A New Algorithm for RNA Secondary Structure Design

Journal of Molecular Biology

Volumn 336, Issue 3, 2004, Pages 607-624

  Andronescu, Mirela ^a   Fejes, Anthony P ^a   Hutter, Frank ^a   Hoos, Holger H ^a   Condon, Anne ^a  

^a UNIVERSITY OF BRITISH COLUMBIA   (Canada)

Author keywords

RNA design; RNA inverse folding; RNA structure; Stochastic local search

Indexed keywords

RNA;

ALGORITHM; COMPUTER PROGRAM; DECOMPOSITION; DNA STRUCTURE; HYDROGEN BOND; NUCLEOTIDE SEQUENCE; PREDICTION; PRIORITY JOURNAL; PROTEIN FOLDING; REVIEW; RNA SEQUENCE; RNA STRUCTURE; STOCHASTIC MODEL;

EID: 0842268067     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2003.12.041     Document Type: Article

References (30)

1. Usman N., McSwiggen J. Catalytic RNA (ribozymes) as drugs. Annu. Rep. Med. Chem. 30:1995;285-294.
2. Cech T. Ribozyme engineering. Curr. Opin. Struct. Biol. 2:1992;605-609.
3. Winfree E., Liu F., Wenzler L., Seeman N. Design and self-assembly of 2D DNA crystals. Nature. 394:1998;539-544.
4. Lyngsø R., Zuker M., Pedersen C. Fast evaluation of internal loops in RNA secondary structure prediction. Bioinformatics. 15:1999;440-445.
5. Hofacker I., Fontana W., Stadler P., Bonhoeffer L., Tacker M., Schuster P. Fast folding and comparison of RNA secondary structures. Chem. Month. 125:1994;167-188.
6. Mathews D.H., Sabina J., Zuker M., Turner D.H. Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure. J. Mol. Biol. 288:1999;911-940.
7. Zuker A., Mathews B., Turner C. Algorithms and thermodynamics for RNA secondary structure prediction: a practical guide. Barszewski J., Clark B. RNA Biochemistry & Biotechnology. 1999;Kluwer Academic Publishers, Dordrecht.
8. Minton S., Johnston M., Philips A., Laird P. Minimizing conflicts: A heuristic repair method for constraint satisfaction and scheduling problems. Artif. Intell. 52:1992;161-205.
9. Heitsch C., Condon A., Hoos H.H. From RNA Secondary Structure to Coding Theory: A Combinatorial Approach. Proceedings of the Eighth International Workshop on DNA Based Computers, LNCS 2568. 2003;Springer, Berlin. pp. 215-228.
10. Seeman N. De novo design of sequences for nucleic acid structural engineering. J. Biomol. Struct. Dyn. 8:1990;573-581.
11. Hoos H.H., Stützle T. Evaluating Las Vegas Algorithms - Pitfalls and Remedies. Proceedings of the 14th Conference on Uncertainty in Artificial Intelligence. 1998;Morgan Kaufman, Los Altos, CA. pp. 238-245.
12. Schuster P., Fontana W., Stadler P., Hofacker I. From sequences to shapes and back: a case study in RNA secondary structures. Proc. R. Soc. Lond. ser. B. 255:1994;279-284.
13. Clark D., Frank J., Gent I., MacIntyre E., Tomov N., Walsh T. Local Search and the Number Of Solutions. Proceedings of the Second International Conference on Principles and Practice of Constraint Programming, LNCS 1118. 1996;Springer, Berlin. pp. 119-133.
14. Hoos, H. H. (1998). Stochastic local search - methods, models, applications. PhD Thesis, Department of Computer Science, Darmstadt University of Technology.
15. Rivas E., Eddy S. A dynamic programming algorithm for RNA structure prediction including pseduoknots. J. Mol. Biol. 285:1999;2053-2068.
16. Gultaev A., van Batenberg F., Pleij C. The computer simulation of RNA folding pathways using a genetic algorithm. J. Mol. Biol. 250:1995;37-51.
17. Andronescu M., Aguirre-Hernández R., Condon A., Hoos H.H. RNAsoft: a suite of RNA secondary structure prediction and design software tools. Nucl. Acids. Res. 31:2003;3416-3422.
18. Steinmann O., Stützle T., Strohmaier A. Tabu search versus random walk. Advances in Artificial Intelligence, LNCS 1303. 1997;Springer, Berlin.
19. Mao C., LaBean T.H., Reif J.H., Seeman N.C. Logical computation using algorithmic self-assembly of DNA triple-crossover molecules. Nature. 407:2000;493-496.
20. Yurke B., Turberfield A., Mills F.S.A.P. Jr, Newmann J. A DNA-fuelled molecular machine made of DNA. Nature. 406:2000;605-608.
21. Fedor M.J. Structure and function of the hairpin ribozyme. J. Mol. Biol. 297:2000;269-291.
22. Antal M., Mougin A., Kis M., Boros E., Steger G., Jakab G., et al. Molecular characterization at the RNA and gene levels of U3 snoRNA from a unicellular green alga, chlamydomonas reinhardtii. Nucl. Acids Res. 28:2000;2959-2968.
23. Szymanski M., Barciszewska M., Erdmann V., Barciszewski J. 5 S ribosomal RNA database. Nucl. Acids Res. 30:2002;176-178.
24. Lafontaine D., Norman D., Lilley D. Structure, folding, and activity of the vs ribozyme: importance of the 2-3-6 helical junction. EMBO J. 20:2001;1415-1424.
25. Sun Z.C.L., Gottlieb R., Zhang B. A selected ribozyme catalyzing diverse dipeptide synthesis. Chem. Biol. 9:2002;619-628.
26. Mobley E., Pan T. Design and isolation of ribozyme-substrate pairs using RNase P-based ribozymes containing altered substrate binding sites. Nucl. Acids Res. 27:1999;4298-4304.
27. Pitulle C., Garcia-Paris M., Zamudio K.R., Pace N.R. Comparative structure analysis of vertebrate ribonuclease P RNA. Nucl. Acids Res. 26:1998;3333-3339.
28. Mackie G. Secondary structure of the mRNA for ribosomal protein S20. Implications for cleavage by ribonuclease E. J. Biol. Chem. 267:1992;1054-1061.
29. Haas E., Armbruster D., Vucson B., Daniels C., Brown J. Comparative analysis of ribonuclease P RNA structure in Archaea. Nucl. Acids Res. 24:1996;1252-1259.
30. Swisher J., Duartel C., Sul L., Pyle A. Visualizing the solvent-inaccessible core of a group ii intron ribozyme. EMBO J. 20:2001;2051-2061.