A population-based temporal logic gate for timing and recording chemical events

Abstract

Single-cell bacterial sensors have numerous applications in human health monitoring, environmental chemical detection, and materials biosynthesis. Such bacterial devices need not only the capability to differentiate between combinations of inputs, but also the ability to process signal timing and duration. In this work, we present a two-input temporal logic gate that can sense and record the order of the inputs, the timing between inputs, and the duration of input pulses. The temporal logic gate design relies on unidirectional DNA recombination with bacteriophage integrases to detect and encode sequences of input events. When implemented in a chromosomally-modified E. coli strain, we can utilize stochastic single cell responses to predict overall heterogeneous population behavior. We show that a stochastic model can be used to predict final population distributions of this E. coli strain, and thus that final differentiated sub populations can be used to deduce the timing and duration of transient chemical events.

Fast and flexible simulation and parameter estimation for synthetic biology using bioscrape

“…Figure 3b depicts the process by which four serine integrase monomers bind to attB and attP DNA recognition sites and recombine them into attL and attR sites. In synthetic biology, this functionality has been leveraged to build synthetic gene circuits for state machines [30], temporal event detection [31], and rewritable memory [32]. However, existing applications of integrases rely on their digital behavior over long time scales (hours), and not much is known about the dynamics of their action upon DNA.…”

Rational programming of history-dependent logic in cellular populations

“…By interleaving target sites for different recombinases, recombination reactions can be made dependent on each other, and the system can transition through different DNA states depending on which recombination reaction occurs first (50,53). Using this concept, researchers started to implement genetic devices tracking the order of occurrence of signals, as well as history-dependent gene expression programs (50,54,55). These history-dependent logic devices operate at the single-cell level, and the most advanced versions use multiple mutant recombination sites recognized by the same enzyme (55).…”

A mechanistic model of the BLADE platform predicts performance characteristics of 256 different synthetic DNA recombination circuits

“…DNA recombination is a highly efficient and reliable method for manipulating genetic sequences in both bacterial and mammalian cells [14,15], and has been used to develop a wide-ranging variety of circuitry in synthetic biology, including genetic switches [16] and logic gates [17,18]. DNA recombinases are specialised proteins that are able to invert, delete or insert sections of DNA flanked by specific attachment sites [19].…”

“…That is, either transitioning the circuit between 'off' and 'on' states is compromised by the lasting effects of the RDF, or the circuit is not viable for therapeutic applications due to the necessity of constant drug induction [37]. Consequently, serine recombinases have been used to design circuitry that exploits unidirectional functions and therefore does not involve transitions back to prior states [38]. Tyrosine recombinases elicit unstable inversion reactions that are not suitable for the design of logic circuitry due to unstable and continuous reversibility ( Fig.…”

“…The analysis of synthetic biological systems through mathematical modelling approaches has become commonplace in the literature [1,2,12,29,38,39] as it offers a highly efficient method of examining the behaviour of a system subject to the perturbation of an array of different variables and parameters. These results can provide answers to experimental hypotheses and hence inform the planning and enactment of subsequent experimental studies, saving time and resources.…”