Team:GreatBay SCIE/Model
Overview
Mathematical modeling is a powerful tool in synthetic and molecular biology, as it allows us to describe the relationship between different parameters and variables during biochemical processes using a set of mathematical equations. In our project, we used mathematical modeling to obtain quantitative solutions to several problems we encounter in our project.
In one of the models, we attempted to use the basic electrophoresis approach to determine the dissociation constant of a given aptamer of amatoxin. Theoretically, by agarose gel electrophoresis of DNA, aptamer bound with the target would experience conformational change, thus being distinguished from free aptamers. The fluorescence, which is the brightness of DNA bands, could quantify the concentration of aptamer-target complex and free aptamer.
Disassociation Constant Model >
The other aims to aid the design of the ALFA test strip: we wish to arrive at a relationship between the given parameters (such as toxin concentration, aptamer concentration, membrane diffusion velocity, sample volume, etc.) and the distance between the start of the test strip and the test line in order to leave enough time for the initial reaction mixture to descend into equilibrium so the amount of excess aptamers could be assessed and reported using colloidal Gold.