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SynBio tools

Binding measurement


Understanding the kinetics of molecular binding is important in optimising engineered biology.

Systems exist to measure these interactions but they only operate on a limited number of samples simultaneously.  This limits the overall throughput of measurement – which is a problem in large experiments such as aptamer screening. The consumables are also bespoke and often expensive.

We wanted to build a highly parallel measurement system for kinetic binding, capable of measuring hundreds of binding events simultaneously on a standard microscope slide.


To tackle the problem, we used a novel interferometric detection approach invented by our optics experts.

Robust, monolithic optics is used to focus two mutually coherent illumination regions on to the slide surface. The interference between the projected regions is imaged to produce a fringe field on the detector. Binding sites and reference sites are located in one illumination region and reference sites only in the other. Common-mode noise is eliminated by measuring the differences between binding and reference sites in the two regions.

Once the concept was established, we used mathematical simulation to optimise the optical layout and built a test rig in our optics lab. Custom MATLAB code was written to log the raw interference data from the sensor and perform the required signal analysis to characterise the change in fringe field – and thus determine the height change – from additional material binding to the slide surface.


Our new approach shows we can measure the binding of small molecules to surfaces over time in a highly parallel format using a standard glass slide.

It opens up the possibility of creating a low-cost open-access instrument for measuring binding kinetics. This addresses the important issue in synthetic biology of providing robust tools that reduce the time taken to characterise and optimise genetic circuits and their outputs.

We’re now working on characterising fully the design – and measuring the limit of detection, and repeatability, for different protein-protein interactions.