Envirome Monitoring with CRISPR Biosensors

In recent years, there has been an increase in low-cost and open-source electronic and chemical sensors that hobbyists, concerned citizens, and grassroots organizations have installed within their local environment. These sensors provide high-quality data on air and water conditions, allowing individuals to collect longitudinal datasets by monitoring how their local ecosystems are changing. Unfortunately, biological sensing, sensing that uses biological molecules to detect a specific chemical or biological substance, has lagged behind. This is primarily due to the high costs associated with laboratory-grade testing and the need for specialized equipment. The ability to use biology to better sense in the biological dimension is key to generating  higher-resolution portraits of our ecosystems, helping us learn more and react quicker to the changes we see.

This project focus on developing biological sensors which leverage the unique collateral cleavage  property Cas12a, a CRISPR nuclease, to create a novel biosensor  [1,2].  This breakthrough allows for highly sequence-specific nucleic acid-targeting biosensors (able to even detect single base changes) that provide a response on the order of minutes rather than days typically needed to culture or sequence samples. These sensors have detected targets present at the attomolar level and have successfully been freeze-dried on a variety of substrates, eliminating the need for cold chain reagent storage. 

This project will serve as the the proof of concept for  paper-based  one-pot SHERLOCK sensors and a companion incubator/reader which are designed for out-of-lab monitoring and fieldwork.  Experiments are being run to test the applicability both as a tool for community-based  microbial water monitoring as well as for microbial monitoring in a  microgravity environment. This project is funded in part by the SEI-TRISH Seed Grant Program and National Geographic. 

Collaborators:  Collins Lab, MIT ; Space Exploration Initiative, MIT Media Lab; Open Ocean Initiative, MIT Media Lab.