Abstract
Biological records are omnipresent in paleontology, history, and climate science. Tree rings and ice cores provide evidence of environmental conditions that have been recorded in the composition of materials that are deposited over time, carrying with them a record of events that have influenced their existence before being buried underneath ice or inside the trunk of a tree. We constructed a proof of concept synthetic circuit that can be used to create a similar chronological record of events in the DNA of a living E. coli. In our system, phage-based serine integrases are employed to sequentially integrate pieces of DNA corresponding to which stimulus is being detected. We show that placing attB and attP sites close together on a piece of DNA prevents intramolecular reactions, and enables repeated integration events to expand a genetic locus proportionally to integrase induction and abundance of plasmid DNA. We also show that dCas9 binding can prevent integrase from reacting with an attachment site, and in so doing we can control which piece of DNA is integrated by the induction of different guide RNAs. These results represent significant steps towards an event logger that is capable of recording the ordering and magnitude of any number of molecular events. Such a system may be useful in studying complex biological phenomena such as biofilm formation, quorum sensing, or signaling in the gut.
