PERFORM Publications

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Title		Authors	PubMed ID
1	Robustness and evolvability: Revisited, redefined and applied	Kharma N; Bédard-Couture R;	39098381 ENCS
2	BioCloneBot: A versatile, low-cost, and open-source automated liquid handler	Wells KC; Kharma N; Jaunky BB; Nie K; Aguiar-Tawil G; Berry D;	38524156 BIOLOGY
3	Digital Microfluidics Chips for the Execution and Real-Time Monitoring of Multiple Ribozymatic Cleavage Reactions	Davis AN; Samlali K; Kapadia JB; Perreault J; Shih SCC; Kharma N;	34514224 BIOLOGY
4	Computer-Aided Design of Active Pseudoknotted Hammerhead Ribozymes.	Najeh S, Zandi K, Djerroud S, Kharma N, Perreault J	32712917 ENCS
5	An Adaptive Defect Weighted Sampling Algorithm to Design Pseudoknotted RNA Secondary Structures.	Zandi K, Butler G, Kharma N	27499762 CSFG
6	RNA-Based Therapy Utilizing Oculopharyngeal Muscular Dystrophy Transcript Knockdown and Replacement.	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	30831428 BIOLOGY

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
Publication:	Methods in molecular biology (Clifton, N.J.)
Keywords:	GlmS ribozyme; HDV ribozyme; Hammerhead ribozyme; Inverse folding; Pistol ribozyme; Pseudoknot; RNA structure; Synthetic biology; Twister ribozyme; VS ribozyme;
PMID:	32712917	Category:	Methods Mol Biol	Date Added:	2020-07-28
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]

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