We also have HPLC for purification of oligonucleotides that we synthesize. Oligonucleotide synthesis is limited to researchers in DeKalb, since our oligos are prepared and purified at or near our cost. Primers used for sequencing should have a Tm of at least 45 C and have a G or C at the 3' end. It is also good to check for potential secondary structure and self-dimer formation. Many commercial plasmid DNA purification kits, such as the cycloprep kit from Amresco, and kits from Qiagen, yield good template.
Problems often arise if phenol is used in any of the DNA purification steps.
Impurities from the phenol can poison the polymerase used in the sequencing reaction. It is always useful to run template DNA on an agarose gel before use in sequencing. The gel will help one to determine if the DNA is undegraded, and if RNA is present in the sample. In addition to plasmid DNA, PCR products can also be used as templates for sequencing. If a single PCR product is seen after electrophoresis, a PCR can be treated to degrade oligos and dNTPs prior to sequencing.