Effects of thermocyclers and primers on the reproducibility of banding patterns in randomly amplified polymorphic DNA analysis

Abstract

The effects of thermocyclers and primers on the reproducibility of banding patterns in randomly amplified polymorphic DNA analysis were tested. Purified Bordetella pertussis DNA was analysed with four primers (12-mer), which did not differ from each other in their GC-content. Three different thermocycler models from two manufacturers were tested. Three of the primers produced consistent banding patterns in separate wells of the reaction plates of individual thermocyclers, and in different thermocycler models. In contrast, the fourth primer showed extensive between-instrument variation, and the within-instrument variation with this primer was acceptable only when the most advanced thermocycler model was used. We conclude that only primers that provide consistent banding patterns in different environments should be chosen for interlaboratory use in randomly amplified polymorphic DNA analysis. The primers showing variability in banding patterns can only be used if they produce consistent results in the thermocycler used.