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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{Ouldridge:2020:10.1038/s41467-020-16353-y,
author = {Ouldridge, T and Turberfield, A and Mullor, Ruiz I and Louis, A and Bath, J and Haley, N and Geraldini, A},
doi = {10.1038/s41467-020-16353-y},
journal = {Nature Communications},
title = {Design of hidden thermodynamic driving for non-equilibrium systems via mismatch elimination during DNA strand displacement},
url = {http://dx.doi.org/10.1038/s41467-020-16353-y},
volume = {11},
year = {2020}
}

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RIS format (EndNote, RefMan)

TY  - JOUR
AB  - Recent years have seen great advances in the development of synthetic self-assembling molecular systems. Designing out-of-equilibrium architectures, however, requires a more subtle control over the thermodynamics and kinetics of reactions. We propose a mechanism for enhancing the thermodynamic drive of DNA strand-displacement reactions whilst barely perturbing forward reaction rates: the introduction of mismatches within the initial duplex. Through a combination of experiment and simulation, we demonstrate that displacement rates are strongly sensitive to mismatch location and can be tuned by rational design. By placing mismatches away from duplex ends, the thermodynamic drive for a strand-displacement reaction can be varied without significantly affecting the forward reaction rate. This hidden thermodynamic driving motif is ideal for the engineering of non-equilibrium systems that rely on catalytic control and must be robust to leak reactions.
AU  - Ouldridge,T
AU  - Turberfield,A
AU  - Mullor,Ruiz I
AU  - Louis,A
AU  - Bath,J
AU  - Haley,N
AU  - Geraldini,A
DO  - 10.1038/s41467-020-16353-y
PY  - 2020///
SN  - 2041-1723
TI  - Design of hidden thermodynamic driving for non-equilibrium systems via mismatch elimination during DNA strand displacement
T2  - Nature Communications
UR  - http://dx.doi.org/10.1038/s41467-020-16353-y
UR  - http://hdl.handle.net/10044/1/79487
VL  - 11
ER  -