Codon Optimization and mRNA Structure Analysis

For the vaccine mRNA to be efficiently translated by the host cells, codon optimization is important. Therefore, the codons of the final vaccine construct were optimized for efficient expression in human cells using several Codon Optimization Tools; JCat [72 (link)], GeneArt Instant Designer by Thermofisher, GenSmart™ Codon optimization by GenScript (GS), Codon Optimization Tool by Integrated DNA Technologies (IDT). The quality of the optimized codons was analyzed Using Rare Codon Analysis tools by GS. This tool can predict the efficiency of the translation of the mRNA expressed as the codon adaptation index (CAI) value. Also, the presence of any tandem unusual codons can be detected, shown as codon frequency distribution (CFD). Based on these parameters, the best-optimized sequence was chosen for further assessment.
The secondary structure of the mRNA construct was predicted using the RNAfold tool of ViennaRNA Package 2.0 [73 (link)]. Both the minimum free energy (MFE) structure and the centroid secondary structure of the mRNA were obtained from this tool along with their MFE.

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Shahrear S, & Islam A.B. (2022). Modeling of MT. P495, an mRNA-based vaccine against the phosphate-binding protein PstS1 of Mycobacterium tuberculosis. Molecular Diversity.

Publication 2022

GenSmart™ Codon optimization Codon Optimization Tool

Adaptation Cells Codon Human Mrna Mrna translation Vaccine

Corresponding Organization :

Other organizations : University of Dhaka

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Variable analysis

independent variables

Codon optimization tools used: JCat, GeneArt Instant Designer, GenSmart™ Codon optimization, Codon Optimization Tool

dependent variables

Codon adaptation index (CAI) value, which predicts the efficiency of the translation of the mRNA
Codon frequency distribution (CFD), which detects the presence of any tandem unusual codons
Minimum free energy (MFE) structure and centroid secondary structure of the mRNA, along with their MFE

control variables

None explicitly mentioned

controls

No positive or negative controls were explicitly mentioned in the input protocol.

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