long PCR primer

[Chen Ho An]

A member of my group did a PCR using a very long oligo ( >80 bases) as
the 3' primer.  However after the PCR product is TA-cloned into pGEM and
sequenced, chunks of the 3' end (~40 bases) seems to have disappear.  I
wonder if this is a general problem of PCR  using long primer or a
problem with the synthesis of the primer? Or may be there is a problem
with the pGEM?  Any suggestion as to what is happening? Also how do you
check that you primer is OK?


-chen