., Woodson S. A. Folding intermediates of a self-splicing RNA: mispairing of the catalytic core. J Mol Biol. 1998 Jul 24;280(4):597–609. doi: 10.1006/jmbi.1998.1901. [DOI] [PubMed] [Google Scholar]
  23. Pan J., Woodson S. A. The effect of long-range loop-loop interactions on folding of the Tetrahymena self-splicing RNA. J Mol Biol. 1999 Dec 10;294(4):955–965. doi: 10.1006/jmbi.1999.3298. [DOI] [PubMed] [Google Scholar]
  24. Pan T. Higher order folding and domain analysis of the ribozyme from Bacillus subtilis ribonuclease P. Biochemistry. 1995 Jan 24;34(3):902–909. doi: 10.1021/bi00003a024. [DOI] [PubMed] [Google Scholar]
  25. Pan T., Sosnick T. R. Intermediates and kinetic traps in the folding of a large ribozyme revealed by circular dichroism and UV absorbance spectroscopies and catalytic activity. Nat Struct Biol. 1997 Nov;4(11):931–938. doi: 10.1038/nsb1197-931. [DOI] [PubMed] [Google Scholar]
  26. Rook M. S., Treiber D. K., Williamson J. R. An optimal Mg(2+) concentration for kinetic folding of the tetrahymena ribozyme. Proc Natl Acad Sci U S A. 1999 Oct 26;96(22):12471–12476. doi: 10.1073/pnas.96.22.12471. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. Rook M. S., Treiber D. K., Williamson J. R. Fast folding mutants of the Tetrahymena group I ribozyme reveal a rugged folding energy landscape. J Mol Biol. 1998 Aug 28;281(4):609–620. doi: 10.1006/jmbi.1998.1960. [DOI] [PubMed] [Google Scholar]
  28. Russell R., Herschlag D. New pathways in folding of the Tetrahymena group I RNA enzyme. J Mol Biol. 1999 Sep 3;291(5):1155–1167. doi: 10.1006/jmbi.1999.3026. [DOI] [PubMed] [Google Scholar]
  29. Sclavi B., Sullivan M., Chance M. R., Brenowitz M., Woodson S. A. RNA folding at millisecond intervals by synchrotron hydroxyl radical footprinting. Science. 1998 Mar 20;279(5358):1940–1943. doi: 10.1126/science.279.5358.1940. [DOI] [PubMed] [Google Scholar]
  30. Treiber D. K., Rook M. S., Zarrinkar P. P., Williamson J. R. Kinetic intermediates trapped by native interactions in RNA folding. Science. 1998 Mar 20;279(5358):1943–1946. doi: 10.1126/science.279.5358.1943. [DOI] [PubMed] [Google Scholar]
  31. Treiber D. K., Williamson J. R. Exposing the kinetic traps in RNA folding. Curr Opin Struct Biol. 1999 Jun;9(3):339–345. doi: 10.1016/S0959-440X(99)80045-1. [DOI] [PubMed] [Google Scholar]
  32. Westhof E., Masquida B., Jaeger L. RNA tectonics: towards RNA design. Fold Des. 1996;1(4):R78–R88. doi: 10.1016/S1359-0278(96)00037-5. [DOI] [PubMed] [Google Scholar]
  33. Wu M., Tinoco I., Jr RNA folding causes secondary structure rearrangement. Proc Natl Acad Sci U S A. 1998 Sep 29;95(20):11555–11560. doi: 10.1073/pnas.95.20.11555. [DOI] [PMC free article] [PubMed] [Google Scholar]
  34. Zarrinkar P. P., Wang J., Williamson J. R. Slow folding kinetics of RNase P RNA. RNA. 1996 Jun;2(6):564–573. [PMC free article] [PubMed] [Google Scholar]
  35. 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]
  36. Zarrinkar P. P., Williamson J. R. The kinetic folding pathway of the Tetrahymena ribozyme reveals possible similarities between RNA and protein folding. Nat Struct Biol. 1996 May;3(5):432–438. doi: 10.1038/nsb0596-432. [DOI] [PubMed] [Google Scholar]

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