scholarly journals Synthetic gene design-The rationale for codon optimization and implications for molecular pharming in plants

2016 ◽  
Vol 114 (3) ◽  
pp. 492-502 ◽  
Author(s):  
Gina R. Webster ◽  
Audrey Y.-H. Teh ◽  
Julian K.-C. Ma
Keyword(s):  
Codon Optimization ◽  
Synthetic Gene ◽  
Molecular Pharming ◽  
Gene Design ◽  
Synthetic Gene Design

Codon Optimization OnLine (COOL): a web-based multi-objective optimization platform for synthetic gene design

2014 ◽  
Vol 30 (15) ◽  
pp. 2210-2212 ◽  
Author(s):  
Ju Xin Chin ◽  
Bevan Kai-Sheng Chung ◽  
Dong-Yup Lee
Keyword(s):  
Codon Optimization ◽  
Synthetic Gene ◽  
Multi Objective Optimization ◽  
Web Based ◽  
Gene Design ◽  
Multi Objective ◽  
Synthetic Gene Design

Synthetic Gene Design Using Codon Optimization On-Line (COOL)

2016 ◽  
pp. 13-34 ◽  
Author(s):  
Kai Yu ◽  
Kok Siong Ang ◽  
Dong-Yup Lee
Keyword(s):  
Codon Optimization ◽  
Synthetic Gene ◽  
Gene Design ◽  
On Line ◽  
Synthetic Gene Design

scholarly journals EuGene: maximizing synthetic gene design for heterologous expression

2012 ◽  
Vol 28 (20) ◽  
pp. 2683-2684 ◽  
Author(s):  
P. Gaspar ◽  
J. L. Oliveira ◽  
J. Frommlet ◽  
M. A. S. Santos ◽  
G. Moura
Keyword(s):  
Heterologous Expression ◽  
Synthetic Gene ◽  
Gene Design ◽  
Synthetic Gene Design

scholarly journals Trans-species synthetic gene design allows resistance pyramiding and broad-spectrum engineering of virus resistance in plants

2018 ◽  
Vol 16 (9) ◽  
pp. 1569-1581 ◽  
Author(s):  
Anna Bastet ◽  
Baptiste Lederer ◽  
Nathalie Giovinazzo ◽  
Xavier Arnoux ◽  
Sylvie German-Retana ◽  
...  
Keyword(s):  
Broad Spectrum ◽  
Virus Resistance ◽  
Synthetic Gene ◽  
Gene Design ◽  
Synthetic Gene Design

Synthetic Gene Design with a Large Number of Hidden Stop Codons

2008 ◽  
Author(s):  
Vinhthuy Phan ◽  
Sudip Saha ◽  
Ashutosh Pandey ◽  
Wong Tit-Yee
Keyword(s):  
Synthetic Gene ◽  
Gene Design ◽  
Stop Codons ◽  
Hidden Stop Codons ◽  
Synthetic Gene Design

scholarly journals Codon pair optimization (CPO): a software tool for synthetic gene design based on codon pair bias to improve the expression of recombinant proteins in Pichia pastoris

2021 ◽  
Vol 20 (1) ◽  
Author(s):  
Yide Huang ◽  
Ting Lin ◽  
Lingfang Lu ◽  
Fan Cai ◽  
Jie Lin ◽  
...  
Keyword(s):  
Pichia Pastoris ◽  
Protein Expression ◽  
Codon Usage ◽  
Codon Optimization ◽  
Software Tool ◽  
Expression Levels ◽  
Gene Design ◽  
Codon Pair Bias ◽  
Codon Pair ◽  
Synthetic Gene Design

Abstract Background Codon optimization is a common method to improve protein expression levels in Pichia pastoris and the current strategy is to replace rare codons with preferred codons to match the codon usage bias. However, codon-pair contexts have a profound effect on translation efficiency by influencing both translational elongation rates and accuracy. Until now, it remains untested whether optimized genes based on codon pair bias results in higher protein expression levels compared to codon usage bias. Results In this study, an algorithm based on dynamic programming was introduced to develop codon pair optimization (CPO) which is a software tool to provide simple and efficient codon pair optimization for synthetic gene design in Pichia pastoris. Two reporters (MT1-MMP E2C6 and ADAM17 A9B8 scFvs) were employed to test the effects of codon pair bias and CPO optimization on their protein expression levels. Four variants of MT1-MMP E2C6 and ADAM17 A9B8 for each were generated, one variant with the best codon-pair context, one with the worst codon-pair context, one with unbiased codon-pair context, and another optimized based on codon usage. The expression levels of variants with the worst codon-pair context were almost undetectable by Western blot and the variants with the best codon-pair context were expressed well. The expression levels on MT1-MMP E2C6 and ADAM17 A9B8 were more than five times and seven times higher in the optimized sequences based on codon-pair context compared to that based on codon usage, respectively. The results indicated that the codon-pair context-based codon optimization is more effective in enhancing expression of protein in Pichia pastoris. Conclusions Codon-pair context plays an important role on the protein expression in Pichia pastoris. The codon pair optimization (CPO) software developed in this study efficiently improved the protein expression levels of exogenous genes in Pichia pastoris, suggesting gene design based on codon pair bias is an alternative strategy for high expression of recombinant proteins in Pichia pastoris.

Exploring codon context bias for synthetic gene design of a thermostable invertase in Escherichia coli

2015 ◽  
Vol 75-76 ◽  
pp. 57-63 ◽  
Author(s):  
Han Bin Pek ◽  
Maximilian Klement ◽  
Kok Siong Ang ◽  
Bevan Kai-Sheng Chung ◽  
Dave Siak-Wei Ow ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Synthetic Gene ◽  
Gene Design ◽  
Codon Context ◽  
Codon Context Bias ◽  
Synthetic Gene Design

scholarly journals EuGene: maximizing synthetic gene design for heterologous expression

2016 ◽  
Vol 32 (7) ◽  
pp. 1120-1120
Author(s):  
Paulo Gaspar ◽  
José Luís Oliveira ◽  
Jörg Frommlet ◽  
Manuel A.S. Santos ◽  
Gabriela Moura
Keyword(s):  
Heterologous Expression ◽  
Synthetic Gene ◽  
Gene Design ◽  
Synthetic Gene Design
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