RiboMaker: computational design of conformation-based riboregulation.
BACKGROUND
The ability to engineer control systems of gene expression is instrumental for synthetic biology. Thus, bioinformatic methods that assist such engineering are appealing because they can guide the sequence design and prevent costly experimental screening. In particular, RNA is an ideal substrate to de novo design regulators of protein expression by following sequence-to-function models.


RESULTS
We have implemented a novel algorithm, RiboMaker, aimed at the computational, automated design of bacterial riboregulation. RiboMaker reads the sequence and structure specifications, which codify for a gene regulatory behaviour, and optimizes the sequences of a small regulatory RNA and a 5'-untranslated region for an efficient intermolecular interaction. To this end, it implements an evolutionary design strategy, where random mutations are selected according to a physicochemical model based on free energies. The resulting sequences can then be tested experimentally, providing a new tool for synthetic biology, and also for investigating the riboregulation principles in natural systems.


METHODS
Web server is available at http://ribomaker.jaramillolab.org/. Source code, instructions and examples are freely available for download at http://sourceforge.net/projects/ribomaker/.
Institute of Systems and Synthetic Biology, CNRS - Université d'Évry Val d'Essonne, F-91000 Évry, France and School of Life Sciences, University of Warwick, Coventry CV4 7AL, United Kingdom.
Guillermo
G
Rodrigo
Institute of Systems and Synthetic Biology, CNRS - Université d'Évry Val d'Essonne, F-91000 Évry, France and School of Life Sciences, University of Warwick, Coventry CV4 7AL, United Kingdom Institute of Systems and Synthetic Biology, CNRS - Université d'Évry Val d'Essonne, F-91000 Évry, France and School of Life Sciences, University of Warwick, Coventry CV4 7AL, United Kingdom.
Alfonso
A
Jaramillo
D020121:5' Untranslated Regions; D000465:Algorithms; D001419:Bacteria / Q000235:genetics; D001483:Base Sequence; D019295:Computational Biology / Q000379:methods; D009690:Nucleic Acid Conformation; D058727:RNA, Small Untranslated / Q000737:chemistry*; D038621:Regulatory Sequences, Ribonucleic Acid; D012984:Software; D058615:Synthetic Biology
D020121:5' Untranslated Regions; D058727:RNA, Small Untranslated; D038621:Regulatory Sequences, Ribonucleic Acid