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high MW dimers - (Jan/27/2012 )

I ran a gel on my PCR product. I have a lot of my product at the right size, but also high molecular weight dimers at 2kb. What could this be possibly?

I know maybe it could be another site the primers could've annealed to and amplified, but since it is a dimer and not a single high molecular weight band, I don't think it is another annealing site for sure. Could it be single stranded DNA? If it is, why does it happen that the PCR generates single stranded DNA ? Thanks


How do you know it's a dimer, did you sequence it? Does it appear in your negative control?
Dimer usually is a "single" band, didn't you mean smear?


may be you need to optimize your PCR by increasing temperature or changing MgCl2 concentration.