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Old 04-14-2010, 08:43 AM   #1
Bruce E
Location: Rochester,MN

Join Date: Jan 2008
Posts: 15
Default Primer Dimers in PEIn libraries

We are preparing PEIn libraries starting with 200 ng of concantenated Raindance products. We used 10X less adapter mix when ligating the adapters to adjust for the lower starting DNA concentration. We also used 1/3 and 2/3 of our purified ligation products in the standard Illumina pcr enrichment step. Analysis on the Agilent bioanalyzer shows a fairly large primer dimer peak. I was wondering if anyone had any suggestions to help reduce this peak. I am considering lowering the concentrations of the 3 primers in the enrichment pcr step. Has anyone tried this? If not does anyone have any other suggestions?
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Old 04-14-2010, 05:46 PM   #2
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Location: Bethesda MD

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We typically observe an abundant primer dimer peak with indexed libraries, even with milligram quantities of starting material. Our (admittedly inelegant) solution is to perform a second round of size selection.

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