Primers Level Up

BY Joshua Ma
October 24, 2013
When we launch new features for Benchling, we never consider them to be the final version. We strongly believe in building out the basics first, getting them out to users, and iterating based on the invaluable feedback they provide.
Benchling used to automatically calculate binding sites for primers. This worked most of the time, but there was no manual override and the number of unique cases our users brought to our attention warranted a simple and flexible solution.

The New Primers

The create primer tab can be accessed via the primers panel or by right clicking a selection.
Now when you create a primer, you specify:

  1. Bases
  2. Location of the first (3′) binding base
  3. Overhang size

For example, a primer with 20 bases bound from positions 10 to 25 on the forward strand has 5 bases of overhang on the 5′ end.

That’s it! We’ve included a handful of goodies that should make your life easier:

  • A preview of the primer you are about to create, indicating matches and overhangs.
  • Quick lookup of enzyme recognition sites.
  • Warnings if an existing primer in your library has the same bases as the primer you’re about to create.

Primer Pairs

You can now link primers to reference PCR products easily.
Select two primers by clicking one and holding down the SHIFT key while clicking the other. The selection will turn blue indicating you’ve selected a valid primer pair.

After you’ve linked two primers, they’re stored in the subpanel to easily bring up the selection:

Up next…

As always, our work is never over! As far as primers go, look out for metadata and descriptions, coming to Benchling in the upcoming weeks.

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