Design a Synthetic Construct

How do I build a modular synthetic sequence in SnapGene?

Open the "Design Synthetic Construct" Tool

Click menu Tools → Design a Synthetic Construct.

In the "Design Synthetic Construct" window set the topology of the new sequence.

  • Use the dropdown to set whether the new sequence will be double-stranded or single stranded
  • Set whether sequence will be "Linear" or "circular"

If linear, specify if the sequence will have 5' phosphorylated ends.

Insert Sequence Elements

Click the buttons to insert sequence elements of different types.

Insert Bases

Click Insert Bases to option the Insert Bases window.

To insert bases you can:

  • Manually type a DNA sequence
  • Paste a plain DNA sequence
  • Paste a formatted DNA sequence in either FASTA, GenBank, EMBL, DDBJ or GCG format
  • Paste a DNA sequence copied from another SnapGene file

Formatted sequence copied from a SnapGene file will, by default, transfer any associated feature, primer or DNA color information. If you don't require this information then uncheck the option to "Transfer features, primers and DNA colors". Click Insert to insert the sequence.

If you paste a specific file format, then the format will be detected. Any features present in the formatted file will automatically be imported with the DNA sequence. Click Insert to insert the sequence.

The new sequence element will be displayed (along with any associated features) and listed in the Design Synthetic Construct window.

Insert Codons

Click Insert Codons to open the "Insert Codons" window.

Set the "Genetic Code" and "Codon Usage Table" for the synthetic coding sequence.

Set the threshold for synonymous codons to be considered rare based on the selected codon usage table. See Import or Create a Codon Usage Table to learn more about using codon usage tables.

Use the dropdown to select the first amino acid to insert.

Synonymous codons will be colored based on the "rare" threshold applied to the synonymous codon frequencies observed in the specified codon usage table.

Use the dropdown to choose an appropriate synonymous codon, then click Insert.

If required, continue to add further amino acids/codons.

Click on an amino acid to switch to an alternate synonymous codon.

Once the desired amino acids/codons are added, click Insert to add the sequence element to your synthetic construct.

Insert Restriction Site

Click Insert Restriction Site to open the "Insert Restriction site".

Use the dropdown to select a restriction site by name, or click and type the enzyme name in the field provided.

Click Insert to add the selected restriction site to your synthetic construct.

Insert Feature

Click Insert Feature to open the "Insert Features" window.

Select and insert features from the SnapGene Standard common features database, or use the drop down to select and use features in the "custom common features" database. See Detect Custom Features for more information on creating a "custom common features" database.

Once you have selected a feature from the list, click Insert to add the feature to your synthetic sequence.

Insert Reverse Translation

Click Insert Reverse Translation to open the "Insert Reverse Translation" window.

Paste or type in an amino acid sequence in the field provided.

Set the Genetic code for reverse translation and choose the method for reverse translation.  See the lesson on Reverse Translation for a summary of the various reverse translation options.

Click Insert to insert the reverse translated sequence element.

Delete a Portion of a Sequence Element

Switch to Sequence view, select the region for deletion, then click menu Edit → Delete Bases (or hit the delete key) to remove the selected nucleotides.

The edited sequence element will be marked as "trimmed". In the above example, removal of the eGFP stop codon allows read through of three manually inserted codons, and a manually added stop codon element.

Modify the Sequence of a Sequence Element

If you modify the sequence of an element, the element will be split into three elements:

  1. [1] The left unchanged portion of the original element.
  2. The Changed region
  3. [2] The righthand unchanged portion of the original Element

Change the Order of Sequence Elements

Select individual sequence elements in the list, and use the arrow to reorder of the elements.

Remove a Sequence Element

Select a sequence element and click the Remove button to remove the element from your synthetic sequence.

Generate and Save your Synthetic Sequence

Once your synthetic sequence is ready, give the sequence an appropriate name then click Synthesize to convert the sequence to a new file.

If you wish to make variations of the synthetic sequence then uncheck the option "and close this window".

Click Save to save your new synthetic sequence to an appropriate location on your computer.

You can now copy the sequence and use it to order a "real" synthetic sequence from a sequence synthesis company.

You can also order a synthetic sequence directly from within SnapGene, see  Order a Synthetic Sequence.