Primers going "loopy" - (Mar/09/2010 )

Hi all,
could it be possible for a primer carrying a mutation (which mispairs with the normal codon seqence) to loop out, and allow taq pol to copy the template strand as normal?

Yes I would say it is possible.

Yes, certainly. This probably won't happen if the looped base is near the 3' end, but in other regions of the primer, it will definitely work (or fail, depending on your point of view).