Cantilever-based optical deflection assay for discrimination of DNA single-nucleotide mismatches

Characterization of single-nucleotide polymorphisms is a major focus of cur rent genomics research. We demonstrate the discrimination of DNA mismatches using an elegantly simple microcantilever-based optical deflection assay, without the need for external labeling. Gold-coated silicon AFM cantilevers were functionalized with thiolated 20- or 25-mer probe DNA oligonucleotide s and exposed to target oligonucleotides of varying sequence in static and now conditions. Hybridization of 10-mer complementary target oligonucleotid es resulted in net positive deflection, while hybridization with targets co ntaining one or two internal mismatches resulted in net negative deflection . Mismatched targets produced a stable and measurable signal when only a fo ur-base pair stretch was complementary to the probe sequence. This techniqu e is readily adaptable to a high-throughput array format and provides a dis tinct positive/negative signal for easy interpretation of oligonucleotide h ybridization.