Bait-and-Switch Molecular Recognition in Nucleic Acid Sensors: Time-Resolved Fluorescence, Single Nucleotide Polymorphism Detection

We investigate the properties of a simple DNA-based nanodevice capable of detecting single nucleotide polymorphisms (SNPs) in unlabelled nucleic acid target sequences. Detection is achieved by a two-stage bait-and-switch process combining complementary-base hybridization and switching as molecular recognition criteria. A probe molecule is constructed from a single DNA strand designed to adopt a partial cruciform structure with a pair of exposed (unhybridized) strands. Upon target binding, a switchable cloverleaf construct (similar to a Holliday junction) is formed where the states are the open and closed junction conformations. Switching between these occurs by junction folding in the presence of divalent ions. A combination of steady-state and time-resolved fluorescence spectroscopy is used to measure Forster resonance energy transfer.