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Full design automation of multi-state RNA devices to program gene expression using energy-based optimization.

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Full design automation of multi-state RNA devices to program gene expression using energy-based optimization.

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Rodrigo Tarrega, G.; Landrain, TE.; Majer, E.; Daros Arnau, JA.; Jaramillo, A. (2013). Full design automation of multi-state RNA devices to program gene expression using energy-based optimization. PLoS Computational Biology. 9(8):1003172-1003172. https://doi.org/10.1371/journal.pcbi.1003172

Por favor, use este identificador para citar o enlazar este ítem: http://hdl.handle.net/10251/59787

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Title: Full design automation of multi-state RNA devices to program gene expression using energy-based optimization.
Author: Rodrigo Tarrega, Guillermo Landrain, Thomas E. Majer, Eszter Daros Arnau, Jose Antonio Jaramillo, Alfonso
UPV Unit: Universitat Politècnica de València. Instituto Universitario Mixto de Biología Molecular y Celular de Plantas - Institut Universitari Mixt de Biologia Molecular i Cel·lular de Plantes
Issued date:
Abstract:
[EN] Small RNAs (sRNAs) can operate as regulatory agents to control protein expression by interaction with the 59 untranslated region of the mRNA. We have developed a physicochemical framework, relying on base pair ...[+]
Subjects: Agents to control protein , Small RNAs (sRNAs)
Copyrigths: Reconocimiento (by)
Source:
PLoS Computational Biology. (issn: 1553-734X ) (eissn: 1553-7358 )
DOI: 10.1371/journal.pcbi.1003172
Publisher:
Public Library of Science
Publisher version: http://dx.doi.org/10.1371/journal.pcbi.1003172
Project ID: info:eu-repo/grantAgreement/EC/FP7/043338
Thanks:
Work supported by the grants FP7-ICT-043338 (BACTOCOM) to AJ, and BIO2011-26741 (Ministerio de Economia y Competitividad, Spain) to JAD. GR is supported by an EMBO long-term fellowship co-funded by Marie Curie actions ...[+]
Type: Artículo

References

Isaacs, F. J., Dwyer, D. J., & Collins, J. J. (2006). RNA synthetic biology. Nature Biotechnology, 24(5), 545-554. doi:10.1038/nbt1208

Isaacs, F. J., Dwyer, D. J., Ding, C., Pervouchine, D. D., Cantor, C. R., & Collins, J. J. (2004). Engineered riboregulators enable post-transcriptional control of gene expression. Nature Biotechnology, 22(7), 841-847. doi:10.1038/nbt986

Lucks, J. B., Qi, L., Mutalik, V. K., Wang, D., & Arkin, A. P. (2011). Versatile RNA-sensing transcriptional regulators for engineering genetic networks. Proceedings of the National Academy of Sciences, 108(21), 8617-8622. doi:10.1073/pnas.1015741108 [+]
Isaacs, F. J., Dwyer, D. J., & Collins, J. J. (2006). RNA synthetic biology. Nature Biotechnology, 24(5), 545-554. doi:10.1038/nbt1208

Isaacs, F. J., Dwyer, D. J., Ding, C., Pervouchine, D. D., Cantor, C. R., & Collins, J. J. (2004). Engineered riboregulators enable post-transcriptional control of gene expression. Nature Biotechnology, 22(7), 841-847. doi:10.1038/nbt986

Lucks, J. B., Qi, L., Mutalik, V. K., Wang, D., & Arkin, A. P. (2011). Versatile RNA-sensing transcriptional regulators for engineering genetic networks. Proceedings of the National Academy of Sciences, 108(21), 8617-8622. doi:10.1073/pnas.1015741108

Mutalik, V. K., Qi, L., Guimaraes, J. C., Lucks, J. B., & Arkin, A. P. (2012). Rationally designed families of orthogonal RNA regulators of translation. Nature Chemical Biology, 8(5), 447-454. doi:10.1038/nchembio.919

Bayer, T. S., & Smolke, C. D. (2005). Programmable ligand-controlled riboregulators of eukaryotic gene expression. Nature Biotechnology, 23(3), 337-343. doi:10.1038/nbt1069

