Excessive Primer Dimers

[kiki06]

Excessive Primer Dimers - are they a concern?

Also how do you get rid of them?!

thanks

Kiki

[kmunson779]

Part of this depends on what you're trying to do. Primer dimers are a problem if they soak up so much primer that you can't get the actual PCR product you're aiming for (or in Sybr Green Real-time PCR, but that's another forum).

To reduce primer dimers, use a hot-start protocol &/or enzyme. If that doesn't work, redesign primers and look for the possibility of primer dimer formation using software tools like Amplify, Vector NTI (Invitrogen, no affiliation), or a web program like IDT's.

[kiki06]

Thanks Kmunson, some great ideas here!

[admin]

Hey kiki,
I hope your primer dimer problem was solved.

I have some tips for other users including:

Decrease your primer concentration

Re-design primers. Check primers carefully for homo-dimer and hetero-dimer formation with OligoAnalyzer or similar primer software.

Try adding formamide to PCR to denature primers better.

Increase your DNA template concentration.

Increase your PCR annealing temperature.

PCR may benefit by adding DMSO (2-5%).

Also, HotStart PCR has less primer dimers than regular Taq polymerase PCR.


I got this information from PCR Troubleshooting
cheers!