Extended shapes for the combinatorial design of RNA sequences

International Journal of Computational Biology and Drug Design

Volumn 2, Issue 4, 2009, Pages 371-384

  Hellmuth, Marc ^a   Merkle, Daniel ^b   Middendorf, Martin ^a  

^a UNIVERSITY OF LEIPZIG   (Germany)

^b UNIVERSITY OF SOUTHERN DENMARK   (Denmark)

Author keywords

Aptamer; Computational biology; Drug design; Extended shapes; NP completeness; Rna design; Rna folding; Secondary structure

Indexed keywords

APTAMER; RNA;

ARTICLE; BASE PAIRING; COMBINATORIAL CHEMISTRY; PROTEIN SECONDARY STRUCTURE; RNA SEQUENCE; RNA STRUCTURE; STRUCTURE ANALYSIS;

EID: 77953667079     PISSN: 17560756     EISSN: 17560764     Source Type: Journal    
DOI: 10.1504/IJCBDD.2009.030767     Document Type: Article

References (16)

1. 2+-dependent RNA-RNA interactions', Nano Lett., Vol. 6, pp. 445-448.
2. Berens, C. and Suess, B. (2005) 'Synthetic riboregulators an alternative means to control gene expression', Gene Ther. Mol. Biol., Vol. 9, pp. 417-422.
3. Clote, P., Leszek, G., Kolpakov, R., Kranakis, E. and Krizanc, D. (2005) 'On realizing shapes in the theory of RNA neutral networks', Journal of Theoretical Biology, Vol. 236, pp. 216-227.
4. Flamm, C., Hofacker, I. L., Mauer-Stroh, S., Stadler, P. F. and Zehl, M. (2001) 'Design of multistable RNA molecules', RNA, Vol. 7, pp. 254-265.
5. Harary, F. (1954) 'On the notion of balance of a signed graph', Michigan Mathematical Journal, Vol. 2, pp. 143-146.
6. Hofacker, I. L. (2009) 'RNA secondary structure analysis using the Vienna RNA package', Curr. Protoc. Bioinform., Vol. 26, pp. 12.2.1-12.2.16.
7. Lee, J. F., Hesselberth, J. R., Ancel Meyers, L. and Ellington, A. D. (2004) 'Aptamer database', Nucleic Acids Res., Vol. 32, pp. D95-D100.
8. Loukakis, E. (2003) 'A dynamic programming algorithm to test a signed graph for balance', Intern. J. Computer Math., Vol. 80, No. 4, pp. 499-507.
9. Reidys, C., Stadler, P. F. and Schuster, P. (1997) 'Generic properties of combinatory maps: neutral networks of RNA secondary structures', Bull. Biol. 59, Vol. 2, pp. 339-397.
10. Severcan, I., Geary, C., Jaeger, L., Bindewald, E., Kasprzak, W. and Shapiro, B. A. (2009) 'Computational and experimental RNA nanoparticle design', Automation in Genomics and Proteomics: An Engineering Case-Based Approach, Chichester, West Sussex, UK, pp. 193-220.
11. Silverman, S. K. (2003) 'Rube goldberg goes (ribo) nuclear? Molecular switches and sensors made from RNA', RNA, Vol. 9, pp. 377-383.
12. Silverman, S. K. (2006) Nucleic Acid Switches and Sensors, Springer, New York.
13. Soukup, G. A. and Breaker, R. R. (1999) 'Engineering precision RNA molecular switches', PNAS, Vol. 96, pp. 3584-3589.
14. Staple, D. W. and Butcher, S. E. (2005) 'Pseudoknots: RNA structures with diverse functions', PLoS Biology 3, Vol. 6, p. e213.
15. von Ahsen, U. (1998) 'Translational fidelity: error-prone vs. hyper-accurate ribosomes', Chem. Biol. 5, Vol. 1, pp. R3-R6.
16. Yannakakis, M. (1981) 'Edge deletion problems', SIAM Journal on Computing, Vol. 10, pp. 297-309.