Section IV: Sequence Analysis FAQ Sheet
Sequence Analysis Troubleshooting Guide
33
Chemistry
Which primer purification method is best for sequencing
primers?
The major factor with a primer that affects DNA sequence quality is the actual
synthesis quality. If a synthesized primer contains little n-1, then high quality sequence
can be obtained. Using other primer purification methods do not affect the quality of
sequence as illustrated below.
Shown below is data generated from a primer that was purified by three different
methods: 1) OPC column, 2) Reverse Phase HPLC and 3) gel filtration. In each case,
because the synthesis quality was high, the sequencing quality was high and the
purification method had little or no effect on the results. The CEQ does, however,
require that all sequencing primers (at a minimum) be desalted (i.e. gel filtration)
before use.
Figure 20: OPC Purified Primer
