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

Project Information

BioCircuit

Grant agreement ID: 677313

DOI 10.3030/677313

Project closed

EC signature date 8 March 2016

Start date 1 August 2016

End date 31 January 2022

Funded under

• EXCELLENT SCIENCE - European Research Council (ERC)

Total cost € 1 887 180,00

EU contribution € 1 887 180,00

Coordinated by

TECHNISCHE UNIVERSITEIT EINDHOVEN
Netherlands

Publications

Peer reviewed articles (24)

Dynamic modulation of proximity-induced enzyme activity using supramolecular polymers

Author(s): Eva Magdalena Estirado, Bas J. H. M. Rosier, Tom F. A. de Greef and Luc Brunsveld
Published in: Chemical Communications, 2020, ISSN 1359-7345
Publisher: Royal Society of Chemistry
DOI: 10.1039/d0cc02120b

Engineered Living Materials based on Adhesin-mediated Trapping of Programmable Cells

Author(s): Maxime C.M. van den Oetelaar; Maarten Merkx; Pim L. Joostens; Tim van der Hek; Yahav Rave; Mick P.A. Verhagen; Kees Verduin; Laura S. van Hazendonk; Guido J.M. Oerlemans; Shuaiqi Guo; Mariska Brüls; Sander R. Keij; Weizhou Xing; Emilien Dubuc; Jetske Stalpers; Simone A.E. Twisk; Bruno V. Eijkens; Roy J. E. A. Boonen; M Marieke Gerth; Ilja K. Voets; Tom F. A. de Greef; Manoj Sharma; Martijn Nijs
Published in: ACS Synthetic Biology, 2020, ISSN 2161-5063
Publisher: American Chemical Society
DOI: 10.1101/734350

Supramolecular interactions between catalytic species allow rational control over reaction kinetics

Author(s): Abraham J. P. Teunissen, Tim F. E. Paffen, Ivo A. W. Filot, Menno D. Lanting, Roy J. C. van der Haas,Tom F. A. de Greef, E. W. Meijer
Published in: Chemical Science, 2019, ISSN 2041-6520
Publisher: Royal Society of Chemistry
DOI: 10.1039/c9sc02357g

Regulating Competing Supramolecular Interactions Using Ligand Concentration

Author(s): Abraham J. P. Teunissen; Tim F. E. Paffen; Gianfranco Ercolani; Tom F. A. de Greef; E. W. Meijer
Published in: VOLUME=138;ISSUE=21;STARTPAGE=6852;ENDPAGE=6860;ISSN=0002-7863;TITLE=Journal of the American Chemical Society, Issue 3, 2016, ISSN 0002-7863
Publisher: American Chemical Society
DOI: 10.1021/jacs.6b03421

Determinants of Ligand-Functionalized DNA Nanostructure-Cell Interactions

Author(s): Glenn A.O. Cremers; Bas J.H.M. Rosier; Ab Meijs; Ab Meijs; Nicholas B. Tito; Sander M.J. van Duijnhoven; Hans van Eenennaam; Lorenzo Albertazzi; Tom F. A. de Greef
Published in: Journal of the American Chemical Society, Issue 2, 2021, ISSN 0002-7863
Publisher: American Chemical Society
DOI: 10.3929/ethz-b-000498818

A Multilayer Microfluidic Platform for the Conduction of Prolonged Cell-Free Gene Expression

Author(s): Ardjan J. van der Linden, Maaruthy Yelleswarapu, Pascal A. Pieters, Zoe Swank, Wilhelm T. S. Huck, Sebastian J. Maerkl, Tom F. A. de Greef
Published in: Journal of Visualized Experiments, 2019, ISSN 1940-087X
Publisher: MYJoVE Corporation
DOI: 10.3791/59655

