smear

[Carhuaz, Rina]

Bio friends:
Using a set of ssr primers I could find some difficult primers in the sense
that they show a nice amplification product on agarose gel, but  horrendous
smear on acrylamide gel which makes difficult or imposible to distinguish a
discrete band.  With great effort  I could succed once and find  a  very
useful band  for my linkage analysis, now I need to apply this difficult
primer to a larger plant-DNA population, however, using the same protocol, I
find  again this tedious smear rather than the expected band.  Can anyone
tell me why this happen?, Does the smear keeps relation with the amplified
genomic region or it is due to  the oligo sequence itself?. I don'I think
the smear might due to PCR components or DNA purity as they work nicely with
other primers.
But the MOST important, please tell me  how to rid me off  this  undesirable
(to say the least) smear.
Thanks a lot in advance for any input.
Rina
Rina Carhuaz Ambia
Pathology lab.
International Potato Center
Lima-Peru