Description of RNA folding by "simulated annealing"

Journal of Molecular Biology

Volumn 255, Issue 1, 1996, Pages 254-266

  Schmitz, Michael ^a   Steger, Gerhard ^a  

^a NONE

Author keywords

Kinetics; Monte carlo; Potato spindle tuber viroid; Secondary structure; Sequential folding

Indexed keywords

RNA POLYMERASE;

ALGORITHM; ARTICLE; COMPUTER SIMULATION; KINETICS; PRIORITY JOURNAL; RNA STRUCTURE; RNA TRANSCRIPTION; SYSTEM ANALYSIS; THERMODYNAMICS;

EID: 0029975949     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1996.0021     Document Type: Article

References (34)

1. Baumstark, T. & Riesner, D. (1995). Only one of four possible secondary structures of the central conserved region of potato spindle tuber viroid is a substrate for processing in a potato nuclear extract. Nucl. Acids Res. 23(21), in the press.
2. Bellman, R. & Kalaba, R. (1960). On kth best policies. SIAM J. Appl. Math. 8, 582-588.
3. Diener, T. O. (1987). Editor of The Viroids. Plenum Press, New York.
4. Gross, H. J., Domdey H., Lossow, C., Jank, P., Raba, M., Alberty H. & Sänger, H. L. (1978). Nucleotide sequence and secondary structure of potato spindle tuber viroid. Nature, 273, 203-208.
5. Gruner, R., Fels, A., Qu, F., Zimmat, R., Steger, G. & Riesner, D. (1995). Interdependence of pathogenicity and replicability with potato spindle tuber viroid (PSTVd). Virology, 209, 60-69.
6. Henco, K. (1979). Viroids: a class of ribonucleic acids with an extraordinary structural and dynamic principle. Thesis, Technische Universität Hannover.
7. Henco, K., Sänger, H. L. & Riesner, D. (1979). Fine structure melting of viroids as studied by kinetic methods. Nucl. Acids Res. 6, 3041-3059.
8. Jaeger, J. A., Turner, D. H. & Zuker, M. (1990). Predicting optimal and suboptimal secondary structure for RNA. Methods Enzymol. 183, 281-306.
9. Kirkpatrick, S., Gelatt, C. D. & Vecchi, M. P. (1983). Optimization by simulated annealing. Science, 220, 671-680.
10. Loss, P., Schmitz, M., Steger, G. & Riesner, D. (1991). Formation of a thermodynamically metastable structure containing hairpin II is critical for infectivity of potato spindle tuber viroid. EMBO J. 10, 719-727.
11. Martinez, H. M. (1984). An RNA folding rule. Nucl. Acids Res. 12, 323-334.
12. McCaskill, J. S. M. (1990). The equilibrium partition function and base pair binding probabilities for RNA secondary structure. Biopolymers, 29, 1105-1119.
13. Metropolis, N., Rosenbluth, A. W., Rosenbluth, M. N., Teller, A. H. & Teller, E. (1953). Equation of state calculations by fast computing machines. J. Chem. Phys. 21, 1087-1092.
14. Mironov, A. & Kister, A. (1986). RNA secondary structure formation during transcription. J. Biomol. Struct. Dynam. 4, 1-9.
15. Mironov, A. A., Dyakonova, L. P. & Kister, A. E. (1985). A kinetic approach to the prediction of RNA secondary structures. J. Biomol. Struct. Dynam. 2, 953-962.
16. Nussinov, R., Pieczenik, G., Griggs, J. R. & Kleitman, D. J. (1978). Algorithms for loop matchings. SIAM J. Appl. Math. 35, 68-82.
17. Pleij, C. W. A. (1990). Pseudoknots: a new motif in the RNA game. Trends Biochem. Sci. 15, 143-147.
18. Qu, F., Heinrich, C., Loss, P., Steger, G., Tien, P. & Riesner, D. (1993). Multiple pathways of reversion in viroids for conservation of structural elements. EMBO J. 12, 2129-2139.
19. Randles, J. W., Steger, G. & Riesner, D. (1982). Structural transitions in viroid-like RNAs associated with cadang-cadang disease, velvet tobacco mottle virus, and Solanum nodiflorum mottle virus. Nucl. Acids Res. 10, 5569-5586.
20. Riesner, D., Henco, K., Rokohl, U, Klotz, G., Kleinschmidt, A. K., Gross, H. J., Domdey H., Jank, P. & Sänger, H. E. (1979). Structure and structure formation of viroids. J. Mol. Biol. 133, 85-115.
21. Rosenbaum, V., Klahn, T., Lundberg, U., Holmgren, E., von Gabain, A. & Riesner, D. (1993). Co-existing structures of an mRNA stability determinant. The 5′ region of the Escherichia coli and Serratia marcescens ompA mRNA. J. Mol. Biol. 229, 656-670.
22. Schindler, I.-M. & Mühlbach, H.-P. (1992). Involvement of nuclear DNA-dependent RNA polymerases into potato spindle tuber viroid replication: a re-evaluation. Plant Sci. 84, 221-229.
23. Schmitz, M. & Steger, G. (1992). Base-pair probability profiles of RNA secondary structures. Comp. Appl. Biosci. 8, 389-399.
24. Schnölzer, M., Haas, B., Ramm, K., Hofmann, H. & Sänger, H. L. (1985). Correlation between structure and pathogenicity of potato spindle tuber viroid (PSTV). EMBO J. 4, 2181-2190.
25. Steger, G., Hofmann, H., Förtsch, J., Gross, H. J., Randles, J. W., Sänger, H. L. & Riesner, D. (1984). Conformational transitions in viroids and virusoids: comparison of results from energy minimization algorithm and from experimental data. J. Biomol. Struct. Dynam. 2, 543-571.
26. Steger, G., Baumstark, T., Mörchen, M., Riesner, D., Tabler, M., Tsagris, & Sänger, H. L. (1992). Structural requirements for viroid processing: correlation between processing data, thermodynamic studies and model calculations. J. Mol. Biol. 227, 719-737.
27. Tinoco, I., Jr, Uhlenbeck, O. C. & Levine, M. D. (1971). Estimation of secondary structure in ribonucleic acids. Nature, 230, 363-367.
28. Tinoco, I., Jr, Puglisi, J. D. & Wyatt, J. R. (1990). RNA folding. Nucl. Acids Mol. Biol. 4, 205-226.
29. Tsagris, M., Tabler, M. & Sänger, H. L. (1987). Oligomeric potato spindle tuber viroid RNA does not process autocatalytically under conditions where other RNAs do. Virology, 157, 227-231.
30. Turner, D. H., Sugimoto, N. & Freier, S. M. (1990). Thermodynamics and kinetics of base-pairing and of DNA and RNA self-assembly and helix-coil transition. In Landolt-Börnstein, Group VII: Biophysics, vol. 1 Nucleic Acids, subvol. c, Spectroscopic and Kinetic Data, Physical Data I. (Saenger, W., ed.), pp. 194-243, Springer Verlag, Berlin.
31. Waterman, M. S. & Smith, T. F. (1978). RNA secondary structure: a complete mathematical analysis. Math. Biosci. 42, 257-266.
32. Williams, A. L. & Tinoco, I., Jr (1986). A dynamic programming algorithm for finding alternative RNA secondary structures. Nucl. Acids Res. 14, 299-315.
33. Wyatt, J. R., Puglisi, J. D. & Tinoco, I., Jr (1989). RNA folding: pseudoknots, loops and bulges. Bioessays, 11, 100-106.
34. Zuker, M. & Stiegler, P. (1981). Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information. Nucl. Acids Res. 9, 133-148.