In this section

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{Irmisch:2020:10.1021/jacs.0c03105,
author = {Irmisch, P and Ouldridge, TE and Seidel, R},
doi = {10.1021/jacs.0c03105},
journal = {Journal of the American Chemical Society},
pages = {11451--11463},
title = {Modelling DNA-strand displacement reactions in the presence of base-pair mismatches},
url = {http://dx.doi.org/10.1021/jacs.0c03105},
volume = {142},
year = {2020}
}

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RIS format (EndNote, RefMan)

TY  - JOUR
AB  - Toehold-mediated strand displacement is the most abundantly used method to achieve dynamic switching in DNA-based nanotechnology. An ‘invader’ strand binds to the ‘toehold’ overhang of a target strand and replaces a target-bound ’incumbent’ strand. Hereby, complementarity of the invader to the single-stranded toehold provides the energetic bias of the reaction. Despite the widespread use of strand displacement reactions for realizing dynamic DNA nanostructures, variants on the basic motif have not been completely characterized. Here we introduce a simple thermodynamic model, which is capable of quantitatively describing the kinetics of strand displacement reactions in the presence of mismatches, using a minimal set of parameters. Furthermore, our model highlights that base pair fraying and internal loop formation are important mechanisms when involving mismatches in the displacement process. Our model should provide a helpful tool for the rational design of strand-displacement reaction networks.
AU  - Irmisch,P
AU  - Ouldridge,TE
AU  - Seidel,R
DO  - 10.1021/jacs.0c03105
EP  - 11463
PY  - 2020///
SN  - 0002-7863
SP  - 11451
TI  - Modelling DNA-strand displacement reactions in the presence of base-pair mismatches
T2  - Journal of the American Chemical Society
UR  - http://dx.doi.org/10.1021/jacs.0c03105
UR  - https://pubs.acs.org/doi/10.1021/jacs.0c03105
UR  - http://hdl.handle.net/10044/1/79655
VL  - 142
ER  -