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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{Climent-Catala:2023:10.1021/acssynbio.3c00599,
author = {Climent-Catala, A and Casas-Rodrigo, I and Iyer, S and Ledesma-Amaro, R and Ouldridge, TE},
doi = {10.1021/acssynbio.3c00599},
journal = {ACS Synthetic Biology},
pages = {3754--3765},
title = {Evaluating DFHBI-responsive RNA light-up aptamers as fluorescent reporters for gene expression},
url = {http://dx.doi.org/10.1021/acssynbio.3c00599},
volume = {12},
year = {2023}
}

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RIS format (EndNote, RefMan)

TY - JOUR
AB - Protein-based fluorescent reporters have been widely used to characterize and localize biological processes in living cells. However, these reporters may have certain drawbacks for some applications, such as transcription-based studies or biological interactions with fast dynamics. In this context, RNA nanotechnology has emerged as a promising alternative, suggesting the use of functional RNA molecules as transcriptional fluorescent reporters. RNA-based aptamers can bind to nonfluorescent small molecules to activate their fluorescence. However, their performance as reporters of gene expression in living cells has not been fully characterized, unlike protein-based reporters. Here, we investigate the performance of three RNA light-up aptamersF30-2xdBroccoli, tRNA-Spinach, and Tornado Broccolias fluorescent reporters for gene expression in Escherichia coli and compare them to a protein reporter. We examine the activation range and effect on the cell growth of RNA light-up aptamers in time-course experiments and demonstrate that these aptamers are suitable transcriptional reporters over time. Using flow cytometry, we compare the variability at the single-cell level caused by the RNA fluorescent reporters and protein-based reporters. We found that the expression of RNA light-up aptamers produced higher variability in a population than that of their protein counterpart. Finally, we compare the dynamical behavior of these RNA light-up aptamers and protein-based reporters. We observed that RNA light-up aptamers might offer faster dynamics compared to a fluorescent protein in E. coli. The implementation of these transcriptional reporters may facilitate transcription-based studies, gain further insights into transcriptional processes, and expand the implementation of RNA-based circuits in bacterial cells.
AU - Climent-Catala,A
AU - Casas-Rodrigo,I
AU - Iyer,S
AU - Ledesma-Amaro,R
AU - Ouldridge,TE
DO - 10.1021/acssynbio.3c00599
EP - 3765
PY - 2023///
SN - 2161-5063
SP - 3754
TI - Evaluating DFHBI-responsive RNA light-up aptamers as fluorescent reporters for gene expression
T2 - ACS Synthetic Biology
UR - http://dx.doi.org/10.1021/acssynbio.3c00599
UR - https://www.ncbi.nlm.nih.gov/pubmed/37991880
UR - https://pubs.acs.org/doi/10.1021/acssynbio.3c00599
UR - http://hdl.handle.net/10044/1/108357
VL - 12
ER -