Amorphous and Evolutionary DNA Nanotechnology

Project Information

AEDNA

Grant agreement ID: 694410

DOI

10.3030/694410

Project closed

EC signature date 25 May 2016

Start date 1 June 2016

End date 31 May 2021

Funded under

• EXCELLENT SCIENCE - European Research Council (ERC)

Total cost

€ 2 157 697,50

EU contribution

€ 2 157 697,50

Coordinated by

TECHNISCHE UNIVERSITAET MUENCHEN
Germany

CORDIS provides links to public deliverables and publications of HORIZON projects.

Links to deliverables and publications from FP7 projects, as well as links to some specific result types such as dataset and software, are dynamically retrieved from OpenAIRE .

Publications

Peer reviewed articles (30)

Establishing Communication Between Artificial Cells

Author(s): Lukas Aufinger, Friedrich C. Simmel
Published in: Chemistry – A European Journal, Issue 25/55, 2019, Page(s) 12659-12670, ISSN 0947-6539
Publisher: John Wiley & Sons Ltd.
DOI: 10.1002/chem.201901726

Bacterial Growth, Communication, and Guided Chemotaxis in 3D-Bioprinted Hydrogel Environments

Author(s): Julia Müller, Anna C. Jäkel, Jonathan Richter, Markus Eder, Elisabeth Falgenhauer, and Friedrich C. Simmel
Published in: ACS Applied Materials and Interfaces, 2022, ISSN 1944-8244
Publisher: American Chemical Society
DOI: 10.1021/acsami.1c20836

Riboswitch-inspired toehold riboregulators for gene regulation in <i>Escherichia coli</i>

Author(s): Tianhe Wang; Friedrich C Simmel
Published in: Nucleic Acids Research, Issue 03051048, 2022, Page(s) 4784–4798, ISSN 0305-1048
Publisher: Oxford University Press
DOI: 10.1093/nar/gkac275

Genetically Encoded Membranes for Bottom‐Up Biology

Author(s): Kilian Vogele, Tobias Pirzer, Friedrich C. Simmel
Published in: ChemSystemsChem, Issue 1/4, 2019, ISSN 2570-4206
Publisher: Wiley-VCH
DOI: 10.1002/syst.201900016

Single Cell Characterization of a Synthetic Bacterial Clock with a Hybrid Feedback Loop Containing dCas9-sgRNA

Author(s): John Henningsen, Matthaeus Schwarz-Schilling, Andreas Leibl, Joaquı́n Gutiérrez, Sandra Sagredo, and Friedrich C. Simmel
Published in: ACS Synthetic BIology, 2020, ISSN 2161-5063
Publisher: American Chemical Society
DOI: 10.1021/acssynbio.0c00438

Programming Diffusion and Localization of DNA Signals in 3D‐Printed DNA‐Functionalized Hydrogels

Author(s): Julia Müller, Anna Christina Jäkel, Dominic Schwarz, Lukas Aufinger, Friedrich C. Simmel
Published in: Small, Issue 16/31, 2020, Page(s) 2001815, ISSN 1613-6810
Publisher: Wiley - V C H Verlag GmbbH & Co.
DOI: 10.1002/smll.202001815

Single DNA Origami Detection by Nanoimpact Electrochemistry

Author(s): Evangelina Pensa, Yash Bogawat, Friedrich C. Simmel, Ibon Santiago
Published in: ChemElectroChem, 2022, ISSN 2196-0216
Publisher: Wiley-VCH
DOI: 10.1002/celc.202101696

A low-cost fluorescence reader for in vitro transcription and nucleic acid detection with Cas13a

Author(s): Florian Katzmeier, Lukas Aufinger, Aurore Dupin, Jorge Quintero, Matthias Lenz, Ludwig Bauer, Sven Klumpe, Dawafuti Sherpa, Benedikt Dürr, Maximilian Honemann, Igor Styazhkin, Friedrich C. Simmel, Michael Heymann
Published in: PLOS ONE, Issue 14/12, 2019, Page(s) e0220091, ISSN 1932-6203
Publisher: Public Library of Science
DOI: 10.1371/journal.pone.0220091