Nakashima, N., & Tamura, T. (2009). Conditional gene silencing of multiple genes with antisense RNAs and generation of a mutator strain of Escherichia coli. Nucleic Acids Research, 37(15), e103-e103. doi:10.1093/nar/gkp498

Callura, J. M., Cantor, C. R., & Collins, J. J. (2012). Genetic switchboard for synthetic biology applications. Proceedings of the National Academy of Sciences, 109(15), 5850-5855. doi:10.1073/pnas.1203808109

Beisel, C. L., Bayer, T. S., Hoff, K. G., & Smolke, C. D. (2008). Model‐guided design of ligand‐regulated RNAi for programmable control of gene expression. Molecular Systems Biology, 4(1), 224. doi:10.1038/msb.2008.62

Qi, L., Lucks, J. B., Liu, C. C., Mutalik, V. K., & Arkin, A. P. (2012). Engineering naturally occurring trans -acting non-coding RNAs to sense molecular signals. Nucleic Acids Research, 40(12), 5775-5786. doi:10.1093/nar/gks168

Carothers, J. M., Goler, J. A., Juminaga, D., & Keasling, J. D. (2011). Model-Driven Engineering of RNA Devices to Quantitatively Program Gene Expression. Science, 334(6063), 1716-1719. doi:10.1126/science.1212209

Rodrigo, G., Landrain, T. E., & Jaramillo, A. (2012). De novo automated design of small RNA circuits for engineering synthetic riboregulation in living cells. Proceedings of the National Academy of Sciences, 109(38), 15271-15276. doi:10.1073/pnas.1203831109

Brantl, S. (2002). Antisense-RNA regulation and RNA interference. Biochimica et Biophysica Acta (BBA) - Gene Structure and Expression, 1575(1-3), 15-25. doi:10.1016/s0167-4781(02)00280-4

Majdalani, N., Vanderpool, C. K., & Gottesman, S. (2005). Bacterial Small RNA Regulators. Critical Reviews in Biochemistry and Molecular Biology, 40(2), 93-113. doi:10.1080/10409230590918702

Selinger, D. W., Cheung, K. J., Mei, R., Johansson, E. M., Richmond, C. S., Blattner, F. R., … Church, G. M. (2000). RNA expression analysis using a 30 base pair resolution Escherichia coli genome array. Nature Biotechnology, 18(12), 1262-1268. doi:10.1038/82367

Yelin, R., Dahary, D., Sorek, R., Levanon, E. Y., Goldstein, O., Shoshan, A., … Rotman, G. (2003). Widespread occurrence of antisense transcription in the human genome. Nature Biotechnology, 21(4), 379-386. doi:10.1038/nbt808

Wang, X.-J., Gaasterland, T., & Chua, N.-H. (2005). Genome Biology, 6(4), R30. doi:10.1186/gb-2005-6-4-r30

Stojanovic, M. N., & Stefanovic, D. (2003). A deoxyribozyme-based molecular automaton. Nature Biotechnology, 21(9), 1069-1074. doi:10.1038/nbt862

Seelig, G., Soloveichik, D., Zhang, D. Y., & Winfree, E. (2006). Enzyme-Free Nucleic Acid Logic Circuits. Science, 314(5805), 1585-1588. doi:10.1126/science.1132493

Yin, P., Choi, H. M. T., Calvert, C. R., & Pierce, N. A. (2008). Programming biomolecular self-assembly pathways. Nature, 451(7176), 318-322. doi:10.1038/nature06451

Ran, T., Kaplan, S., & Shapiro, E. (2009). Molecular implementation of simple logic programs. Nature Nanotechnology, 4(10), 642-648. doi:10.1038/nnano.2009.203

Penchovsky, R., & Breaker, R. R. (2005). Computational design and experimental validation of oligonucleotide-sensing allosteric ribozymes. Nature Biotechnology, 23(11), 1424-1433. doi:10.1038/nbt1155

Salis, H. M., Mirsky, E. A., & Voigt, C. A. (2009). Automated design of synthetic ribosome binding sites to control protein expression. Nature Biotechnology, 27(10), 946-950. doi:10.1038/nbt.1568

