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Computer-Aided Design of Active Pseudoknotted Hammerhead Ribozymes.

Author(s): Najeh S, Zandi K, Djerroud S, Kharma N, Perreault J

Methods Mol Biol. 2021;2167:91-111 Authors: Najeh S, Zandi K, Djerroud S, Kharma N, Perreault J

Article GUID: 32712917
An Adaptive Defect Weighted Sampling Algorithm to Design Pseudoknotted RNA Secondary Structures.

Author(s): Zandi K, Butler G, Kharma N

Front Genet. 2016;7:129 Authors: Zandi K, Butler G, Kharma N

Article GUID: 27499762
RNA-Based Therapy Utilizing Oculopharyngeal Muscular Dystrophy Transcript Knockdown and Replacement.

Author(s): Abu-Baker A, Kharma N, Perreault J, Grant A, Shekarabi M, Maios C, Dona M, Neri C, Dion PA, Parker A, Varin L, Rouleau GA

Mol Ther Nucleic Acids. 2019 Apr 15;15:12-25 Authors: Abu-Baker A, Kharma N, Perreault J, Grant A, Shekarabi M, Maios C, Dona M, Neri C, Dion PA, Parker A, Varin L, Rouleau GA

Article GUID: 30831428
Title:Computer-Aided Design of Active Pseudoknotted Hammerhead Ribozymes.
Authors:Najeh S,  Zandi K,  Djerroud S,  Kharma N,  Perreault J
Link:https://www.ncbi.nlm.nih.gov/pubmed/32712917
DOI:10.1007/978-1-0716-0716-9_7
Category:Methods Mol Biol
PMID:32712917
Dept Affiliation: ENCS
1 Centre Armand-Frappier Santé Biotechnologie, Institut National de la Recherche Scientifique (INRS), Laval, QC, Canada.
2 Software Engineering and Computer Science Department, Concordia University, Montreal, QC, Canada.
3 Electrical and Computer Engineering Department, Concordia University, Montreal, QC, Canada. kharma@ece.concordia.ca.
4 Centre Armand-Frappier Santé Biotechnologie, Institut National de la Recherche Scientifique (INRS), Laval, QC, Canada. jonathan.perreault@iaf.inrs.ca.

Description:

Computer-Aided Design of Active Pseudoknotted Hammerhead Ribozymes.

Methods Mol Biol. 2021;2167:91-111

Authors: Najeh S, Zandi K, Djerroud S, Kharma N, Perreault J

Abstract

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.

PMID: 32712917 [PubMed - in process]