Emergence of Colloidal Patterns in ac Electric Fields

Author(s): Florian Katzmeier, Bernhard Altaner, Jonathan List, Ulrich Gerland, and Friedrich C. Simmel
Published in: Physical Review Letters, 2022, ISSN 0031-9007
Publisher: American Physical Society
DOI: 10.1103/physrevlett.128.058002

Barcoded DNA origami structures for multiplexed optimization and enrichment of DNA-based protein-binding cavities

Author(s): Ali Aghebat Rafat, Sandra Sagredo, Melissa Thalhammer, Friedrich C. Simmel
Published in: Nature Chemistry, Issue 12/9, 2020, Page(s) 852-859, ISSN 1755-4330
Publisher: Nature Publishing Group
DOI: 10.1038/s41557-020-0504-6

Synthetic cell–based materials extract positional information from morphogen gradients

Author(s): Aurore Dupin, Lukas Aufinger, Igor Styazhkin, Florian Rothfischer, Benedikt K. Kaufmann, Sascha Schwarz, Nikolas Galensowske, Hauke Clausen-Schaumann, Friedrich C. Simmel
Published in: Science Advances, 2022, ISSN 2375-2548
Publisher: AAAS
DOI: 10.1126/sciadv.abl9228

Steady-State Operationof a Cell-Free Genetic Band-Detection Circuit

Author(s): Anna Jäkel, Lukas Aufinger, Friedrich C. Simmel
Published in: ACS Synthetic Biology, 2022, ISSN 2161-5063
Publisher: American Chemical Society
DOI: 10.1021/acssynbio.2c00195

Growth of Giant Peptide Vesicles Driven by Compartmentalized Transcription–Translation Activity

Author(s): Thomas Frank, Kilian Vogele, Aurore Dupin, Friedrich C. Simmel, Tobias Pirzer
Published in: Chemistry – A European Journal, Issue 26/72, 2020, Page(s) 17356-17360, ISSN 0947-6539
Publisher: John Wiley & Sons Ltd.
DOI: 10.1002/chem.202003366

Transcriptional Interference in Toehold Switch-Based RNA Circuits

Author(s): Elisabeth Falgenhauer, Andrea Mückl, Matthaeus Schwarz-Schilling, and Friedrich C. Simmel
Published in: ACS Synthetic Biology, 2022, ISSN 2161-5063
Publisher: American Chemical Society
DOI: 10.1021/acssynbio.1c00486

Self-organizing materials built with DNA

Author(s): Friedrich C. Simmel, Rebecca Schulman
Published in: MRS Bulletin, Issue 42/12, 2017, Page(s) 913-919, ISSN 0883-7694
Publisher: Materials Research Society
DOI: 10.1557/mrs.2017.271

A DNA Nanorobot Uprises against Cancer

Author(s): Hari R. Singh, Enzo Kopperger, Friedrich C. Simmel
Published in: Trends in Molecular Medicine, Issue 24/7, 2018, Page(s) 591-593, ISSN 1471-4914
Publisher: Elsevier BV
DOI: 10.1016/j.molmed.2018.05.001

Artificial Gel-Based Organelles for Spatial Organization of Cell-Free Gene Expression Reactions

Author(s): Lukas Aufinger, Friedrich C. Simmel
Published in: Angewandte Chemie International Edition, Issue 57/52, 2018, Page(s) 17245-17248, ISSN 1433-7851
Publisher: John Wiley & Sons Ltd.
DOI: 10.1002/anie.201809374

Towards synthetic cells using peptide-based reaction compartments

Author(s): Kilian Vogele, Thomas Frank, Lukas Gasser, Marisa A. Goetzfried, Mathias W. Hackl, Stephan A. Sieber, Friedrich C. Simmel, Tobias Pirzer
Published in: Nature Communications, Issue 9/1, 2018, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-018-06379-8

Functional Surface-immobilization of Genes Using Multistep Strand Displacement Lithography

Author(s): Günther Pardatscher, Matthaeus Schwarz-Schilling, Sandra Sagredo, Friedrich C. Simmel
Published in: Journal of Visualized Experiments, Issue 140, 2018, ISSN 1940-087X
Publisher: MYJoVE Corporation
DOI: 10.3791/58634

