101 things you (maybe) didn’t know about MacVector: #16 – Using A Primer Database

If you have accumulated a collection of primers in your freezer, then you should consider storing the sequences in a primer database within MacVector so that you can rapidly scan any new plasmids for potential primer binding sites. Plus, you’ll have a nice electronic record of all your primer sequences.

Start by choosing File | New | Nucleic Acid Subsequence, then click on the Add button to open up the subsequence editor;

Here you can give your primer a name, type or paste in the sequence and add a comment. Note that you can enter values into the Allowed mismatch field so that even imperfect binding sites will be reported when searching with the primers. Repeat for each primer and save the database to a location on your hard drive. It will save with a .nsub extension.

Once you have created a primer file, you can scan any nucleic acid sequence for primer binding sites using the Analyze | Nucleic Acid Subsequence… menu item;

Make sure you Choose… your primer database file in the File section. The nucleic acid subsequence analysis function is very similar to a restriction enzyme analysis – you have the option of viewing lists of primer binding sites, viewing lists of primers that don’t bind and/or displaying the binding sites on the graphical map of the sequence. You can even right-click on a primer and create a feature representing that binding site;

Finally, if you want even finer control over which potential primer binding sites are reported, you can force certain residues to always match during the scan. In the subsequence editor, simply place an X underneath each residue that you absolutely want to match. For example, you would typically need to have the last few 3′ residues be a perfect match for a PCR or sequencing reaction to work with any efficiency, so you might force the last five residues to match;

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