Excessive Primer Dimers
 

Excessive Primer Dimers - are they a concern?

Also how do you get rid of them?!

thanks

Kiki :)

Re: Excessive Primer Dimers
 

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 [Only registered and activated users can see links. Click Here To Register...], Vector NTI (Invitrogen, no affiliation), or a web program like [Only registered and activated users can see links. Click Here To Register...]'s.

Re: Excessive Primer Dimers
 

Thanks Kmunson, some great ideas here!

:)

Re: Excessive Primer Dimers
 

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 [Only registered and activated users can see links. Click Here To Register...]
cheers!