How do I analyze primers (oligonucleotides) to obtain extinction coefficient, hairpin formation, self-dimerization or hetero-dimerization information?
SnapGene reports %GC, molecular weight and Tm in Primer view. To access further information about primers SnapGene can pass your primer sequences to the IDT "OligoAnalyzer" form.
You can create a free login at IDT, via https://sg.idtdna.com/site/account, to use IDT "OligoAnalyzer".
Open a DNA sequence
Open a DNA sequence that has primers annotated on the sequence. See the User Guide chapter on Primers to learn more about creating, adding and using primers in SnapGene.
Select one or more primers for analysis in Map view, Sequence view or Primers view.
Analyze Selected Primers
Click Primers → Analyze Selected Primers.
Log into the IDT Website
Create an Account on the IDT website https://https://sg.idtdna.com/ to perform your primer analysis.
SnapGene will open a separate tab in your default web browser for each primer and automatically fill each IDT form with your primer sequences.
1. Use the buttons to the right of the window to obtain detailed information about each primer.
2. Use the modifications "drop-downs" to add chemical modifications to your primer, then click "Analyze" to obtain detailed information about the modified primer.
Use the IDT website "Instructions" page to learn how to use this IDT tool.
