Single-chain polymorphism analysis in long QT syndrome using planar waveguide fluorescent biosensors.

Rapid detection of single nucleotide polymorphisms (SNPs) has potential applications in both genetic screening and pharmacogenomics. Planar waveguide fluorescent biosensor technology was employed to detect SNPs using a simple hybridization assay with the complementary strand ("capture oligo") immobilized on the waveguide. This technology allows real-time measurements of DNA hybridization kinetics. Under normal conditions, both the wild-type sequence and the SNP-containing sequence will hybridize with the capture oligo, but with different reaction kinetics and equilibrium duplex concentrations. A "design of experiments" approach was used to maximize the differences in the kinetics profiles of the two. Nearly perfect discrimination can be achieved at short times (2 min) with temperatures that destabilize or melt the heteroduplex while maintaining the stability of the homoduplex. The counter ion content of the solvent was shown to have significant effect not only on the melting point of the heteroduplex and the homoduplex but also on the hybridization rate. Changes in both the stability and the difference between the hybridization rates of the hetero- and homoduplex were observed with varying concentrations of three different cations (Na(+), K(+), Mg(2+)). With the difference in hybridization rates maximized, discrimination between the hetero- and the homoduplex can be obtained at lower, less rigorous temperatures at hybridization times of 7.5 min or longer.