Binary Probes for Nucleic Acid Analysis

The advances in the development of binary probe (BPs) and their improved selectivity in comparison with other hybridization-based techniques were studied. The first BP, which used Förster resonance energy transfer (FRET), was suggested in 1988. A commonly adopted BP architecture employs the different affinity mode BPs. In this design one strand with a longer analyte binding arm binds tightly to the position abutting to the single-nucleotide polymorphisms (SNP) site. A second shorter analyte binding arm interrogates the SNP site by forming stable hybrid only with the perfectly matched sequence. The design of BPs employs self-assembly of more than two nucleic acid components. The same principle is adopted by DNA nanotechnology, which deals with constructing objects and functionally active assemblies from DNA molecules. Newly designed constructs based on aptamers, DNA junctions, and DNA enzymes offer an opportunity to utilize DNA probes that avoid direct covalent attachment with organic dyes.