Designed Asymmetric Protein Assembly on a Symmetric Scaffold

Author(s): Lenne J. M. Lemmens, Job A. L. Roodhuizen, Tom F. A. de Greef, Albert J. Markvoort, Luc Brunsveld
Published in: Angewandte Chemie, 2020, ISSN 1433-7851
Publisher: John Wiley & Sons Ltd.
DOI: 10.1002/anie.202003626

Proximity-induced caspase-9 activation on a DNA origami-based synthetic apoptosome

Author(s): Bas J. H. M. Rosier, Albert J. Markvoort, Berta Gumí Audenis, Job A. L. Roodhuizen, Anniek den Hamer, Luc Brunsveld, Tom F. A. de Greef
Published in: Nature Catalysis, Issue 3/3, 2020, Page(s) 295-306, ISSN 2520-1158
Publisher: Nature Springer
DOI: 10.1038/s41929-019-0403-7

Assembly of Dynamic Supramolecular Polymers on a DNA Origami Platform

Author(s): Jurgen Schill,Bas J. H. M. Rosier,Berta Gumí Audenis, Eva Magdalena Estirado,Tom F. A. de Greef, Luc Brunsveld
Published in: Angewandte Chemie, 2021, ISSN 1433-7851
Publisher: John Wiley & Sons Ltd.
DOI: 10.1002/ange.202016244

Hierarchical control of enzymatic actuators using DNA-based switchable memories

Author(s): Lenny H. H. Meijer, Alex Joesaar, Erik Steur, Wouter Engelen, Rutger A. van Santen, Maarten Merkx, Tom F. A. de Greef
Published in: Nature Communications, Issue 8/1, 2017, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-017-01127-w

DNA-Based Nanodevices Controlled by Purely Entropic Linker Domains

Author(s): Davide Mariottini, Andrea Idili, Minke A. D. Nijenhuis, Tom F. A. de Greef, Francesco Ricci
Published in: Journal of the American Chemical Society, Issue 140/44, 2018, Page(s) 14725-14734, ISSN 0002-7863
Publisher: American Chemical Society
DOI: 10.1021/jacs.8b07640

Cell-free microcompartmentalised transcription–translation for the prototyping of synthetic communication networks

Author(s): Emilien Dubuc, Pascal A Pieters, Ardjan J van der Linden, Jan CM van Hest, Wilhelm TS Huck, Tom FA de Greef
Published in: Current Opinion in Biotechnology, Issue 58, 2019, Page(s) 72-80, ISSN 0958-1669
Publisher: Elsevier BV
DOI: 10.1016/j.copbio.2018.10.006

Sigma Factor-Mediated Tuning of Bacterial Cell-Free Synthetic Genetic Oscillators

Author(s): Maaruthy Yelleswarapu, Ardjan J. van der Linden, Bob van Sluijs, Pascal A. Pieters, Emilien Dubuc, Tom F. A. de Greef, Wilhelm T. S. Huck
Published in: ACS Synthetic Biology, Issue 7/12, 2018, Page(s) 2879-2887, ISSN 2161-5063
Publisher: American Chemical Society
DOI: 10.1021/acssynbio.8b00300

DNA-based communication in populations of synthetic protocells

Author(s): 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
Published in: Nature Nanotechnology, Issue 14/4, 2019, Page(s) 369-378, ISSN 1748-3387
Publisher: Nature Publishing Group
DOI: 10.1038/s41565-019-0399-9

Pathway Control in Cooperative vs. Anti-Cooperative Supramolecular Polymers

Author(s): Lorena Herkert, Jörn Droste, Kalathil K. Kartha, Peter A. Korevaar, Tom F. A. de Greef, Michael Ryan Hansen, Gustavo Fernández
Published in: Angewandte Chemie International Edition, 2019, ISSN 1433-7851
Publisher: John Wiley & Sons Ltd.
DOI: 10.1002/anie.201905064

Counterion-Dependent Mechanisms of DNA Origami Nanostructure Stabilization Revealed by Atomistic Molecular Simulation

