RNA folding at elementary step resolution

RNA

Volumn 6, Issue 3, 2000, Pages 325-338

  Flamm, Christoph ^a,d   Fontana, Walter ^b,c   Hofacker, Ivo L ^a   Schuster, Peter ^a  

^a UNIVERSITY OF VIENNA   (Austria)

^b SANTA FE INSTITUTE   (United States)

^c INSTITUTE FOR ADVANCED STUDY   (United States)

^d Inst Theor Chem Molec S   (Austria)

Author keywords

Conformational spaces; Foldability; RNA folding kinetics; RNA secondary structure

Indexed keywords

RNA;

ALGORITHM; ARTICLE; KINETICS; PRIORITY JOURNAL; PROTEIN FOLDING; PROTEIN SECONDARY STRUCTURE; RNA ANALYSIS; RNA CONFORMATION; RNA SEQUENCE; RNA STRUCTURE; STOCHASTIC MODEL;

ALGORITHMS; BASE SEQUENCE; ENERGY TRANSFER; KINETICS; MOLECULAR SEQUENCE DATA; NUCLEIC ACID CONFORMATION; RNA; RNA, TRANSFER, PHE; THERMODYNAMICS;

EID: 0034021259     PISSN: 13558382     EISSN: None     Source Type: Journal    
DOI: 10.1017/S1355838200992161     Document Type: Article

References (27)

1. Banerjee AR, Jaeger JA, Turner DH. 1993. Thermal unfolding of a group I ribozyme:The low-temperature transition is primarily disruption of tertiary structure. Biochemistry 32:153-163.
2. Breton N, Jacob C, Daegelen P. 1997. Prediction of sequentially optimal RNA secondary structures. J Biomol Struct Dyn 14:727-740.
3. Fontana W, Schuster P. 1987. A computer model of evolutionary optimization. Biophys Chem 26:123-147.
4. Galzitskaya OV, Finkelstein AV. 1996. Computer simulation of secondary structure folding of random and "edited" RNA chains. J Chem Phys 105:319-325.
5. Gardiner CW. 1985. Handbook of stochastic methods for physics, chemistry and the natural sciences, 2nd ed. Berlin:Springer-Verlag.
6. Gillespie DT. 1976. A general method for numerically simulating the stochastic time evolution of coupled chemical reactions. J Comp Phys 22:403-434.
7. Gillespie DT. 1977. Exact stochastic simulation of coupled chemical reactions. J Phys Chem 81:2340-2361.
8. Gultyaev AP, van Batenburg FHD, Pleij CWA. 1995. The computer simulation of RNA folding pathways using a genetic algorithm. J Mol Biol 250:37-51.
9. Gutell RR. 1993. Evolutionary characteristics of RNA:Inferring higher order structure from patterns of sequence variation. Curr Opin Struct Biol 3:313-322.
10. Hofacker IL, Fontana W, Stadler PF, Bonhoeffer S, Tacker M, Schuster P. 1994. Fast folding and comparison of RNA secondary structures. Monatsh Chem 125:167-188.
11. Huynen M, Gutell R, Konings D. 1997. Assessing the reliability of RNA folding using statistical mechanics. J Mol Biol 267:1104-1112.
12. Jacob C, Breton N, Daegelen P. 1997a. Stochastic theories of the activated complex and the activated collision:The RNA example. J Chem Phys 107:2903-2912.
13. Jacob C, Breton N, Daegelen P, Peccoud J. 1997b. Probability distribution of the chemical states of a closed system and thermodynamic law of mass action from kinetics:The RNA example. J Chem Phys 107:2913-2919.
14. Kawasaki K. 1966. Diffusion constants near the critical point for time-dependent lsing models. Phys Rev 145:224-230.
15. McCaskill JS. 1990. The equilibrium partition function and base pair binding probabilities for RNA secondary structure. Biopolymers 29:1105-1119.
16. Metropolis N, Rosenbluth AW, Rosenbluth MN, Teller AH, Teller E. 1953. Equation of state calculations by fast computing machines. J Chem Phys 21:1087-1092.
17. Mironov A, Lebedev VF. 1993. A kinetic model of RNA folding. Bio-Systems 30:49-56.
18. Morgan SR, Higgs PG. 1996. Evidence for kinetic effects in the folding of large RNA molecules. J Chem Phys 105:7152-7157.
19. Nussinov R, Jacobson AB. 1980. Fast algorithm for predicting the secondary structure of single-stranded RNA. Proc Natl Acad Sd USA 77:6309-6313.
20. Pörschke D. 1974. Model calculations on the kinetics of oligonucleotide double helix coil transitions. Evidence for a fast chain sliding reaction. Biophys Chem 2:83-96.
21. Schmitz M, Steger G. 1996. Description of RNA folding by simulated annealing. J Mol Biol 225:254-266.
22. Suvernev AA, Frantsuzov PA. 1995. Statistical description of nucleic acid secondary structure folding. J Biomol Struct Dyn 13:135-144.
23. Tacker M, Stadler PF, Bornberg-Bauer EG, Hofacker IL, Schuster P. 1996. Algorithm independent properties of RNA secondary structure predictions. Eur Biophys J 25:115-130.
24. Thirumalai D, Woodson SA. 1996. Kinetics of folding of proteins and RNA. Acc Chem Res 29:433-439.
25. Waterman MS, Smith TF. 1978. RNA secondary structure:A complete mathematical analysis. Math Biosci 42:257-266.
26. Wuchty S, Fontana W, Hofacker IL, Schuster P. 1999. Complete suboptimal folding of RNA and the stability of secondary structures. Biopolymers 49:145-165.
27. Zuker M, Stiegler P. 1981. Optimal computer folding of larger RNA sequences using thermodynamics and auxiliary information. Nucleic Acids Res 9:133-148.