Keyword search (4,163 papers available)

"Synthetic biology" Keyword-tagged Publications:

Title Authors PubMed ID
1 Benzylisoquinoline Alkaloid Production in Yeast via Norlaudanosoline Improves Titer, Selectivity, and Yield Narcross L; Pyne ME; Kevvai K; Siu KH; Dueber JE; Martin VJJ; 41779670
BIOLOGY
2 A Bacteroides synthetic biology toolkit to build an in vivo malabsorption biosensor McCallum G; Burckhardt JC; He J; Hong A; Potvin-Trottier L; Tropini C; 41610848
BIOLOGY
3 Robustness and evolvability: Revisited, redefined and applied Kharma N; Bédard-Couture R; 39098381
ENCS
4 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
5 Functional Synthetic Biology Aldulijan I; Beal J; Billerbeck S; Bouffard J; Chambonnier G; Ntelkis N; Guerreiro I; Holub M; Ross P; Selvarajah V; Sprent N; Vidal G; Vignoni A; 37073284
BIOLOGY
6 Advancing Undergraduate Synthetic Biology Education: Insights from a Canadian iGEM Student Perspective Diep P; Boucinha A; Kell BJ; Yeung BA; Chen XA; Tsyplenkov D; Serra D; Escobar A; Gnanapragasam A; Emond CA; Sajtovich VA; Mahadevan R; Kilkenny DM; Gini-Newman G; Kaern M; Ingalls B; 34237221
BIOLOGY
7 Using Models to (Re-)Design Synthetic Circuits. McCallum G, Potvin-Trottier L 33405217
BIOLOGY
8 Computer-Aided Design of Active Pseudoknotted Hammerhead Ribozymes. Najeh S, Zandi K, Djerroud S, Kharma N, Perreault J 32712917
ENCS
9 Reconstituting Plant Secondary Metabolism in Saccharomyces cerevisiae for Production of High-Value Benzylisoquinoline Alkaloids. Pyne ME, Narcross L, Fossati E, Bourgeois L, Burton E, Gold ND, Martin VJ 27417930
CSFG

 

Title:Computer-Aided Design of Active Pseudoknotted Hammerhead Ribozymes.
Authors:Najeh SZandi KDjerroud SKharma NPerreault 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 ribozymeHDV ribozymeHammerhead ribozymeInverse foldingPistol ribozymePseudoknotRNA structureSynthetic biologyTwister ribozymeVS 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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