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Computer-Aided Design of Active Pseudoknotted Hammerhead Ribozymes

Najeh, Sabrine, Zandi, Kasra, Djerroud, Samia, Kharma, Nawwaf et Perreault, Jonathan ORCID: https://orcid.org/0000-0003-4726-6319 (2021). Computer-Aided Design of Active Pseudoknotted Hammerhead Ribozymes In: Ribozymes: Methods and Protocols. Methods in Molecular Biology (2167). Humana Press, New York, p. 91-111.

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Résumé

Pseudoknots are important motifs for stabilizing the structure of functional RNAs. As an example, pseudoknotted hammerhead ribozymes are highly active compared to minimal ribozymes. The design of new RNA sequences that retain the function of a model RNA structure includes taking in account pseudoknots presence in the structure, which is usually a challenge for bioinformatics tools. Our method includes using "Enzymer", a software for designing RNA sequences with desired secondary structures that may include pseudoknots. Enzymer implements an efficient stochastic search and optimization algorithm to sample RNA sequences from low ensemble defect mutational landscape of an initial design template to generate an RNA sequence that is predicted to fold into the desired target structure.

Type de document: Chapitre de livre
Mots-clés libres: -
Centre: Centre INRS-Institut Armand Frappier
Date de dépôt: 15 juill. 2021 00:39
Dernière modification: 15 févr. 2022 21:07
URI: https://espace.inrs.ca/id/eprint/11718

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