Molecular Analytical Robotics Assays

Leistungen

Upon assembly of a functional DNA pore, which is verified to insert itself in biological membrane environments, the pore will be analysed using electron cryo-tomography. Subsequently, 4D-models will be created.

4D-model of archaellum

Upon expression, purification and biochemical analysis of several wildtype and mutated archaellum subunits, the proteins will be analysed using electron cryo-microscopy. We will use the archaellum proteins from different archaea such as S. acidocaldarius, P.furiosus, M. jannaschii and Archaeoglobus fulgidus. We will also image the intact archaellar motor in situ in Haloferax volcanii cells. It is expected this variety of model organisms will ensure that structural information can be obtained. Subsequently, 4D-models will be created: a description of the mechanism that accounts for function.

DNA origami design software

Based on existing DNA origami design software a novel bioinformatic toolkit will be created to enable the automated protein embedding function into the DNA scaffold using the 4D models from WP3

Collaborative website

A website that will facilitate internal and external communication and dissemination.

Data management plan

A Data Management Plan will be elaborated within the first six months of the project, guaranteeing an appropriate disclosure of research data to the public and standardised data management within the project. The types of data that will be generated and collected within the project comprise design data (oligonucleotide sequences, technical drawings, etc.), laboratory test data (images, reaction parameters, etc.), software and metadata (final results/scientific insights, documentation, reports, publications, etc.). Three different levels of confidentiality will be defined according to IP issues and marketing strategies: classified data, IPR relevant data and public data.

Veröffentlichungen

Structure and interactions of the archaeal motility repression module ArnA–ArnB that modulates archaellum gene expression in Sulfolobus acidocaldarius

Autoren: Lena Hoffmann, Katrin Anders, Lisa F. Bischof, Xing Ye, Julia Reimann, Sunia Khadouma, Trong K. Pham, Chris van der Does, Phillip C. Wright, Lars-Oliver Essen, Sonja-Verena Albers
Veröffentlicht in: Journal of Biological Chemistry, Ausgabe 294/18, 2019, Seite(n) 7460-7471, ISSN 0021-9258
Herausgeber: American Society for Biochemistry and Molecular Biology Inc.
DOI: 10.1074/jbc.ra119.007709

In silico modelling of DNA nanostructures

Autoren: Tadija Kekic, Ivan Barisic
Veröffentlicht in: Computational and Structural Biotechnology Journal, Ausgabe 18, 2020, Seite(n) 1191-1201, ISSN 2001-0370
Herausgeber: Elsevier
DOI: 10.1016/j.csbj.2020.05.016

The Brownian and Flow‐Driven Rotational Dynamics of a Multicomponent DNA Origami‐Based Rotor

Autoren: Yasaman Ahmadi, Ashley L. Nord, Amanda J. Wilson, Christiane Hütter, Fabian Schroeder, Morgan Beeby, Ivan Barišić
Veröffentlicht in: Small, Ausgabe 16/22, 2020, Seite(n) 2001855, ISSN 1613-6810
Herausgeber: Wiley - V C H Verlag GmbbH & Co.
DOI: 10.1002/smll.202001855

Positioning of the Motility Machinery in Halophilic Archaea

Autoren: Zhengqun Li, Yoshiaki Kinosita, Marta Rodriguez-Franco, Phillip Nußbaum, Frank Braun, Floriane Delpech, Tessa E. F. Quax, Sonja-Verena Albers
Veröffentlicht in: mBio, Ausgabe 10/3, 2019, Seite(n) e00377-19, ISSN 2150-7511
Herausgeber: American Society for Microbiology
DOI: 10.1128/mBio.00377-19

Propulsive nanomachines: the convergent evolution of archaella, flagella and cilia

Autoren: Morgan Beeby, Josie L Ferreira, Patrick Tripp, Sonja-Verena Albers, David R Mitchell
Veröffentlicht in: FEMS Microbiology Reviews, Ausgabe 44/3, 2020, Seite(n) 253-304, ISSN 0168-6445
Herausgeber: Blackwell
DOI: 10.1093/femsre/fuaa006

Gene-therapy Inspired Polycation Coating for Protection of DNA Origami Nanostructures

Autoren: Yasaman Ahmadi, Ivan Barisic
Veröffentlicht in: Journal of Visualized Experiments, Ausgabe 143, 2019, ISSN 1940-087X
Herausgeber: MYJoVE Corporation
DOI: 10.3791/58771

Expanding the archaellum regulatory network - the eukaryotic protein kinases ArnC and ArnD influence motility of Sulfolobus acidocaldarius

Autoren: Lena Hoffmann, Andreas Schummer, Julia Reimann, Maria F. Haurat, Amanda J. Wilson, Morgan Beeby, Bettina Warscheid, Sonja-V. Albers
Veröffentlicht in: MicrobiologyOpen, Ausgabe 6/1, 2017, Seite(n) e00414, ISSN 2045-8827
Herausgeber: John Wiley and Sons Inc.
DOI: 10.1002/mbo3.414

