RNAblueprint: Flexible multiple target nucleic acid sequence design

Bioinformatics

Volumn 33, Issue 18, 2017, Pages 2850-2858

  Hammer, Stefan ^a,b   Tschiatschek, Birgit ^b   Flamm, Christoph ^a,c   Hofacker, Ivo L ^a,b,d   Findeiß, Sven ^a,b  

^a Department of Analytical Chemistry   (United States)

^b Research Group Bioinformatics and Computational Biology   (United States)

^c UNIVERSITY OF VIENNA   (Austria)

^d UNIVERSITY OF COPENHAGEN   (Denmark)

Author keywords

[No Author keywords available]

Indexed keywords

RNA;

CHEMISTRY; CONFORMATION; MOLECULAR MODEL; PROCEDURES; SOFTWARE; SYNTHETIC BIOLOGY;

MODELS, MOLECULAR; NUCLEIC ACID CONFORMATION; RNA; SOFTWARE; SYNTHETIC BIOLOGY;

EID: 85028724882     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btx263     Document Type: Article

References (26)

1. Abfalter,I.G. et al. (2003) Design of multi-stable nucleic acid sequences. In: Mewes,H.W. et al. (eds.) In: Proceedings of the German Conference on Bioinformatics (GCB). Belleville Verlag, Michael Farin, München, vol. 1, pp. 1-7.
2. Berens,C. and Suess,B. (2015) Riboswitch engineering-making the allimportant second and third steps. Curr. Opin. Biotechnol., 31, 10-15.
3. Chappell,J. et al. (2015) Creating small transcription activating RNAs. Nat. Chem. Biol., 11, 214-220.
4. Espah-Borujeni,A. et al. (2015) Automated physics-based design of synthetic riboswitches from diverse RNA aptamers. Nucleic Acids Res., gkv1289.
5. Flamm,C. et al. (2001) Design of multistable RNA molecules. RNA, 7, 254-265.
6. Garcia-Martin,J.A. et al. (2015) RNAiFold 2.0: a web server and software to design custom and rfam-based RNA molecules. Nucleic Acids Res., 43, W513-W521.
7. Green,A.A. et al. (2014) Toehold switches: de-novo-designed regulators of gene expression. Cell, 159, 925-939.
8. Hofacker,I.L. et al. (1994) Fast folding and comparison of RNA secondary structures. Monatshefte Für Chemie/Chem. Mon., 125, 167-188.
9. Höner zu Siederdissen,C. et al. (2013) Computational design of RNAs with complex energy landscapes. Biopolymers, 99, 1124-1136.
10. Isaacs,F.J. et al. (2004) Engineered riboregulators enable post-transcriptional control of gene expression. Nat. Biotechnol., 22, 841-847.
11. Janssen,S. and Giegerich,R. (2015) The RNA shapes studio. Bioinformatics, 31, 423-425.
12. Lorenz,R. et al. (2011) ViennaRNA Package 2.0. Algorithms Mol. Biol., 6, 26.
13. Lorenz,R. et al. (2016) RNA folding with hard and soft constraints. Algorithms Mol. Biol., 11, 8.
14. Lyngso,R.B. et al. (2012) Frnakenstein: multiple target inverse RNA folding. BMC Bioinformatics, 13, 260.
15. Maon,Y. et al. (1986) Parallel ear decomposition search (EDS) and STnumbering in graphs. Theor. Comp. Sci., 47, 277-298.
16. Michael Mitzenmacher,E.U. (2005) Probability and Computing: Randomized Algorithms and Probabilistic Analysis. Cambridge University, Puerto Rico.
17. Neupert,J. et al. (2008) Design of simple synthetic RNA thermometers for temperature-controlled gene expression in Escherichia coli. Nucleic Acids Res., 36, e124.
18. Qi,L. et al. (2012) Engineering naturally occurring trans-acting non-coding RNAs to sense molecular signals. Nucleic Acids Res, 40, 5775-5786.
19. Reinharz,V. et al. (2013) A weighted sampling algorithm for the design of RNA sequences with targeted secondary structure and nucleotide distribution. Bioinformatics, 29, i308-i315.
20. Rodrigo,G. and Jaramillo,A. (2014) RiboMaker: computational design of conformation-based riboregulation. Bioinformatics, 30, 2508-2510.
21. Rodrigo,G. et al. (2012) De novo automated design of small RNA circuits for engineering synthetic riboregulation in living cells. Proc. Natl. Acad. Sci. U. S. A., 109, 15271-15276.
22. Taneda,A. (2015) Multi-objective optimization for RNA design with multiple target secondary structures. BMC Bioinformatics, 16, 280.
23. Wachsmuth,M. et al. (2013) De novo design of a synthetic riboswitch that regulates transcription termination. Nucleic Acids Res., 41, 2541-2551.
24. Wolfe,B.R. and Pierce,N.A. (2015) Sequence design for a test tube of interacting nucleic acid strands. ACS Synth. Biol., 4, 1086-1100.
25. Zadeh,J.N. et al. (2011a) Nucleic acid sequence design via efficient ensemble defect optimization. J. Comput. Chem., 32, 439-452.
26. Zadeh,J.N. et al. (2011b) NUPACK: analysis and design of nucleic acid systems. J. Comput. Chem., 32, 170-173.