Molecular Analytical Robotics Assays

Risultati finali

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.

Pubblicazioni

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

Autori: 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
Pubblicato in: Journal of Biological Chemistry, Numero 294/18, 2019, Pagina/e 7460-7471, ISSN 0021-9258
Editore: American Society for Biochemistry and Molecular Biology Inc.
DOI: 10.1074/jbc.ra119.007709

In silico modelling of DNA nanostructures

Autori: Tadija Kekic, Ivan Barisic
Pubblicato in: Computational and Structural Biotechnology Journal, Numero 18, 2020, Pagina/e 1191-1201, ISSN 2001-0370
Editore: Elsevier
DOI: 10.1016/j.csbj.2020.05.016

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

Autori: Yasaman Ahmadi, Ashley L. Nord, Amanda J. Wilson, Christiane Hütter, Fabian Schroeder, Morgan Beeby, Ivan Barišić
Pubblicato in: Small, Numero 16/22, 2020, Pagina/e 2001855, ISSN 1613-6810
Editore: Wiley - V C H Verlag GmbbH & Co.
DOI: 10.1002/smll.202001855

Positioning of the Motility Machinery in Halophilic Archaea

Autori: Zhengqun Li, Yoshiaki Kinosita, Marta Rodriguez-Franco, Phillip Nußbaum, Frank Braun, Floriane Delpech, Tessa E. F. Quax, Sonja-Verena Albers
Pubblicato in: mBio, Numero 10/3, 2019, Pagina/e e00377-19, ISSN 2150-7511
Editore: American Society for Microbiology
DOI: 10.1128/mBio.00377-19

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

Autori: Morgan Beeby, Josie L Ferreira, Patrick Tripp, Sonja-Verena Albers, David R Mitchell
Pubblicato in: FEMS Microbiology Reviews, Numero 44/3, 2020, Pagina/e 253-304, ISSN 0168-6445
Editore: Blackwell
DOI: 10.1093/femsre/fuaa006

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

Autori: Yasaman Ahmadi, Ivan Barisic
Pubblicato in: Journal of Visualized Experiments, Numero 143, 2019, ISSN 1940-087X
Editore: MYJoVE Corporation
DOI: 10.3791/58771

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

Autori: Lena Hoffmann, Andreas Schummer, Julia Reimann, Maria F. Haurat, Amanda J. Wilson, Morgan Beeby, Bettina Warscheid, Sonja-V. Albers
Pubblicato in: MicrobiologyOpen, Numero 6/1, 2017, Pagina/e e00414, ISSN 2045-8827
Editore: John Wiley and Sons Inc.
DOI: 10.1002/mbo3.414

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

Autori: Yasaman Ahmadi, Elisa De Llano, Ivan Barišić
Pubblicato in: Nanoscale, Numero 10/16, 2018, Pagina/e 7494-7504, ISSN 2040-3364
Editore: Royal Society of Chemistry
DOI: 10.1039/C7NR09461B

ArnS, a kinase involved in starvation-induced archaellum expression

Autori: M. Florencia Haurat, Ana Sofia Figueiredo, Lena Hoffmann, Lingling Li, Katharina Herr, Amanda J. Wilson, Morgan Beeby, Jörg Schaber, Sonja-Verena Albers
Pubblicato in: Molecular Microbiology, Numero 103/1, 2017, Pagina/e 181-194, ISSN 0950-382X
Editore: Blackwell Publishing Inc.
DOI: 10.1111/mmi.13550

Multiscale Visualization and Scale-Adaptive Modification of DNA Nanostructures

Autori: Haichao Miao, Elisa De Llano, Johannes Sorger, Yasaman Ahmadi, Tadija Kekic, Tobias Isenberg, M. Eduard Groller, Ivan Barisic, Ivan Viola
Pubblicato in: IEEE Transactions on Visualization and Computer Graphics, Numero 24/1, 2018, Pagina/e 1014-1024, ISSN 1077-2626
Editore: 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

Autori: H. Miao, E. De Llano, T. Isenberg, M. E. Gröller, I. Barišić, I. Viola
Pubblicato in: Computer Graphics Forum, Numero 37/3, 2018, Pagina/e 403-413, ISSN 0167-7055
Editore: Blackwell Publishing Inc.
DOI: 10.1111/cgf.13429

Adenita: interactive 3D modelling and visualization of DNA nanostructures

Autori: Elisa de Llano, Haichao Miao, Yasaman Ahmadi, Amanda J Wilson, Morgan Beeby, Ivan Viola, Ivan Barisic
Pubblicato in: Nucleic Acids Research, Numero 48/15, 2020, Pagina/e 8269-8275, ISSN 0305-1048
Editore: Oxford University Press
DOI: 10.1093/nar/gkaa593

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

Autori: 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
Pubblicato in: Nature Microbiology, Numero 5/1, 2020, Pagina/e 216-225, ISSN 2058-5276
Editore: Nature
DOI: 10.1038/s41564-019-0622-3

Protein phosphorylation and its role in archaeal signal transduction

Autori: Dominik Esser, Lena Hoffmann, Trong Khoa Pham, Christopher Bräsen, Wen Qiu, Phillip C. Wright, Sonja-Verena Albers, Bettina Siebers
Pubblicato in: FEMS Microbiology Reviews, Numero 40/5, 2016, Pagina/e 625-647, ISSN 1574-6976
Editore: OXFORD UNIVERSITY PRESS
DOI: 10.1093/femsre/fuw020

Interactive Exploded Views for Molecular Structures

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

Diritti di proprietà intellettuale

AUTONOMOUS SENSING MOLECULES (ASM)

Numero candidatura/pubblicazione: EP 16801263
Data: 2016-11-25

MOLECULAR ROBOT

Numero candidatura/pubblicazione: EP 16806004
Data: 2016-11-25

NANOSTRUCTURES WITH CATALYTIC ACTIVITY

Numero candidatura/pubblicazione: EP 16801262
Data: 2016-11-25

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Risultati finali

Pubblicazioni

Diritti di proprietà intellettuale

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