How to Use the Primer Dimer Checker
Step 1: Enter your forward primer sequence in the first box and reverse primer in the second box.
Step 2: Click Check Primer Dimers. The tool checks three types of problems — self-dimer for each primer and inter-primer dimer between the two primers.
Step 3: Check the risk level. Low risk means your primers are fine. High risk means you should consider redesigning to reduce complementarity at the 3' end.
What are Primer Dimers?
Primer dimers form when primers bind to themselves or to each other instead of to the template. This wastes primers and polymerase, and can produce a faint band at ~50–100bp on your gel even when there is no template.
5' ATGCGATCG 3'
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3' GCTAGCGTA 5'
// Inter-primer dimer — fwd binds to rev:
5' ATGCGATCG 3'
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3' CGATCGATCG 5'
// 3' end complementarity is most dangerous
How to Fix Primer Dimers
Change 1–3 bases at the 3' end of one or both primers to break the complementarity. Even a single base change at the 3' end can eliminate dimer formation. Avoid ending primers with runs of G or C that match the other primer.