D. H. Kim and J. J. Rossi, Strategies for silencing human disease using RNA interference, Nature Reviews Genetics, vol.126, issue.3, pp.173-184, 2007.
DOI : 10.1038/nrg2006

L. J. Scherer and J. J. Rossi, Approaches for the sequence-specific knockdown of mRNA, Nature Biotechnology, vol.21, issue.12, pp.1457-1465, 2003.
DOI : 10.1038/nbt915

A. Serganov and D. J. Patel, Ribozymes, riboswitches and beyond: regulation of gene expression without proteins, Nature Reviews Genetics, vol.97, issue.10, pp.776-790, 2007.
DOI : 10.1038/nrg2172

M. Amarzguioui and H. Prydz, Hammerhead ribozyme design and application, Cellular and Molecular Life Sciences (CMLS), vol.54, issue.11, pp.1175-1202, 1998.
DOI : 10.1007/s000180050247

A. Khvorova, A. Lescoute, E. Westhof, and S. D. Jayasena, Sequence elements outside the hammerhead ribozyme catalytic core enable intracellular activity, Nature Structural Biology, vol.10, issue.9, pp.708-712, 2003.
DOI : 10.1038/nsb959

M. De-la-pena, S. Gago, and R. Flores, Peripheral regions of natural hammerhead ribozymes greatly increase their self-cleavage activity, The EMBO Journal, vol.22, issue.20, pp.5561-5570, 2003.
DOI : 10.1093/emboj/cdg530

T. Ohmichi and E. T. Kool, The virtues of self-binding: high sequence specificity for RNA cleavage by self-processed hammerhead ribozymes, Nucleic Acids Research, vol.28, issue.3, pp.776-783, 2000.
DOI : 10.1093/nar/28.3.776

D. Lévesque, F. P. Brì-ere, and J. P. Perreault, A Modern Mode of Activation for Nucleic Acid Enzymes, PLoS ONE, vol.46, issue.7, p.673, 2007.
DOI : 10.1371/journal.pone.0000673.s007

T. Kuwabara, M. Warashina, T. Tanabe, K. Tani, S. Asano et al., A Novel Allosterically trans-Activated Ribozyme, the Maxizyme, with Exceptional Specificity In Vitro and In Vivo, Molecular Cell, vol.2, issue.5, pp.617-627, 1998.
DOI : 10.1016/S1097-2765(00)80160-4

R. R. Breaker, Engineered allosteric ribozymes as biosensor components, Current Opinion in Biotechnology, vol.13, issue.1, pp.31-39, 2002.
DOI : 10.1016/S0958-1669(02)00281-1

N. K. Vaish, F. Dong, L. Andrews, R. E. Schweppe, N. G. Ahn et al., Monitoring post-translational modification of proteins with allosteric ribozymes, Nature Biotechnology, vol.11, issue.8, pp.810-815, 2002.
DOI : 10.1038/nbt719

N. Rusk, Microbiology: Prokaryotic RNAi, Nature Methods, vol.9, issue.3, pp.220-221, 2012.
DOI : 10.1016/j.molcel.2011.10.023

S. Lewin and W. W. Hauswirth, Ribozyme gene therapy: applications for molecular medicine, Trends in Molecular Medicine, vol.7, issue.5, pp.221-228, 2001.
DOI : 10.1016/S1471-4914(01)01965-7

E. M. Purnick and R. Weiss, The second wave of synthetic biology: from modules to systems, Nature Reviews Molecular Cell Biology, vol.307, issue.6, pp.410-422, 2009.
DOI : 10.1038/nrm2698

B. Brais, Oculopharyngeal muscular dystrophy: A polyalanine myopathy, Current Neurology and Neuroscience Reports, vol.124, issue.Pt3, pp.76-82, 2009.
DOI : 10.1007/s11910-009-0012-y

B. Brais, J. P. Bouchard, Y. G. Xie, D. L. Rochefort, N. Chrétien et al., Short GCG expansions in the PABP2 gene cause oculopharyngeal muscular dystrophy, Nature Genetics, vol.146, issue.2, pp.164-167, 1998.
DOI : 10.1016/0960-8966(93)90119-5

E. Rodríguez-lebrónlebr´lebrón, M. Docarmo-costa, K. Luna-cancalon, T. M. Peron, S. Fischer et al., Silencing mutant ATXN3 expression resolves molecular phenotypes in SCA3 transgenic mice, Mol. Ther, vol.21, 1909.

J. Hu, M. Matsui, K. T. Gagnon, J. C. Schwartz, S. Gabillet et al., Allele-specific silencing of mutant huntingtin and ataxin-3 genes by targeting expanded CAG repeats in mRNAs, Nature Biotechnology, vol.3, issue.5, pp.478-484, 2009.
DOI : 10.1038/nbt.1539

B. Nawrot, S. Antoszczyk, M. Maszewska, T. Kuwabara, M. Warashina et al., -driven and CTE-helicase associated hammerhead ribozymes, European Journal of Biochemistry, vol.19, issue.19, pp.3962-3970, 2003.
DOI : 10.1046/j.1432-1033.2003.03784.x
URL : https://hal.archives-ouvertes.fr/hal-00309347

M. Zoumadakis and M. Tabler, Comparative analysis of cleavage rates after systematic permutation of the NUX??? consensus target motif for hammerhead ribozymes, Nucleic Acids Research, vol.23, issue.7, pp.1192-1196, 1995.
DOI : 10.1093/nar/23.7.1192

T. Shimayama, S. Nishikawa, and K. Taira, Generality of the NUX rule: kinetic analysis of the results of systematic mutations in at Institut Pasteur Mediathèque Scientifique on, nar.oxfordjournals.org/ Downloaded from e39 Nucleic Acids Research, p.12, 1995.

