what do you mean by "low quality"? do you get short sequences? small peaks? lots of "N" signals in the middle?

Low quality sequence can derive from several sources (examples)

1: mismatch primer, especially in the 5' or 3' ends of the primer

2: poly G and poly C sequences

3: high concentration of salts in the sample

4: secondary structures in the DNA

i would recommend that you verify that your sample is clean from any salt or protein contamination. if the sample is contaminate, perform phenol-ethanol percipitation.

change primer to a primer that is 100% matched and ask the sequencing unit to preform the sequencing according to the primer TM to avoid 2nd structures. possibly add DMSO (1.5%) to the reaction.

sometimes, using a different sequencer also help (not very scientific though)

good luck!

Hi Henry,

Did you 'gel-purify' the PCR product and directly used for sequencing? Try to use a quality kit (such as Qiagen) for this purpose. If problem persistence, try to simply clone the PCR product into a sequencing vector, then sequence with your gene primers or the universal primers.

What about the quality of purified product? use magnetic beads kits