We clean them up with Ampure XP beads. It will retain only longer fragments (what size fragments are retained can be controlled by varying the ratio of Ampure to sample), thus oligos and primer dimer along with any other short fragments will be removed. Have you tried tweaking the amount of template vs. primer (i.e. use more template or less primer)?

Hi

Thanks for helping! Are these magnetic beads, and do I need a magnetic stand as well? I've tried increasing the template, reducing the primers, different annealing temperatures, adding glycerol/spermidine etc etc. I'm all out of good ideas...

You could run your sample out on a gel, cut out the products larger than the primer dimers and do a gel cleanup.

Hi

I usually clean the PCR product twice for Illumina sequencing, first with column purification (MinElute PCR purification kit) and then by a paramagnetic bead clean up (AMPure XP). Following clean up, run 1-2 ul on 1.5 % agarose gel. Then I dont see any primer dimer on the gel.

You can try those

Thanks everyone! I was thinking about cutting the bands from the gel, but with so little product I fear that most will be list... also it is a lot of work with 300 samples...

'I've tried increasing the template, reducing the primers, different annealing temperatures, adding glycerol/spermidine etc etc. I'm all out of good ideas...'

Try increasing Tm i.e. melting temperature a few degrees. Hope it helps!