Author(s): Job A. L. Roodhuizen, Philip J. T. M. Hendrikx, Peter A. J. Hilbers, Tom F. A. de Greef, Albert J. Markvoort
Published in: ACS Nano, 2019, ISSN 1936-0851
Publisher: American Chemical Society
DOI: 10.1021/acsnano.9b05650

Incorporation of native antibodies and Fc-fusion proteins on DNA nanostructures via a modular conjugation strategy

Author(s): Bas J. H. M. Rosier, Glenn A. O. Cremers, Wouter Engelen, Maarten Merkx, Luc Brunsveld, Tom F. A. de Greef
Published in: Chem. Commun., Issue 53/53, 2017, Page(s) 7393-7396, ISSN 1359-7345
Publisher: Royal Society of Chemistry
DOI: 10.1039/C7CC04178K

Small-Molecule-Induced and Cooperative Enzyme Assembly on a 14-3-3 Scaffold

Author(s): Anniek den Hamer, Lenne J. M. Lemmens, Minke A. D. Nijenhuis, Christian Ottmann, Maarten Merkx, Tom F. A. de Greef, Luc Brunsveld
Published in: ChemBioChem, Issue 18/3, 2017, Page(s) 331-335, ISSN 1439-4227
Publisher: John Wiley & Sons Ltd.
DOI: 10.1002/cbic.201600631

Antibody-controlled actuation of DNA-based molecular circuits

Author(s): Wouter Engelen, Lenny H. H. Meijer, Bram Somers, Tom F. A. de Greef, Maarten Merkx
Published in: Nature Communications, Issue 8, 2017, Page(s) 14473, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/ncomms14473

Non-equilibrium supramolecular polymerization

Author(s): Alessandro Sorrenti, Jorge Leira-Iglesias, Albert J. Markvoort, Tom F. A. de Greef, Thomas M. Hermans
Published in: Chem. Soc. Rev., 2017, ISSN 0306-0012
Publisher: Royal Society of Chemistry
DOI: 10.1039/C7CS00121E

A plug-and-play platform of ratiometric bioluminescent sensors for homogeneous immunoassays

Author(s): Yan Ni, Bas J. H. M. Rosier, Eva A. van Aalen, Eva T. L. Hanckmann, Lieuwe Biewenga, Anna-Maria Makri Pistikou, Bart Timmermans, Chris Vu, Sophie Roos, Remco Arts, Wentao Li, Tom F. A. de Greef, Marcel M. G. J. van Borren, Frank J. M. van Kuppeveld, Berend-Jan Bosch & Maarten Merkx
Published in: Nature Communications, 2021, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-021-24874-3

Efficient Small-Scale Conjugation of DNA to Primary Antibodies for Multiplexed Cellular Targeting

Author(s): Glenn A. O. Cremers, Bas J. H. M. Rosier, Roger Riera Brillas, Lorenzo Albertazzi, and Tom F. A. de Greef
Published in: Bioconjugate Chem., 2019, ISSN 1043-1802
Publisher: American Chemical Society
DOI: 10.1021/acs.bioconjchem.9b00490

Cell-Free Characterization of Coherent Feed-Forward Loop-Based Synthetic Genetic Circuits

Author(s): Pascal A. Pieters, Bryan L. Nathalia, Ardjan J. van der Linden, Peng Yin, Jongmin Kim, Wilhelm T. S. Huck, and Tom F. A. de Greef
Published in: ACS Synthetic Biology, 2021, ISSN 2161-5063
Publisher: American Chemical Society
DOI: 10.1101/2021.01.11.426179

Light-Activated Signaling in DNA-Encoded Sender–Receiver Architectures

Author(s): Shuo Yang, Pascal A. Pieters, Alex Joesaar, Bas W. A. Bögels, Rens Brouwers, Iuliia Myrgorodska, Stephen Mann, Tom F. A. de Greef
Published in: ACS Nano, Issue 14/11, 2020, Page(s) 15992-16002, ISSN 1936-0851
Publisher: American Chemical Society
DOI: 10.1021/acsnano.0c07537