Signalling and differentiation in emulsion-based multi-compartmentalized in vitro gene circuits

Author(s): Aurore Dupin, Friedrich C. Simmel
Published in: Nature Chemistry, Issue 11/1, 2019, Page(s) 32-39, ISSN 1755-4330
Publisher: Nature Publishing Group
DOI: 10.1038/s41557-018-0174-9

Out-of-Plane Aptamer Functionalization of RNA Three-Helix Tiles

Author(s): Aradhana Chopra, Sandra Sagredo, Guido Grossi, Ebbe Andersen, Friedrich Simmel
Published in: Nanomaterials, Issue 9/4, 2019, Page(s) 507, ISSN 2079-4991
Publisher: MDPI
DOI: 10.3390/nano9040507

Switching the activity of Cas12a using guide RNA strand displacement circuits

Author(s): Lukas Oesinghaus, Friedrich C. Simmel
Published in: Nature Communications, Issue 10/1, 2019, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-019-09953-w

Principles and Applications of Nucleic Acid Strand Displacement Reactions

Author(s): Friedrich C. Simmel, Bernard Yurke, Hari R. Singh
Published in: Chemical Reviews, Issue 119, 2019, Page(s) 6326-6369, ISSN 0009-2665
Publisher: American Chemical Society
DOI: 10.1021/acs.chemrev.8b00580

Controlling Chirality across Length Scales using DNA

Author(s): Alessandro Cecconello, Friedrich C. Simmel
Published in: Small, Issue 15, 2019, Page(s) 1805419, ISSN 1613-6810
Publisher: Wiley - V C H Verlag GmbbH & Co.
DOI: 10.1002/smll.201805419

Algorithmic Design of 3D Wireframe RNA Polyhedra

Author(s): Antti Elonen, Ashwin Karthick Natarajan, Ibuki Kawamata, Lukas Oesinghaus, Abdulmelik Mohammed, Jani Seitsonen, Yuki Suzuki, Friedrich C. Simmel, Anton Kuzyk, and Pekka Orponen
Published in: ACS Nano, Issue 19360851, 2022, ISSN 1936-0851
Publisher: American Chemical Society
DOI: 10.1021/acsnano.2c06035

Complex dynamics in a synchronized cell-free genetic clock

Author(s): Lukas Aufinger, Johann Brenner, Friedrich C. SImmel
Published in: Nature Communications, Issue 20411723, 2022, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-022-30478-2

Rational design of hybrid DNA–RNA triplex structures as modulators of transcriptional activity <i>in vitro</i>

Author(s): Alessandro Cecconello; Massimiliano Magro; Fabio Vianello; Friedrich C Simmel
Published in: Nucleic Acids Research, Issue 50, 2023, Page(s) 13172–13182, ISSN 0305-1048
Publisher: Oxford University Press
DOI: 10.1093/nar/gkac1131

Controlling gene expression in mammalian cells using multiplexed conditional guide RNAs for Cas12a

Author(s): Lukas Oesinghaus; Friedrich C. Simmel
Published in: Angewandte Chemie Int. Ed., Issue 60, 2021, Page(s) 23894-23902, ISSN 0044-8249
Publisher: Wiley-VCH
DOI: 10.1101/2021.04.16.440136

Small Antisense DNA-Based Gene Silencing Enables Cell-Free Bacteriophage Manipulation and Genome Replication

Author(s): Kilian Vogele, Elisabeth Falgenhauer, Sophie von Schönberg, Friedrich C. Simmel, Tobias Pirzer
Published in: ACS Synthetic Biology, Issue 10/3, 2021, Page(s) 459-465, ISSN 2161-5063
Publisher: American Chemical Society
DOI: 10.1021/acssynbio.0c00402

Evaluation of an E. coli cell extract prepared by lysozyme‐assisted sonication via gene expression, phage assembly and proteomics

Author(s): Elisabeth Falgenhauer, Sophie von Schönberg, Chen Meng, Andrea Mückl, Kilian Vogele, Quirin Emslander, Christina Ludwig, Friedrich Christian Simmel
Published in: ChemBioChem, 2021, ISSN 1439-4227
Publisher: John Wiley & Sons Ltd.
DOI: 10.1002/cbic.202100257