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Old 04-10-2012, 07:22 AM   #6
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Location: Utah

Join Date: Mar 2010
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In theory they can, but I haven't personally seen much of a problem from it. If you're using a gel cut purification method, you should get rid of those hybrid molecules as well because they will migrate differently from a regular amplicon duplex.

I wonder if you could get rid of those hybrid duplexes by treating the library with mung bean or S1 nuclease before doing the AMPure purification. That should destroy the single stranded parts of those molecules and leave your double stranded amplicons alone. I suppose that's worth a try for anyone having trouble with short reads that might be caused by such hybrid duplexes.
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