PERFORM Publications

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Title		Authors	PubMed ID
1	Using Models to (Re-)Design Synthetic Circuits.	McCallum G, Potvin-Trottier L	33405217 BIOLOGY
2	Computer-Aided Design of Active Pseudoknotted Hammerhead Ribozymes.	Najeh S, Zandi K, Djerroud S, Kharma N, Perreault J	32712917 ENCS
3	Metabolomic and lipidomic analyses of chronologically aging yeast.	Richard VR, Bourque SD, Titorenko VI	25213255 BIOLOGY
4	A Cell-Free Content Mixing Assay for SNARE-Mediated Multivesicular Body-Vacuole Membrane Fusion.	Karim MA, Samyn DR, Brett CL	30317513 BIOLOGY
5	Visualization of SNARE-Mediated Organelle Membrane Hemifusion by Electron Microscopy.	Mattie S, Kazmirchuk T, Mui J, Vali H, Brett CL	30317518 BIOLOGY
6	Identification of Genes Involved in the Degradation of Lignocellulose Using Comparative Transcriptomics.	Gruninger RJ, Reid I, Forster RJ, Tsang A, McAllister TA	28417376 CSFG
7	Isolation and Preparation of Extracellular Proteins from Lignocellulose Degrading Fungi for Comparative Proteomic Studies Using Mass Spectrometry	Robert J Gruninger	28417377 CSFG
8	Introduction: Overview of Fungal Genomics.	de Vries RP, Grigoriev IV, Tsang A	29876804 CSFG
9	Fungal Genomic DNA Extraction Methods for Rapid Genotyping and Genome Sequencing.	Bellemare A, John T, Marqueteau S	29876805 CSFG
10	Mass Spectrometry-Based Proteomics	Marcos Rafael Di Falco	29876812 CSFG
11	Evolutionary Adaptation to Generate Mutants.	de Vries RP, Lubbers R, Patyshakuliyeva A, Wiebenga A, Benoit-Gelber I	29876815 BIOLOGY
12	Manual Gene Curation and Functional Annotation.	McDonnell E, Strasser K, Tsang A	29876819 CSFG
13	Evaluating Programs for Predicting Genes and Transcripts with RNA-Seq Support in Fungal Genomes.	Reid I	29876820 CSFG
14	Phylogenetic Analysis of Protein Family.	Song L, Wu S, Tsang A	29876824 CSFG

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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