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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:2022:nar/gkac590,
author = {Ouldridge, T and Hertel, S and Spinney, R and Xu, S and Morris, R and Lee, L},
doi = {nar/gkac590},
journal = {Nucleic Acids Research},
pages = {7829--7841},
title = {The stability and number of nucleating interactions determine DNA hybridisation rates in the absence of secondary structure},
url = {http://dx.doi.org/10.1093/nar/gkac590},
volume = {50},
year = {2022}
}

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RIS format (EndNote, RefMan)

TY  - JOUR
AB  - The kinetics of DNA hybridisation are fundamental to biological processes and DNA-based technologies.However, the precise physical mechanisms that determine why different DNA sequences hybridise at differentrates are not well understood. Secondary structure is one predictable factor that influences hybridisation ratesbut is not sufficient on its own to fully explain the observed sequence-dependent variance. In this context, wemeasured hybridisation rates of 43 different DNA sequences that are not predicted to form secondarystructure and present a parsimonious physically justified model to quantify our observations. Accounting onlyfor the combinatorics of complementary nucleating interactions and their sequence-dependent stability, themodel achieves good correlation with experiment with only two free parameters. Our results indicate thatgreater repetition of Watson-Crick pairs increases the number of initial states able to proceed to fullhybridisation, with the stability of those pairings dictating the likelihood of such progression, thus providingnew insight into the physical factors underpinning DNA hybridisation rates.
AU  - Ouldridge,T
AU  - Hertel,S
AU  - Spinney,R
AU  - Xu,S
AU  - Morris,R
AU  - Lee,L
DO  - nar/gkac590
EP  - 7841
PY  - 2022///
SN  - 0305-1048
SP  - 7829
TI  - The stability and number of nucleating interactions determine DNA hybridisation rates in the absence of secondary structure
T2  - Nucleic Acids Research
UR  - http://dx.doi.org/10.1093/nar/gkac590
UR  - https://academic.oup.com/nar/article/50/14/7829/6649941
UR  - http://hdl.handle.net/10044/1/97924
VL  - 50
ER  -