What is back translation?
Back translation is the process of turning an AA sequence into a DNA sequence. You can leverage Benchling's nucleotide codon optimization tool to generate a back translated sequence that matches your desired constraints.
To begin, select the part of an AA sequence you wish to optimize and right click. Then, click "Back Translate."
Specify your parameters
You have several parameters to set:
Organism: Specify the target organism you wish to express the sequence in. The algorithm will create a sequence whose codons match the codon frequencies of the specified organism. If you don't see the organism you need, let us know!
GC Content: Select a range of desired GC content. The algorithm will attempt to create a sequence that matches the specified range.
Uridine: mRNA uridine depletion. Depleting uridine in transcribed mRNA has been implicated in reducing immunogenicity of RNA.
Avoid creating specific restriction sites
Click "Add cut site to avoid" to select restriction enzymes for which you want to avoid creating recognition sites in the resulting DNA sequence.
Preview your optimization
After specifying your parameters, click "Preview Optimization."
Based on your inputs, the codon optimization algorithm generates an optimized DNA sequence. Review the summary to determine you're satisfied with the result.
If you are satisfied, click "Save as new sequence." If you are not satisfied with the result, click "Back" and change your input parameters.