This year, the BIOMOD team at Colorado State University researched into a revolutionary new way to sense viral RNA by concentrating a molecular beacon in a protein crystal. The crystal has pores that allow the molecular beacon to enter and covalently attach to the crystal. The beacon is designed to have a fluorophore on one end and a quencher on the other end. When the beacon is attached to the crystal, the quencher should absorb most of the fluorescence, but when its complementary sequence comes and pairs to the beacon, it will open and the quencher will be too far away to absorb the fluorescence. This will allow for visible detection of the virus. Protein crystals then act as a carrier for the molecular beacon and can be used to amplify the fluorescence signal by concentrating the beacons in a small area.
The design of our biosensor was carefully assessed using a variety of programs. By following the methods provided in the computational notebook, beacons can be designed and optimized for a virus with ease. Once designs have been chosen, molecular dynamic simulations and laboratory experiments can be done for proof of concept. Check out the computational notebook in the link below.