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Abstract
Many of the most important applications predicted to arise from Synthetic Biology will require engineered cellular memory with the capability to store data in a rewritable and reversible manner upon induction by transient stimuli. DNA recombination provides an ideal platform for cellular data storage and has allowed the development of a rewritable recombinase addressable data (RAD) module, capable of efficient data storage within a chromosome. Here, we develop the first detailed mechanistic model of DNA recombination, and validate it against a new set of in vitro data on recombination efficiencies across a range of different concentrations of integrase and gp3. Investigation of in vivo recombination dynamics using our model reveals the importance of fully accounting for all mechanistic features of DNA recombination in order to accurately predict the effect of different switching strategies on RAD module performance, and highlights its usefulness as a design tool for building future synthetic circuitry.
Highlights
S YNTHETIC Biology is a relatively young field with immense potential in numerous applications at the interface of engineering and biology [1]–[5]
One integrase dimer bound to attB and attP is necessary to mediate the integration reaction [11], [13]–[21], [23]–[26], [28]–[54], which is unidirectional [11], [13], [14], BOWYER et al.: MECHANISTIC MODELING OF A REWRITABLE RECOMBINASE ADDRESSABLE DATA MODULE
The dissociation of gp3 gives rise to the intermediate DBPI4R complex and, with recombination dynamics revealed the importance of fully accounting for all mechanistic details in models of DNA recombination, in order to accurately predict the effect of different switching strategies on recombinase addressable data (RAD) module performance
Summary
S YNTHETIC Biology is a relatively young field with immense potential in numerous applications at the interface of engineering and biology [1]–[5]. One integrase dimer bound to attB and attP is necessary to mediate the integration reaction [11], [13]–[21], [23]–[26], [28]–[54], which is unidirectional (irreversible) [11], [13], [14], BOWYER et al.: MECHANISTIC MODELING OF A REWRITABLE RECOMBINASE ADDRESSABLE DATA MODULE [17], [18], [20], [24], [26], [28]–[30], [32], [35], [37], [38], [42], [43], [45], [48], [50]–[57] This gives the following additional dynamics: DBP + I2 k4 DBPI2. In each case the full system of ODEs is solved numerically in order to determine the total register, that is, no attempt is made to reduce complexity as we look to retain mechanistic detail
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