We developed a biodevice capable of detecting miR-21 and miR-92a based on Ma et al. (2022)’s LIRA (Loop Initiated RNA Activator) design. As far as we know, our team was the first to develop such system based on the LIRA framework. The sequence encoded in the part will form a multi-arm RNA junction once transcribed inside the bacterial cell. The multi-arm junction, which includes from upstream are miR21 binding site and miR92a binding site in the form of a hairpin loop for each binding site, an rbs sequence, and followed by start codon acts as an OR-gate mechanism that will open when miR-21 or miR-92a is present in the environment and is taken up by the bacterium, thus allowing for the translation of elements downstream of the part. Here is our new basic part BBa_K4914000, we got this from our Toehold LIRA Optimization Design Process which can be seen on the Model Page.

Our new composite part BBa_K4914001 consists of the T7 minimal promoter BBa_K1614000 , the LIRA sequence BBa_K4914000, the aeBlue chromoprotein coding sequence BBa_K864401, and double terminator BBa B0010, BBa B0012. The composite part could be transcribed as a functional RNA that could detect miR-21 or miR-92a, and express aeBlue chromoprotein in response.

To address minimal wetlab data and implementation of LIRA switch, we construct analogical ON-OFF metrics based on simulated secondary structure of LIRA switch. Some considerations included such as probabilities of secondary structure from sub-sequence RBS to start codon, concentration rank result of each complex prediction in simulation, and mathematically modeled logical projection of several complexes probabilities.

The ON-OFF performance of biomarkers largely depends on the accuracy performance of the LIRA switch. The LIRA switch itself can be customized. To address how important LIRA properties are in ON-OFF performance, we developed a multivariate regression pipeline using several schemes such as feature selection and AutoML.

A new mathematical model idea that modeling the LIRA expression system using OR Gate by considering probabilities of each complex equally in order to project prediction of AeBlue chromoprotein expression as a result of ColDBlue biodevice.