In this study, we performed a RNAfold analysis to investigate alterations in secondary structures of mRNAs in SARS-CoV-2 vaccines due to codon optimization. The emerging G-quadruplexes are favorable binding sites of RNA binding proteins like helicases that inevitably affect epigenetic reprogramming of the cell by altering transcription, translation and replication. Importantly, when codon optimization increases the GC content of synthetic mRNAs, there can be an inevitable enrichment of G-quartets which potentially form G-quadruplex structures. In SARS-CoV-2 mRNA vaccines codon optimizations can result in differential secondary conformations that inevitably affect a protein’s function with significant consequences to the cell. If you are working with an organism not listed in the Codon Optimization Tool’s Organism list, or do not see the information you need, contact that fall outside of the rules used by the tool.Codon optimization describes the process used to increase protein production by use of alternative but synonymous codon changes. We also provide a step-by-step tutorial for using the Codon Optimization Tool. Access IDT’s free, online Codon Optimization Tool and get started. Instead of spending days designing and constructing your synthetic gene, use the Codon Optimization Tool to order your gene in minutes through IDT, and spend the saved time advancing your research, while we make your genes or gene fragments. Get started using the Codon Optimization Tool See the DECODED article, Using a codon optimization tool -how it works and advantages, for more discussion on this topic. Additional factors, such as mRNA stability, protein maturation, translation speed, chaperone expression, promoter design, etc. While codon optimization is important for optimal protein expression, it does not guarantee higher expression levels. Codons used less than 10% of the time in the chosen organism are shown in gray, struck-through text.Ī caveat: Does codon optimization equal higher expression? Those selected for the final sequence are highlighted as a gray box. Codons chosen by the tool are shown in blue. Codon view for Manual Optimization. The Manual Optimization screen splits each codon into an individual box. Order sequence using the blue Order item button.įigure 3. To manually optimize your original sequence, click on Map Codons Only and then Manual Optimization (Figure 2) to change codon usage for any amino acid or stop codon in your sequence (Figure 3).ħ. (Optional available only for amino acid sequences) Click on Manual Optimization (Figure 2) to change codon usage for any amino acid or stop codon in your sequence (Figure 3).Ī.Note: multiple clicks on the Optimize button will generate slightly different sequences. Click on Optimize (lower right orange button).Obtain results in one of the following ways: You can then edit the sequence by changing the reading frame shift and by indicating start/stop codons.Ħ. (optional) To designate a specific part of the sequence for optimization, click on Highlight Codons. Paste in your sequence (Bulk entry is also available in a variety of input formats).ĥ. Select your Organism for expression from the pulldown list (If working with cell lines, select the animal or plant origin).Ĥ. Select the desired Product Type of either gBlocks™ Gene Fragments, Megamer™ ssDNA Fragment, eBlocks™ Gene Fragments, or Gene to set the complexity rules that the tool will use.ģ. Select the Sequence Type by clicking either DNA Bases or Amino Acids.Ģ. Use of the Codon Optimization Tool is straightforward (see Figure 1 for a screen shot of the tool interface):ġ. The tool also makes it easy to adjust a sequence that has difficult secondary structure, a repetitive motif, or high/low GC content for compatibility with IDT manufacturing requirements for genes and gene fragments.Įasy steps for using the Codon Optimization Tool coli into account, which would be considered codon optimization for E. coli system, the DNA sequence should be changed taking the codon usage of E. For example, if a human protein from nature is going to be expressed using an E. The main design consideration is to optimize a DNA or protein sequence from one host organism for expression in another by reassigning codon usage. The IDT Codon Optimization Tool simplifies designing synthetic genes, single-stranded, and double-stranded DNA fragments for expression in a variety of organisms. Target Capture Probe Design & Ordering Tool.Library Concentration Conversion Calculator.Alt-R Predesigned Cas9 crRNA Selection Tool.SYBR Green dye assay and PrimeTime probe assays.PCR Allele Competitive Extension (PACE) genotyping.Drug target identification via CRISPR screening.
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