A single-input binary counting module based on serine integrase site-specific recombination

Zhao, J., Pokhilko, A., Ebenhöh, O., Rosser, S. J. and Colloms, S. D. (2019) A single-input binary counting module based on serine integrase site-specific recombination. Nucleic Acids Research, 47(9), pp. 4896-4909. (doi:10.1093/nar/gkz245) (PMID:30957849) (PMCID:PMC6511857)

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Abstract

A device that counts and records the number of events experienced by an individual cell could have many uses in experimental biology and biotechnology. Here, we report a DNA-based ‘latch’ that switches between two states upon each exposure to a repeated stimulus. The key component of the latch is a DNA segment whose orientation is inverted by the actions of ϕC31 integrase and its recombination directionality factor (RDF). Integrase expression is regulated by an external input, while RDF expression is controlled by the state of the latch, such that the orientation of the invertible segment switches efficiently each time the device receives an input pulse. Recombination occurs over a time scale of minutes after initiation of integrase expression. The latch requires a delay circuit, implemented with a transcriptional repressor expressed in only one state, to ensure that each input pulse results in only one inversion of the DNA segment. Development and optimization of the latch in living cells was driven by mathematical modelling of the recombination reactions and gene expression regulated by the switch. We discuss how N latches built with orthogonal site-specific recombination systems could be chained together to form a binary ripple counter that could count to 2N − 1.

Item Type:Articles
Status:Published
Refereed:Yes
Glasgow Author(s) Enlighten ID:Colloms, Dr Sean and Rosser, Professor Susan and Pokhilko, Dr Alexandra and Zhao, Miss Jia
Authors: Zhao, J., Pokhilko, A., Ebenhöh, O., Rosser, S. J., and Colloms, S. D.
College/School:College of Medical Veterinary and Life Sciences > Institute of Molecular Cell and Systems Biology
Journal Name:Nucleic Acids Research
Publisher:Oxford University Press
ISSN:0305-1048
ISSN (Online):1362-4962
Published Online:08 April 2019
Copyright Holders:Copyright © 2019 The Authors
First Published:First published in Nucleic Acids Research 47(9):4896–4909
Publisher Policy:Reproduced under a Creative Commons License

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Project CodeAward NoProject NamePrincipal InvestigatorFunder's NameFunder RefLead Dept
589142A platform for rapid and precise DNA module rearrangements in Synthetic BiologyWilliam StarkBiotechnology and Biological Sciences Research Council (BBSRC)BB/K003356/1RI MOLECULAR CELL & SYSTEMS BIOLOGY