A new assay for single nucleotide polymorphism analysis based on displacement reactions in PNA–DNA double helices

In this article, we describe a new method for single nucleotide polymorphism analysis using the displacement reaction of the DNA in a PNA–DNA double helix by the target DNA. Thereby, the probe consists of a TMR-labeled PNA and a Cy5-labeled DNA forming a FRET system. Due to the displacement of the labeled DNA strand by the target DNA, the FRET is invalidated and the fluorescence of the donor dye (TMR) increases. Investigations of the exchange reaction show that increasing salt concentration and temperature accelerate the exchange rate.