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BioCircuit SIGNED

Programmable BioMolecular Circuits: Emulating Regulatory Functions in Living Cells Using a Bottom-Up Approach

Total Cost €

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EC-Contrib. €

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Partnership

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Project "BioCircuit" data sheet

The following table provides information about the project.

Coordinator
TECHNISCHE UNIVERSITEIT EINDHOVEN 

Organization address
address: GROENE LOPER 3
city: EINDHOVEN
postcode: 5612 AE
website: www.tue.nl/en

contact info
title: n.a.
name: n.a.
surname: n.a.
function: n.a.
email: n.a.
telephone: n.a.
fax: n.a.

 Coordinator Country Netherlands [NL]
 Total cost 1˙887˙180 €
 EC max contribution 1˙887˙180 € (100%)
 Programme 1. H2020-EU.1.1. (EXCELLENT SCIENCE - European Research Council (ERC))
 Code Call ERC-2015-STG
 Funding Scheme ERC-STG
 Starting year 2016
 Duration (year-month-day) from 2016-08-01   to  2021-07-31

 Partnership

Take a look of project's partnership.

# participants  country  role  EC contrib. [€] 
1    TECHNISCHE UNIVERSITEIT EINDHOVEN NL (EINDHOVEN) coordinator 1˙887˙180.00

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 Project objective

Programmable biomolecular circuits have received increasing attention in recent years as the scope of chemistry expands from the synthesis of individual molecules to the construction of chemical networks that can perform sophisticated functions such as logic operations and feedback control. Rationally engineered biomolecular circuits that robustly execute higher-order spatiotemporal behaviours typically associated with intracellular regulatory functions present a unique and uncharted platform to systematically explore the molecular logic and physical design principles of the cell. The experience gained by in-vitro construction of artificial cells displaying advanced system-level functions deepens our understanding of regulatory networks in living cells and allows theoretical assumptions and models to be refined in a controlled setting. This proposal combines elements from systems chemistry, in-vitro synthetic biology and micro-engineering and explores generic strategies to investigate the molecular logic of biology’s regulatory circuits by applying a physical chemistry-driven bottom-up approach. Progress in this field requires 1) proof-of-principle systems where in-vitro biomolecular circuits are designed to emulate characteristic system-level functions of regulatory circuits in living cells and 2) novel experimental tools to operate biochemical networks under out-of-equilibrium conditions. Here, a comprehensive research program is proposed that addresses these challenges by engineering three biochemical model systems that display elementary signal transduction and information processing capabilities. In addition, an open microfluidic droplet reactor is developed that will allow, for the first time, high-throughput analysis of biomolecular circuits encapsulated in water-in-oil droplets. An integral part of the research program is to combine the computational design of in-vitro circuits with novel biochemistry and innovative micro-engineering tools.

 Publications

year authors and title journal last update
List of publications.
2019 Job A. L. Roodhuizen, Philip J. T. M. Hendrikx, Peter A. J. Hilbers, Tom F. A. de Greef, Albert J. Markvoort
Counterion-Dependent Mechanisms of DNA Origami Nanostructure Stabilization Revealed by Atomistic Molecular Simulation
published pages: , ISSN: 1936-0851, DOI: 10.1021/acsnano.9b05650
ACS Nano 2019-09-26
2019 Alex Joesaar, Shuo Yang, Bas Bögels, Ardjan van der Linden, Pascal Pieters, B. V. V. S. Pavan Kumar, Neil Dalchau, Andrew Phillips, Stephen Mann, Tom F. A. de Greef
DNA-based communication in populations of synthetic protocells
published pages: 369-378, ISSN: 1748-3387, DOI: 10.1038/s41565-019-0399-9
Nature Nanotechnology 14/4 2019-08-29
2019 Lorena Herkert, Jörn Droste, Kalathil K. Kartha, Peter A. Korevaar, Tom F. A. de Greef, Michael Ryan Hansen, Gustavo Fernández
Pathway Control in Cooperative vs. Anti-Cooperative Supramolecular Polymers
published pages: , ISSN: 1433-7851, DOI: 10.1002/anie.201905064
Angewandte Chemie International Edition 2019-08-06
2017 Bas J. H. M. Rosier, Glenn A. O. Cremers, Wouter Engelen, Maarten Merkx, Luc Brunsveld, Tom F. A. de Greef
Incorporation of native antibodies and Fc-fusion proteins on DNA nanostructures via a modular conjugation strategy
published pages: 7393-7396, ISSN: 1359-7345, DOI: 10.1039/C7CC04178K
Chem. Commun. 53/53 2019-07-08
2017 Anniek den Hamer, Lenne J. M. Lemmens, Minke A. D. Nijenhuis, Christian Ottmann, Maarten Merkx, Tom F. A. de Greef, Luc Brunsveld
Small-Molecule-Induced and Cooperative Enzyme Assembly on a 14-3-3 Scaffold
published pages: 331-335, ISSN: 1439-4227, DOI: 10.1002/cbic.201600631
ChemBioChem 18/3 2019-07-08
2017 Alessandro Sorrenti, Jorge Leira-Iglesias, Albert J. Markvoort, Tom F. A. de Greef, Thomas M. Hermans
Non-equilibrium supramolecular polymerization
published pages: , ISSN: 0306-0012, DOI: 10.1039/C7CS00121E
Chem. Soc. Rev. 2019-07-08
2018 Davide Mariottini, Andrea Idili, Minke A. D. Nijenhuis, Tom F. A. de Greef, Francesco Ricci
DNA-Based Nanodevices Controlled by Purely Entropic Linker Domains
published pages: 14725-14734, ISSN: 0002-7863, DOI: 10.1021/jacs.8b07640
Journal of the American Chemical Society 140/44 2019-05-09
2018 Maaruthy Yelleswarapu, Ardjan J. van der Linden, Bob van Sluijs, Pascal A. Pieters, Emilien Dubuc, Tom F. A. de Greef, Wilhelm T. S. Huck
Sigma Factor-Mediated Tuning of Bacterial Cell-Free Synthetic Genetic Oscillators
published pages: 2879-2887, ISSN: 2161-5063, DOI: 10.1021/acssynbio.8b00300
ACS Synthetic Biology 7/12 2019-05-09
2019 Emilien Dubuc, Pascal A Pieters, Ardjan J van der Linden, Jan CM van Hest, Wilhelm TS Huck, Tom FA de Greef
Cell-free microcompartmentalised transcription–translation for the prototyping of synthetic communication networks
published pages: 72-80, ISSN: 0958-1669, DOI: 10.1016/j.copbio.2018.10.006
Current Opinion in Biotechnology 58 2019-05-09

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