Effects of sample matrix and injection plug on dsDNA migration in capillary gel electrophoresis

Reproducible DNA migration times are required for accurate basepair assignment in restriction fragment mapping and polymerase chain reaction product identification. Our data shows DNA migration time shifts with changes in sample ionic strength. Secondly, loss of resolution with replaceable polyacrylamide gels was observed when increasing the length of the sample plug with pressure injection. An easy way to correct for the migration time shifts is to incorporate an internal DNA standard directly into the separation process by consecutively injecting the DNA sample and the DNA standard. This allows for compensation of any possible migration time variation caused by high ionic strength sample matrices. Also high-resolution separations can be maintained with large injection volumes (long injection plug) by using consecutive injections of 0.1 M Tris-acetate buffer and the DNA sample.