When I run my 17mer DNA oligos on PAGE gel I can see a smear above my DNA band. Does anyone know a possible reason or how to minimize this? I have attached a gel image here as well.
Without protocol it is difficult to tell for sure. However, I guess that some of you oligos could form intermolecular or intramolecular structures. Urea is fully effective as denaturant only at high temperature (optimum is around 50-55 C). That is why gel need to be pre-run.