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Old 04-18-2012, 11:46 AM   #7
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Originally Posted by ajthomas View Post
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.
A primer dimer is pretty short. I was assuming that the amplicon ends up double stranded throughout its length. It just has the primer dimer riding one adapter end, with the rest of the complement-to-the-adapter strand peeled back to allow this. This would only increase the molecular weight of the duplex by the molecular weight of a single strand of the primer dimer. Not enough to remove using size selection unless your cut is very narrow.

Unless you had a pretty bad primer dimer issue, the concentration of these hitchhikers would be low enough to ignore, though.
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