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Codon Optimization Tool Makes Synthetic Genes Easy

The recently updated IDT Codon Optimization tool simplifies designing synthetic genes and gBlocks® Gene Fragments for expression in a variety of organisms. The tool allows researchers to take a DNA or protein sequence from one host organism and optimize it for expression in another. The tool also makes it easy to adjust a sequence that has difficult secondary structure, a repetitive motif, or GC content ≥ 65% for compatibility with gBlocks Gene Fragments or Gene manufacturing requirements.

The tool is simple to use. First, select the desired Product Type as either Gene or gBlocks Gene Fragments. Selecting the product type determines the rule set that the Codon Optimization Tool will use. Next, select the Sequence Type to enter DNA Bases or Amino Acids. Paste or type in your sequence and select the codon table (Codon Organism) and the number of codon-optimized sequence results you wish to review from the dropdown menus (Figure 1).

Figure 1. Sequence Entry for the Codon Optimization Tool. Selecting Gene or gBlocks® Gene Fragments determines the correct rules for optimization. Select DNA Bases or Amino Acids and enter the appropriate sequence for optimization. Finally, select from the dropdown list of organisms and either 5 or 10 results to return. Click Optimize (red arrow) to get your results.

The Codon Optimization Tool randomly chooses codons with a bias that is similar to the natural bias observed in the organism’s genome. Rare codons that are present less than 10% of the time for that organism are not included. Multiple, randomized sequences are generated and ranked according to their relative ease of manufacturing in order to facilitate the fast delivery of your gBlocks Gene Fragments or Gene constructs (Figure 2).

Figure 2. Ranking of Codon-Optimized Sequences. The sequence results delivered are ranked based on their ease of manufacturing for the specified product type (Gene or gBlocks® Gene Fragments). Any additional services or restriction sites that conflict with manufacturing will be displayed in this screen. Click the Select Sequence button below the desired sequence (red arrow) for the codon view.

Once a sequence result has been selected, the codon usage for that result is displayed for your review in the Manual Optimization view. At this point, you can make desired changes to any individual codons by simply clicking on the location for the change. Any changes to optimized codons are clearly highlighted in light blue (Figure 3). Keep in mind that making multiple, manual changes may increase the difficulty of manufacturing the final sequence, and increase the time it takes to deliver your construct.

Figure 3. Codon View and Manual Optimization. After selecting a desired sequence, the Manual Optimization screen appears. In the large shaded box, codons chosen by the tool are shown in bold text. Those selected for the final sequence are highlighted (examples shown in gold boxes), with manually selected codons highlighted in bright blue-green (curved red arrows). Codons that are used <10% of the time in the organism of interest are shown in gray, struck-through text (examples shown in red boxes).

If you have made several changes and would like to start afresh on the manual optimization screen, simply click the Reset Optimization button at the bottom of the window to return to the automatic selections.

Instead of spending days making your synthetic gene, use the Codon Optimization tool to order your gene in minutes through IDT and spend those days advancing your research while we make your Gene or gBlocks Gene Fragments.

Author: Hans Packer, PhD, is a Scientific Writer at IDT.

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