Stanford Advisors

All Publications

  • Modular Aptamer Switches for the Continuous Optical Detection of Small-Molecule Analytes in Complex Media. Advanced materials (Deerfield Beach, Fla.) Hariri, A. A., Cartwright, A. P., Dory, C., Gidi, Y., Yee, S., Thompson, I. A., Fu, K., Yang, K., Wu, D., Maganzini, N., Feagin, T., Young, B. E., Afshar, B. H., Eisenstein, M., Digonnet, M., Vuckovic, J., Soh, H. T. 2023: e2304410


    Aptamers are a promising class of affinity reagents because signal transduction mechanisms can be built into the reagent, so that they can directly produce a physically measurable output signal upon target binding. However, endowing the signal transduction functionality into an aptamer remains a trial-and-error process that can compromise its affinity or specificity and typically requires knowledge of the ligand binding domain or its structure. In this work, we describe a design architecture that can convert an existing aptamer into a "reversible aptamer-switch" whose kinetic and thermodynamic properties can be tuned without a priori knowledge of the ligand binding domain or its structure. Finally, by combining these aptamer-switches with evanescent-field based optical detection hardware that rejects sample autofluorescence, we demonstrate the first optical biosensor system that can continuously measure multiple biomarkers (dopamine and cortisol) in complex samples (artificial cerebrospinal fluid and undiluted plasma) with second-scale time resolution at physiologically relevant concentration ranges. This article is protected by copyright. All rights reserved.

    View details for DOI 10.1002/adma.202304410

    View details for PubMedID 37975267

  • An antibody-based molecular switch for continuous small-molecule biosensing. Science advances Thompson, I. A., Saunders, J., Zheng, L., Hariri, A. A., Maganzini, N., Cartwright, A. P., Pan, J., Yee, S., Dory, C., Eisenstein, M., Vuckovic, J., Soh, H. T. 2023; 9 (38): eadh4978


    We present a generalizable approach for designing biosensors that can continuously detect small-molecule biomarkers in real time and without sample preparation. This is achieved by converting existing antibodies into target-responsive "antibody-switches" that enable continuous optical biosensing. To engineer these switches, antibodies are linked to a molecular competitor through a DNA scaffold, such that competitive target binding induces scaffold switching and fluorescent signaling of changing target concentrations. As a demonstration, we designed antibody-switches that achieve rapid, sample preparation-free sensing of digoxigenin and cortisol in undiluted plasma. We showed that, by substituting the molecular competitor, we can further modulate the sensitivity of our cortisol switch to achieve detection at concentrations spanning 3.3 nanomolar to 3.3 millimolar. Last, we integrated this switch with a fiber optic sensor to achieve continuous sensing of cortisol in a buffer and blood with <5-min time resolution. We believe that this modular sensor design can enable continuous biosensor development for many biomarkers.

    View details for DOI 10.1126/sciadv.adh4978

    View details for PubMedID 37738337