Analyses of secondary structures in DNA by pyrosequencing.

A common problem in conventional DNA sequencing is the occurrence of DNA sequence compressions during gel electrophoresis, leading to misreading of the sequence. These compressions are usually due to secondary structures in the DNA fragment. In this study, we present a non-gel-based DNA sequencing technique that facilitates analysis of such DNA regions. A part of the polymorphic pertussis toxin promoter region in five different Bordetella species was successfully resolved by the new technique. The obtained sequence data revealed four related palindromic sequences. The ability of different DNA polymerases to read through such secondary structures is also described.