Optimal sensitivity in molecular recognition

Molecular recognition of DNA sequences is classically achieved by DNA hybridization of complementary sequences. In the context of mismatch detection, a sequence discrimination sensitivity is defined. Classical denatured DNA probes are compared to molecular beacons (DNA probes with a stem-loop structure). Molecular beacons are shown to optimize the sequence discrimination sensitivity, by a proper design of the stem length and content. This paper discusses the issue of experimental signal-to-noise in genetic sequence detection, and gives a quantitative analysis and optimization of single-mismatch detection sensitivity.