A. Panjkovich and F. Melo, Comparison of different melting temperature calculation methods for short DNA sequences, Bioinformatics, vol.21, issue.6, pp.711-722, 2005.
DOI : 10.1093/bioinformatics/bti066

J. Santalucia and D. Hicks, The Thermodynamics of DNA Structural Motifs, Annual Review of Biophysics and Biomolecular Structure, vol.33, issue.1, pp.415-440, 2004.
DOI : 10.1146/annurev.biophys.32.110601.141800

J. Sambrook and D. W. Russell, Molecular Cloning: A Laboratory Manual, 2001.

Y. Ding, C. Y. Chan, and C. E. Lawrence, Sfold web server for statistical folding and rational design of nucleic acids, Nucleic Acids Research, vol.32, issue.Web Server, pp.135-141, 2004.
DOI : 10.1093/nar/gkh449

Y. Shao, S. Wu, C. Y. Chan, J. R. Klapper, E. Schneider et al., A structural analysis of in vitro catalytic activities of hammerhead ribozymes, BMC Bioinformatics, vol.8, issue.1, p.469, 2007.
DOI : 10.1186/1471-2105-8-469

J. F. Milligan, D. R. Groebe, G. W. Witherall, and O. C. Uhlenbeck, Oligoribonucleotide synthesis using T7 RNA polymerase and synthetic DNA templates, Nucleic Acids Research, vol.15, issue.21, pp.8783-8798, 1987.
DOI : 10.1093/nar/15.21.8783

K. Deb, Multi-objective optimization using evolutionary algorithms, 2001.

A. Mercatanti, C. Lande, and L. Citti, A Computational Approach to Predict Suitable Target Sites for trans-Acting Minimal Hammerhead Ribozymes, Methods Mol. Biol, vol.848, pp.337-356
DOI : 10.1007/978-1-61779-545-9_21

N. R. Markham and M. Zuker, UNAFold, Bioinformatics, Volume II:Structure, Function and Applications Methods in Molecular Biology, pp.3-31, 2008.
DOI : 10.1007/978-1-60327-429-6_1

J. F. Lucier, L. J. Bergeron, F. P. Brì-ere, R. Ouellette, S. A. Elela et al., RiboSubstrates: a web application addressing the cleavage specificities of ribozymes in designated genomes, BMC Bioinformatics, vol.7, issue.1, p.480, 2006.
DOI : 10.1186/1471-2105-7-480

A. L. Edwards and R. T. Batey, Riboswitches: a common RNA regulatory element, Nat. Educ, vol.3, p.9, 2010.

E. R. Lee, J. L. Baker, Z. Weinberg, N. Sudarsan, and R. R. Breaker, An Allosteric Self-Splicing Ribozyme Triggered by a Bacterial Second Messenger, Science, vol.329, issue.5993, pp.845-848, 2010.
DOI : 10.1126/science.1190713

R. R. Breaker, Engineered allosteric ribozymes as biosensor components, Current Opinion in Biotechnology, vol.13, issue.1, pp.31-39, 2002.
DOI : 10.1016/S0958-1669(02)00281-1

A. D. Ellington and J. W. Szostak, In vitro selection of RNA molecules that bind specific ligands, Nature, vol.346, issue.6287, pp.818-822, 1990.
DOI : 10.1038/346818a0

S. Shen, G. Rodrigo, S. Prakash, E. Majer, T. E. Landrain et al., Dynamic signal processing by ribozyme-mediated RNA circuits to control gene expression, Nucleic Acids Research, vol.43, issue.10, pp.5158-5170, 2015.
DOI : 10.1093/nar/gkv287

R. Penchovsky and R. R. Breaker, Computational design and experimental validation of oligonucleotide-sensing allosteric ribozymes, Nature Biotechnology, vol.20, issue.11, pp.1424-1433, 2005.
DOI : 10.1093/nar/gkg599

S. Millington-ward, B. O-'neill, G. Tuohy, N. Al-jandal, A. S. Kiang et al., Strategems in vitro for gene therapies directed to dominant mutations, Human Molecular Genetics, vol.6, issue.9, pp.1415-1426, 1997.
DOI : 10.1093/hmg/6.9.1415

V. Saksmerprome, M. Roychowdhury-saha, S. Jayasena, A. Khvorova, and D. H. Burke, Artificial tertiary motifs stabilize trans-cleaving hammerhead ribozymes under conditions of submillimolar divalent ions and high temperatures, RNA, vol.10, issue.12, pp.1916-1924, 2004.
DOI : 10.1261/rna.7159504