Laidler, K. J., & King, M. C. (1983). Development of transition-state theory. The Journal of Physical Chemistry, 87(15), 2657-2664. doi:10.1021/j100238a002

Sosnick, T. R., & Pan, T. (2003). RNA folding: models and perspectives. Current Opinion in Structural Biology, 13(3), 309-316. doi:10.1016/s0959-440x(03)00066-6

Yurke, B. (2003). Genetic Programming and Evolvable Machines, 4(2), 111-122. doi:10.1023/a:1023928811651

Bandyra, K. J., Said, N., Pfeiffer, V., Górna, M. W., Vogel, J., & Luisi, B. F. (2012). The Seed Region of a Small RNA Drives the Controlled Destruction of the Target mRNA by the Endoribonuclease RNase E. Molecular Cell, 47(6), 943-953. doi:10.1016/j.molcel.2012.07.015

Dawid, A., Cayrol, B., & Isambert, H. (2009). RNA synthetic biology inspired from bacteria: construction of transcription attenuators under antisense regulation. Physical Biology, 6(2), 025007. doi:10.1088/1478-3975/6/2/025007

Lioliou, E., Romilly, C., Romby, P., & Fechter, P. (2010). RNA-mediated regulation in bacteria: from natural to artificial systems. New Biotechnology, 27(3), 222-235. doi:10.1016/j.nbt.2010.03.002

Dirks, R. M., Bois, J. S., Schaeffer, J. M., Winfree, E., & Pierce, N. A. (2007). Thermodynamic Analysis of Interacting Nucleic Acid Strands. SIAM Review, 49(1), 65-88. doi:10.1137/060651100

Das, R., Karanicolas, J., & Baker, D. (2010). Atomic accuracy in predicting and designing noncanonical RNA structure. Nature Methods, 7(4), 291-294. doi:10.1038/nmeth.1433

Vogel, J., & Luisi, B. F. (2011). Hfq and its constellation of RNA. Nature Reviews Microbiology, 9(8), 578-589. doi:10.1038/nrmicro2615

Friedland, A. E., Lu, T. K., Wang, X., Shi, D., Church, G., & Collins, J. J. (2009). Synthetic Gene Networks That Count. Science, 324(5931), 1199-1202. doi:10.1126/science.1172005

Rodrigo, G., Carrera, J., Landrain, T. E., & Jaramillo, A. (2012). Perspectives on the automatic design of regulatory systems for synthetic biology. FEBS Letters, 586(15), 2037-2042. doi:10.1016/j.febslet.2012.02.031

Chin, J. W. (2006). Modular approaches to expanding the functions of living matter. Nature Chemical Biology, 2(6), 304-311. doi:10.1038/nchembio789

McCaskill, J. S. (1990). The equilibrium partition function and base pair binding probabilities for RNA secondary structure. Biopolymers, 29(6-7), 1105-1119. doi:10.1002/bip.360290621

Chitsaz, H., Salari, R., Sahinalp, S. C., & Backofen, R. (2009). A partition function algorithm for interacting nucleic acid strands. Bioinformatics, 25(12), i365-i373. doi:10.1093/bioinformatics/btp212

Hofacker, I. L., Fontana, W., Stadler, P. F., Bonhoeffer, L. S., Tacker, M., & Schuster, P. (1994). Fast folding and comparison of RNA secondary structures. Monatshefte f�r Chemie Chemical Monthly, 125(2), 167-188. doi:10.1007/bf00818163

Andronescu, M., Zhang, Z. C., & Condon, A. (2005). Secondary Structure Prediction of Interacting RNA Molecules. Journal of Molecular Biology, 345(5), 987-1001. doi:10.1016/j.jmb.2004.10.082

Mathews, D. H., Sabina, J., Zuker, M., & Turner, D. H. (1999). Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure. Journal of Molecular Biology, 288(5), 911-940. doi:10.1006/jmbi.1999.2700

Kirkpatrick, S., Gelatt, C. D., & Vecchi, M. P. (1983). Optimization by Simulated Annealing. Science, 220(4598), 671-680. doi:10.1126/science.220.4598.671

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