Method for preparing single-stranded DNA templates for Pyrosequencing using vector ligation and universal biotinylated primers.

Marco Groth, Klaus Huse, Kathrin Reichwald, Stefan Taudien, Jochen Hampe, Philip Rosenstiel, Gerd Birkenmeier, Stefan Schreiber, Matthias Platzer
Year of publication:
Journal title abbreviated:
Anal. Biochem.
Journal title long:
Analytical biochemistry
Impact factor:
In Pyrosequencing, the addition of nucleotides to a primer-template hybrid is monitored by enzymatic conversion of chemical energy into detectable light. The technique yields both qualitative and quantitative sequence information because the chemical energy is released by a stoichiometric split off of pyrophosphates from incorporated deoxynucleotide triphosphates and a defined nucleotide dispensation order is given. Because Pyrosequencing works best if single-stranded DNA templates are used, template generation usually requires PCR with a target-specific biotinylated primer and a subsequent purification involving interaction of the biotin label with immobilized streptavidin. To circumvent the need for numerous and expensive template-specific biotinylated primers, we developed a method that uses the ligation of amplified DNA fragments into a plasmid vector, thereby facilitating subsequent PCR using a universal vector-specific biotinylated primer. This approach allows easy and straightforward isolation of single-stranded templates of any PCR product. As a proof of principle, we used the method for genotyping two single-nucleotide polymorphisms in the human genes CARD15 and A2M and for characterization of four multisite variations in the human DEFB104 gene.