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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{Liu:2021:10.1021/acssynbio.1c00336,
author = {Liu, H and Hong, F and Smith, F and Goertz, J and Ouldridge, T and Stevens, MM and Yan, H and ulc, P},
doi = {10.1021/acssynbio.1c00336},
journal = {ACS Synthetic Biology},
pages = {3066--3073},
title = {Kinetics of RNA and RNA:DNA hybrid strand displacement},
url = {http://dx.doi.org/10.1021/acssynbio.1c00336},
volume = {10},
year = {2021}
}

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RIS format (EndNote, RefMan)

TY  - JOUR
AB  - In nucleic acid nanotechnology, strand displacement is a widely used mechanism where one strand from a hybridized duplex is exchanged with an invading strand that binds to a toehold, a single-stranded region on the duplex. It is used to perform logic operations on a molecular level, initiate cascaded reactions, or even for in vivo diagnostics and treatments. While systematic experimental studies have been carried out to probe the kinetics of strand displacement in DNA with different toehold lengths, sequences, and mismatch positions, there has not been a comparable investigation of RNA or RNA-DNA hybrid systems. Here, we experimentally study how toehold length, toehold location (5' or 3' end of the strand), and mismatches influence the strand displacement kinetics. We observe reaction acceleration with increasing toehold length and placement of the toehold at the 5' end of the substrate. We find that mismatches closer to the interface of toehold and duplex slow down the reaction more than remote mismatches. A comparison of RNA and DNA displacement with hybrid displacement (RNA invading DNA or DNA invading RNA) is partly explainable by the thermodynamic stabilities of the respective toehold regions, but also suggests that the rearrangement from B-form to A-form helix in the case of RNA invading DNA might play a role in the kinetics.
AU  - Liu,H
AU  - Hong,F
AU  - Smith,F
AU  - Goertz,J
AU  - Ouldridge,T
AU  - Stevens,MM
AU  - Yan,H
AU  - ulc,P
DO  - 10.1021/acssynbio.1c00336
EP  - 3073
PY  - 2021///
SN  - 2161-5063
SP  - 3066
TI  - Kinetics of RNA and RNA:DNA hybrid strand displacement
T2  - ACS Synthetic Biology
UR  - http://dx.doi.org/10.1021/acssynbio.1c00336
UR  - https://www.ncbi.nlm.nih.gov/pubmed/34752075
UR  - https://pubs.acs.org/doi/10.1021/acssynbio.1c00336
UR  - http://hdl.handle.net/10044/1/92445
VL  - 10
ER  -