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Research

Biological systems - including the simplest cells - exhibit a broad range of functions to thrive in their environment. Research in the Imperial College Centre for Synthetic Biology is focused on the possibility of engineering the underlying biochemical processes to solve many of the challenges facing society, from healthcare to sustainable energy. In particular, we model, analyse, design and build biological and biochemical systems in living cells and/or in cell extracts, both exploring and enhancing the engineering potential of biology.

As part of our research we develop novel methods to accelerate the celebrated Design-Build-Test-Learn synthetic biology cycle. As such research in the Centre for Synthetic Biology highly multi- and interdisciplinary covering computational modelling and machine learning approaches; automated platform development and genetic circuit engineering ; multi-cellular and multi-organismal interactions, including gene drive and genome engineering; metabolic engineering; in vitro/cell-free synthetic biology; engineered phages and directed evolution; and biomimetics, biomaterials and biological engineering.

Publications

Citation

BibTex format

@article{Mukherjee:2024:10.1021/jacs.3c14673,
author = {Mukherjee, R and Sengar, A and Cabello, Garcia J and Ouldridge, T},
doi = {10.1021/jacs.3c14673},
journal = {Journal of the American Chemical Society},
pages = {18916--18926},
title = {Kinetic proofreading can enhance specificity in a non-enzymatic DNA strand displacement network},
url = {http://dx.doi.org/10.1021/jacs.3c14673},
volume = {146},
year = {2024}
}

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RIS format (EndNote, RefMan)

TY  - JOUR
AB  - Kinetic proofreading is used throughout natural systems to enhance the specificity of molecular recognition. At its most basic level, kinetic proofreading uses a supply of chemical fuel to drive a recognition interaction out of equilibrium, allowing a single free-energy difference between correct and incorrect targets to be exploited two or more times. Despite its importance in biology, there has been little effort to incorporate kinetic proofreading into synthetic systems in which molecular recognition is important, such as nucleic acid nanotechnology. In this article, we introduce a DNA strand displacement-based kinetic proofreading motif, showing that the consumption of a DNA-based fuel can be used to enhance molecular recognition during a templated dimeri zation reaction. We then show that kinetic proofreading can enhance the specificity with which a probe discriminates single nucleo tide mutations, both in terms of the initial rate with which the probe reacts and the long-time behaviour.
AU  - Mukherjee,R
AU  - Sengar,A
AU  - Cabello,Garcia J
AU  - Ouldridge,T
DO  - 10.1021/jacs.3c14673
EP  - 18926
PY  - 2024///
SN  - 0002-7863
SP  - 18916
TI  - Kinetic proofreading can enhance specificity in a non-enzymatic DNA strand displacement network
T2  - Journal of the American Chemical Society
UR  - http://dx.doi.org/10.1021/jacs.3c14673
UR  - https://pubs.acs.org/doi/10.1021/jacs.3c14673
UR  - http://hdl.handle.net/10044/1/112671
VL  - 146
ER  -