Mechanistic modelling of a recombinase‐based two‐input temporal logic gate

Abstract

Site-specific recombinases (SSRs) mediate efficient manipulation of DNA sequences in vitro and in vivo. In particular, serine integrases have been identified as highly effective tools for facilitating DNA inversion, enabling the design of genetic switches that are capable of turning the expression of a gene of interest on or off in the presence of a SSR protein. The functional scope of such circuitry can be extended to biological Boolean logic operations by incorporating two or more distinct integrase inputs. To date, mathematical modelling investigations have captured the dynamical properties of integrase logic gate systems in a purely qualitative manner, and thus such models are of limited utility as tools in the design of novel circuitry. Here, the authors develop a detailed mechanistic model of a twoinput temporal logic gate circuit that can detect and encode sequences of input events. Their model demonstrates quantitative agreement with time-course data on the dynamics of the temporal logic gate, and is shown to subsequently predict dynamical responses relating to a series of induction separation intervals. The model can also be used to infer functional variations between distinct integrase inputs, and to examine the effect of reversing the roles of each integrase on logic gate output.

Serine Integrases: Advancing Synthetic Biology

“…103 A mechanistic model of this two-input temporal logic gate has been developed. 104 The serine-interase logic and memory devices discussed up to this point rearrange DNA to produce stable, heritable, permanent outputs. While such devices are ideal for recording one-off historical events such as the presence of an environmental signal, rewritable devices are being developed to enable counting of real-time, dynamic biological processes such as cell divisions.…”

Low-Burden Biological Feedback Controllers for Near-Perfect Adaptation

“…Initially, we have Δ, Θ = 1; variation from this value represents introduction of a disturbance. Integrase/excisionase mediated DNA flipping is described by where r on,off are scaling factors for the rates of DNA inversion, K I , X are equilibrium constants that determine the concentration of each protein required for the half-maximum flipping rate to be achieved, and the order four Hill functions arise due to four molecules of each protein being required (one dimer at each recognition site) to perform DNA inversion. , A summary of the model parameters is provided in Table , and the numerical values used in simulations are discussed in Supplementary Section 1.…”

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

“…These results can provide answers to experimental hypotheses and hence inform the planning and enactment of subsequent experimental studies, saving time and resources. The dissemination of mathematical modelling approaches is important in establishing a wide-ranging archive of useful tools for the design and implementation of novel circuitry across synthetic biology [40][41][42][43][44][45]. In this paper, we present the first mechanistic mathematical model of the 2-input BLADE platform developed in [8].…”