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. 2000 Mar;6(3):325–338. doi: 10.1017/s1355838200992161

RNA folding at elementary step resolution.

C Flamm 1, W Fontana 1, I L Hofacker 1, P Schuster 1
PMCID: PMC1369916  PMID: 10744018

Abstract

We study the stochastic folding kinetics of RNA sequences into secondary structures with a new algorithm based on the formation, dissociation, and the shifting of individual base pairs. We discuss folding mechanisms and the correlation between the barrier structure of the conformational landscape and the folding kinetics for a number of examples based on artificial and natural sequences, including the influence of base modification in tRNAs.

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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. Breton N., Jacob C., Daegelen P. Prediction of sequentially optimal RNA secondary structures. J Biomol Struct Dyn. 1997 Jun;14(6):727–740. doi: 10.1080/07391102.1997.10508175. [DOI] [PubMed] [Google Scholar]
  3. Fontana W., Schuster P. A computer model of evolutionary optimization. Biophys Chem. 1987 May 9;26(2-3):123–147. doi: 10.1016/0301-4622(87)80017-0. [DOI] [PubMed] [Google Scholar]
  4. Gultyaev A. P., van Batenburg F. H., Pleij C. W. The computer simulation of RNA folding pathways using a genetic algorithm. J Mol Biol. 1995 Jun 30;250(1):37–51. doi: 10.1006/jmbi.1995.0356. [DOI] [PubMed] [Google Scholar]
  5. Huynen M., Gutell R., Konings D. Assessing the reliability of RNA folding using statistical mechanics. J Mol Biol. 1997 Apr 18;267(5):1104–1112. doi: 10.1006/jmbi.1997.0889. [DOI] [PubMed] [Google Scholar]
  6. McCaskill J. S. The equilibrium partition function and base pair binding probabilities for RNA secondary structure. Biopolymers. 1990 May-Jun;29(6-7):1105–1119. doi: 10.1002/bip.360290621. [DOI] [PubMed] [Google Scholar]
  7. Mironov A. A., Lebedev V. F. A kinetic model of RNA folding. Biosystems. 1993;30(1-3):49–56. doi: 10.1016/0303-2647(93)90061-g. [DOI] [PubMed] [Google Scholar]
  8. Nussinov R., Jacobson A. B. Fast algorithm for predicting the secondary structure of single-stranded RNA. Proc Natl Acad Sci U S A. 1980 Nov;77(11):6309–6313. doi: 10.1073/pnas.77.11.6309. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Pörschke D. Model calculations on the kinetics of oligonucleotide double helix coil transitions. Evidence for a fast chain sliding reaction. Biophys Chem. 1974 Aug;2(2):83–96. doi: 10.1016/0301-4622(74)80028-1. [DOI] [PubMed] [Google Scholar]
  10. Schmitz M., Steger G. Description of RNA folding by "simulated annealing". J Mol Biol. 1996 Jan 12;255(1):254–266. doi: 10.1006/jmbi.1996.0021. [DOI] [PubMed] [Google Scholar]
  11. Suvernev A. A., Frantsuzov P. A. Statistical description of nucleic acid secondary structure folding. J Biomol Struct Dyn. 1995 Aug;13(1):135–144. doi: 10.1080/07391102.1995.10508826. [DOI] [PubMed] [Google Scholar]
  12. Wuchty S., Fontana W., Hofacker I. L., Schuster P. Complete suboptimal folding of RNA and the stability of secondary structures. Biopolymers. 1999 Feb;49(2):145–165. doi: 10.1002/(SICI)1097-0282(199902)49:2<145::AID-BIP4>3.0.CO;2-G. [DOI] [PubMed] [Google Scholar]
  13. Zuker M., Stiegler P. Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information. Nucleic Acids Res. 1981 Jan 10;9(1):133–148. doi: 10.1093/nar/9.1.133. [DOI] [PMC free article] [PubMed] [Google Scholar]

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