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Old 04-08-2012, 06:20 AM   #4
pmiguel
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Location: Purdue University, West Lafayette, Indiana

Join Date: Aug 2008
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Non-denaturing gel cuts will not get rid of primer dimer strands annealed to full length amplicon strands. And the primer dimer strands will anneal to the full length strands, right? They share adapter sequence.

Roche recommends "double AmPure" at reduced AmPure concentrations. Same problem, I guess. But some of the primer dimers probably do exchange off the full length amplicons during the process. So each added cycle of size selection probably helps.

Might also want to try tuning the PCR reactions to minimize primer dimer formation. Lower primer concentrations, etc.

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Phillip
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