Template secondary structure promotes polymerase jumping during PCR amplification

Pairs of primers flanking known miniTn10 transposon insertion sites were us ed to confirm the presence of the transposon in DNA isolated from Legionell a pneumophila mutants. It was expected that the polymerase chain reaction p roducts derived from the mutant template would be larger than those from th e wild-type (WT) template due to the presence of the 1.8-kb transposon. Ins tead, it was observed that the mutant template yielded a product of almost the same size as that yielded by WT template. We present evidence to indica te that the aberrant product from the mutant template is a direct result of secondary structure of the template resulting from an inverted repeat sequ ence present in the miniTn10 transposon.