Adaptive molecular recognition strategies for multimodal sensing in biological systems
Embargo Date
2027-05-22
OA Version
Citation
Abstract
The growing demand for rapid, accurate, and accessible diagnostic tools has underscored the need for generalizable systems in molecular sensing, capable of addressing diverse biological targets and evolving threats. This dissertation advances the field by developing innovative molecular recognition strategies for multimodal sensing, with a focus on creating adaptable platforms for antigen detection and ribonucleic acid (RNA) regulation. First, I introduce the Rapid and Modular Nanobody Assay (RAMONA), a versatile platform that leverages nanobody-coiled coil conjugates for programmable antigen detection and modular integration with downstream readout methods. Its compatibility with cell-free systems and robustness to environmental factors enable on-demand biomanufacturing and rapid adaptation for diverse target detection, thereby facilitating scalable deployment in low-resource settings. Building on this, I present nanobody-oligo conjugates that integrate RAMONA with Cas12a for signal amplification, leveraging oligo manipulation techniques to conditionally activate Cas12a’s multiple turnover activity upon target antigen binding. In the RNA context, I explore programmable translational regulation via the development of de novo pseudoknots (PKs) in mammalian cells. I describe a computational algorithm for de novo PK design and experimental methods to evaluate their impact on translation, highlighting design considerations beyond traditional parameters for nucleic acid design. Insights from this pioneering work manipulating an emerging class of translational regulators lay the groundwork for a generalizable framework to generate “designer” PKs capable of tunable RNA regulation. Such devices have potential to offer a compact and adaptable solution to overcome limitations in payload capacity for existing delivery vehicles.
Overall, this work advances programmable molecular sensing strategies to expand the scope of capabilities for antigen and RNA detection. The findings presented here pave the way for future innovations in adaptive biological sensing, with broad implications for global public health preparedness and response.
Description
2025
License
Attribution-NonCommercial-NoDerivatives 4.0 International