In our approach to human practices, we followed one of the underlying characteristics of synthetic biology: resemblance to the field of designing electronic circuits. We created a circuit kit that emulates in hardware the designed biological constructs.

System implemented with the kit

As we described here, our team engineered a fluorescence-based sensor that provides information on both transcription strength and translation efficiency. The sensor is noninvasive, easily applied to a variety of promoters, and capable of providing results in a time frame that is short when compared to current technologies. The sensor is based on the use of an RNA aptamer (termed Spinach) and a fluorogen activating protein (FAP). Both the Spinach and FAP become fluorescent in response to binding with dye molecules.

The combination of FAP and Spinach allows to quantitatively determine relationships involving mRNA and protein, such as translational efficiency. The sensor utilizes the relationship between the rates of production of biosensors and the gene's translational efficiency and transcription rate. Spinach can be used to quantify the RNA concentration in a cell, whereas FAP is used to tag proteins.

In order to present features of the biosensor (link to the description) that we designed, and to make it more accessible to others, we built an affordable, microcontroller-based, hardware platform, and developed associated, open-source, digital simulation software.

We gave several presentations about synthetic biology and our project to high school students enrolled in the Summer Academy of Math and Science. To bridge the gap between the background of a high school student and the complexity of our project, we built and demonstrated an affordable, microcontroller-based, hardware platform and associated, open-source, digital simulation software.

The combined hardware/software platform allows the students to directly manipulate electronic components, by changing the current and/or voltage. These electronic components are formal equivalents of the BioBricks used in building the sensor, such as the promoter, the FAP, and the Spinach. Manipulating the electronic components allows for measuring with our kit the electronic equivalents of PoPs and translational efficiency. The microscope is simulated using LEDs and a photoresistor.

The software that is used in the platform is based on the model that we derived for the analysis of the sensor. We have also created a GUI that allows users to interact with the components of the model and read the results from the table and graphical output representing fluorescence of mRNA and protein over time.

The hardware/software platform allows for comparing different promoters and observing which ones are the strongest. The kit allows for a convenient hands-on experience that helps students understand how all parts of the model affect the mRNA and protein production, without working in the wet lab.