some primer pairs may cause problems using standard PCR conditions.
Usually the critical things to change are the MgCl2 concentration
and/or the pH in the buffer, to a lesser effect the template DNA
concentration. We use the Invitrogen PCR optimizer kit. It basically
consists of different premade buffers you can try out. We test each
new primer pair according to the kits protocol. Often the buffer
composition is not critical but occasionally one gets results that
vary from no band at all, smears, additional bands to the correct
band only depending on the buffer. It is really worthwhile trying
out. Especially in mapping experiments where the DNA quality/amount
may be limiting and hence the PCR buffer conditions should be
Hope this helps.