PT  - JOURNAL ARTICLE
AU  - Tripathy, Soumya P.
AU  - Ponnapati, Manvitha
AU  - Jacobson, Joseph
AU  - Chatterjee, Pranam
TI  - Sub-Picomolar Detection of SARS-CoV-2 RBD via Computationally-Optimized Peptide Beacons
AID  - 10.1101/2021.06.04.447114
DP  - 2021 Jan 01
TA  - bioRxiv
PG  - 2021.06.04.447114
4099  - http://biorxiv.org/content/early/2021/06/04/2021.06.04.447114.short
4100  - http://biorxiv.org/content/early/2021/06/04/2021.06.04.447114.full
AB  - The novel coronavirus SARS-CoV-2 continues to pose a significant global health threat. Along with vaccines and targeted therapeutics, there is a critical need for rapid diagnostic solutions. In this work, we employ deep learning-based protein design to engineer molecular beacons that function as conformational switches for high sensitivity detection of the SARS-CoV-2 spike protein receptor binding domain (S-RBD). The beacons contain two peptides, together forming a heterodimer, and a binding ligand between them to detect the presence of S-RBD. In the absence of S-RBD (OFF), the peptide beacons adopt a closed conformation that opens when bound to the S-RBD and produces a fluorescence signal (ON), utilizing a fluorophore-quencher pair at the two ends of the heterodimer stems. Two candidate beacons, C17LC21 and C21LC21, can detect the S-RBD with limits of detection (LoD) in the sub-picomolar range. We envision that these beacons can be easily integrated with on-chip optical sensors to construct a point-of-care diagnostic platform for SARS-CoV-2.Competing Interest StatementP.C., M.P., S.P.T and J.M.J. are listed as inventors for U.S. Provisional Patent Application 63/182,537 entitled "Peptide Based Probes For the Detection of SARS-CoV-2."