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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{Khara:2017:nar/gkx1282,
author = {Khara, DC and Schreck, JS and Tomov, TE and Berger, Y and Ouldridge, TE and Doye, JPK and Nir, E},
doi = {nar/gkx1282},
journal = {Nucleic Acids Research},
pages = {1553--1561},
title = {DNA bipedal motor walking dynamics: an experimental and theoretical study of the dependency on step size},
url = {http://dx.doi.org/10.1093/nar/gkx1282},
volume = {46},
year = {2017}
}

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RIS format (EndNote, RefMan)

TY  - JOUR
AB  - We present a detailed coarse-grained computer simulation and single molecule fluorescence study of the walking dynamics and mechanism of a DNA bipedal motor striding on a DNA origami. In particular, we study the dependency of the walking efficiency and stepping kinetics on step size. The simulations accurately capture and explain three different experimental observations. These include a description of the maximum possible step size, a decrease in the walking efficiency over short distances and a dependency of the efficiency on the walking direction with respect to the origami track. The former two observations were not expected and are non-trivial. Based on this study, we suggest three design modifications to improve future DNA walkers. Our study demonstrates the ability of the oxDNA model to resolve the dynamics of complex DNA machines, and its usefulness as an engineering tool for the design of DNA machines that operate in the three spatial dimensions.
AU  - Khara,DC
AU  - Schreck,JS
AU  - Tomov,TE
AU  - Berger,Y
AU  - Ouldridge,TE
AU  - Doye,JPK
AU  - Nir,E
DO  - nar/gkx1282
EP  - 1561
PY  - 2017///
SN  - 0305-1048
SP  - 1553
TI  - DNA bipedal motor walking dynamics: an experimental and theoretical study of the dependency on step size
T2  - Nucleic Acids Research
UR  - http://dx.doi.org/10.1093/nar/gkx1282
UR  - http://hdl.handle.net/10044/1/55610
VL  - 46
ER  -