Multiplexed nucleic acid sensing with single-molecule FRET.

Multiplex detection of biomolecules is important in bionanotechnology and clinical diagnostics. Multiplexing using engineered solutions such as microarrays, synthetic nanopores, and DNA barcodes are promising but they require sophisticated design/engineering and typically yield semi-quantitative information. Single-molecule FRET (smFRET) is an attractive tool in this regard as it enables both sensitive and quantitative detection. However, multiplexing with smFRET remains a great challenge as it requires either multiple excitation sources, an antenna system created by multiple FRET pairs, or multiple acceptors of the donor fluorophore, which not only complicates the labeling schemes but also data analysis due to overlapping of FRET efficiencies (EFRET). Here, we address these currently outstanding issues by designing interconvertible hairpin-based sensors (iHabSs) with non-overlapping EFRET utilizing a single donor/acceptor pair and demonstrate a high-confidence multiplex-detection of unlabeled nucleic acid sequences. We validated the reliability of our approach by systematically omitting one target at a time. Further, we demonstrate that these iHabSs are fully recyclable, sensitive with a limit of detection of ~200 pM, and are able to discriminate against single base mismatches. The multiplexed approach developed here has the potential to benefit the fields of biosensing and diagnostics by allowing a simultaneous and quantitative detection of unlabeled nucleic acid biomarkers.