Selective quenching of unhybridized fluorescent probes by gold nanoparticles for rapid SNP genotyping using conventional PCR

We detect single nucleotide polymorphisms (SNP) in genomic DNA that has been amplified using a standard PCR protocol where a short fluorescently tagged probe sequence and a single denaturation and annealing step have been added. We utilize the ability of ionically treated gold nanoparticles to selectively adsorb unhybridized probes in the modified PCR product and quench their fluorescence. The method eliminates the time and expense of gel electrophoresis while retaining the ability to use an ordinary thermal cycler for PCR amplification. We describe an application to genotyping Fatty Zucker rats and validate the method against fluorogenic real-time PCR with double blind studies.