The engineering of logic gates in living cells is inspired by electronic designs. Recombinase logic gates are modular, compact, function in many species and can hold memory. The recombination reaction which inverts or excises DNA is irreversible and have applications in memory associated systems that involve end-point measurements such as biosensing and diagnostics. Memory of logic states are written in the DNA and can be retrieved by PCR and DNA sequencing even if the cells die. Recombinase logic gates are built in different arrangements of recombination sites and regulatory elements.
In 2018 a research group by Jerome Bonnet at University of Montpellier, France, presented a framework for the systematic design of logic gates in an autonomous multicellular consortium based on site-specific recombinases. The group used a Distributed Muliticellular Computation (DMC) approach. The type of recombinase used was serine integrase which catalyze site-specific recombination which can result in excision or inversion depending on whether the attachment sites are oriented in parallel or antiparallel. The researchers have made their framework accessible on the web platform Composable Asynchronous Logic using Integrase Networks (CALIN) where truth tables can be used as inputs for retrieving DNA designs and sequence outputs.
Bonnet’s group designed switches based on integrase-mediated excision. The IDENTITY element (ID-element) has a recombination site flanked transcriptional terminator placed between the promoter and output gene, so that when excised, the gene is expressed. Their NOT-element is composed of a promoter flanked by recombination sites that drives the output gene so that in the presence of signal, the gene is not expressed. Their system is arranged in a hierarchial composition. Cell-cell communication channels are not needed, nor do the cells need to be spatially separated. The autonomous multicellular consortia operates without an external physical device. The researchers noted that cultivating a high number of strains together could pose some challenges.
In 2019 Bonnet’s group demonstrated the application of their framework in the building of a recombinase logic device family that supports up to 4-input Boolean logic in a multicellular system.