(Poly)cation-induced protection of conventional and wireframe DNA origami nanostructures

Autoren: Yasaman Ahmadi, Elisa De Llano, Ivan Barišić
Veröffentlicht in: Nanoscale, Ausgabe 10/16, 2018, Seite(n) 7494-7504, ISSN 2040-3364
Herausgeber: Royal Society of Chemistry
DOI: 10.1039/C7NR09461B

ArnS, a kinase involved in starvation-induced archaellum expression

Autoren: M. Florencia Haurat, Ana Sofia Figueiredo, Lena Hoffmann, Lingling Li, Katharina Herr, Amanda J. Wilson, Morgan Beeby, Jörg Schaber, Sonja-Verena Albers
Veröffentlicht in: Molecular Microbiology, Ausgabe 103/1, 2017, Seite(n) 181-194, ISSN 0950-382X
Herausgeber: Blackwell Publishing Inc.
DOI: 10.1111/mmi.13550

Multiscale Visualization and Scale-Adaptive Modification of DNA Nanostructures

Autoren: Haichao Miao, Elisa De Llano, Johannes Sorger, Yasaman Ahmadi, Tadija Kekic, Tobias Isenberg, M. Eduard Groller, Ivan Barisic, Ivan Viola
Veröffentlicht in: IEEE Transactions on Visualization and Computer Graphics, Ausgabe 24/1, 2018, Seite(n) 1014-1024, ISSN 1077-2626
Herausgeber: Institute of Electrical and Electronics Engineers
DOI: 10.1109/TVCG.2017.2743981

DimSUM: Dimension and Scale Unifying Map for Visual Abstraction of DNA Origami Structures

Autoren: H. Miao, E. De Llano, T. Isenberg, M. E. Gröller, I. Barišić, I. Viola
Veröffentlicht in: Computer Graphics Forum, Ausgabe 37/3, 2018, Seite(n) 403-413, ISSN 0167-7055
Herausgeber: Blackwell Publishing Inc.
DOI: 10.1111/cgf.13429

Adenita: interactive 3D modelling and visualization of DNA nanostructures

Autoren: Elisa de Llano, Haichao Miao, Yasaman Ahmadi, Amanda J Wilson, Morgan Beeby, Ivan Viola, Ivan Barisic
Veröffentlicht in: Nucleic Acids Research, Ausgabe 48/15, 2020, Seite(n) 8269-8275, ISSN 0305-1048
Herausgeber: Oxford University Press
DOI: 10.1093/nar/gkaa593

The structure of the periplasmic FlaG–FlaF complex and its essential role for archaellar swimming motility

Autoren: Chi-Lin Tsai, Patrick Tripp, Shamphavi Sivabalasarma, Changyi Zhang, Marta Rodriguez-Franco, Rebecca L. Wipfler, Paushali Chaudhury, Ankan Banerjee, Morgan Beeby, Rachel J. Whitaker, John A. Tainer, Sonja-Verena Albers
Veröffentlicht in: Nature Microbiology, Ausgabe 5/1, 2020, Seite(n) 216-225, ISSN 2058-5276
Herausgeber: Nature
DOI: 10.1038/s41564-019-0622-3

Protein phosphorylation and its role in archaeal signal transduction

Autoren: Dominik Esser, Lena Hoffmann, Trong Khoa Pham, Christopher Bräsen, Wen Qiu, Phillip C. Wright, Sonja-Verena Albers, Bettina Siebers
Veröffentlicht in: FEMS Microbiology Reviews, Ausgabe 40/5, 2016, Seite(n) 625-647, ISSN 1574-6976
Herausgeber: OXFORD UNIVERSITY PRESS
DOI: 10.1093/femsre/fuw020

Interactive Exploded Views for Molecular Structures

Autoren: Maximilian Sbardellati, Haichao Miao, Hsiang-Yun Wu, Eduard Gröller, Ivan Barisic, Ivan Viola
Veröffentlicht in: VCBM 19: Eurographics Workshop on Visual Computing for Biology and Medicine, 2019, ISBN 978-3-03868-081-9
Herausgeber: The Eurographics Association
DOI: 10.2312/vcbm.20191237

Rechte des geistigen Eigentums

AUTONOMOUS SENSING MOLECULES (ASM)

Antrags-/Publikationsnummer: EP 16801263
Datum: 2016-11-25

MOLECULAR ROBOT

Antrags-/Publikationsnummer: EP 16806004
Datum: 2016-11-25

NANOSTRUCTURES WITH CATALYTIC ACTIVITY

Antrags-/Publikationsnummer: EP 16801262
Datum: 2016-11-25

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Leistungen

Veröffentlichungen

Rechte des geistigen Eigentums

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