DNA Scaffold Embedded Protein Emulation Complexes – or for short D-SEPECs – are self-assembling nanostructures which
have artificial catalytic centres emulating existing proteins embedded within the scaffold.
A proof-of-concept D-SEPEC is planned to be developed during Work Package 4 of the MARA project.
Scientists working within the MARA project at the AIT Austrian Institute of Technology have developed the software ADENITA for the design of complex DNA nanostructures. Some highlights of this tool are that proteins can be embedded in the designs and that the designs are available on an atomic scale. A public version will be released in February, and the first structures designed with ADENITA are currently being visualised in vitro. To that end, Imperial College London is working to image DNA origami constructs using electron microscopy and electron cryo-microscopy to verify correct assembly and to monitor the dynamics of these structures. The team has already successfully imaged a number of structures in 2-D, and are now working to determine 3-D structures.
In the same time at AIT, first artificial DNA-based enzymes – the D-SEPECs – are undergoing rigorous trails to confirm the already-observed effect of the hydrolysis of ATP, which is one of the most important chemical reaction catalysed by enzymes.
The contribution of Work Package 3 is to determine how a set of naturally-occurring molecular machines work;
this understanding will ultimately form the basis for designing the MORO for the MARA project.
As such, Work Package 3 is a set of different but inter-related research projects by the consortium of Imperial College London,
Albert-Ludwigs-Universität Freiburg, and Aarhus University.
Together, Imperial College and Albert-Ludwigs-Universität Freiburg have been working to understand how the molecular propeller used by exotic “archaea“ microbes operates. This ongoing collaboration has led to development of a variety of methodologies for optimal growth of two archaea, Sulfolobus acidocaldarius and Haloferax volcanii. Work is now underway to use electron cryo-tomography to directly visualize the functional molecular propeller in the cell. If successful, these efforts will guide the design of the rotary component of the MORO. Imperial College and Albert-Ludwigs-Universität Freiburg are also completing a comprehensive literary review of molecular propellers across all life on earth, to be published in the coming months.
At the same time, Aarhus University have been researching the mechanism of an “ion channel” that could be used in the MORO to attack cancer cells or invading pathogens. The insertion of such an ion channel into the cell membrane will disrupt the natural salt ion balance and ultimately destroy the targeted cell. The ion channel has been expressed and purified from mammalian cells and is being investigated by state-of-the-art electron microscopy, to study its ion selectivity mechanism. The recent emergence of DNA-based nanopores, which can be inserted into biological membranes and maintain ion selectivity are also being investigated. These could potentially be integrated in the MORO and the entire complex is to be analysed by electron cryo-tomography resulting in 4D-models of a mobile cell lysing nanobot.
ArchaeaBot is an underwater robotic installation by Anna Dumitriu and Alex May that explores what ‘life’ might mean in a
post-singularity and post-climate change future. The project is being supported through a EMAP/EMARE artists residency at
LABoral Centro de Arte y Creación Industrial in Spain via funding from Creative Europe and with generous support from Arts
The artists have based their project on research funded by MARA; specifically the work on archaea being carried out at Imperial College London and Albert-Ludwigs-Universität Freiburg, combined with the latest innovations in artificial intelligence and machine learning, in order to create a hypothetical hybrid species for the end of the world.
The work is the result of collaboration with Amanda Wilson (Research Associate. Imperial College London) within the framework of the EU MARA project, and Daniel Polani (Professor of Artificial Intelligence in the School of Computer Science at the University of Hertfordshire).
ArchaeaBot is a motorised swimming robot, designed to emulate a Sulfolobus acidocaldarius cell, the model organism being used to investigate the structure of the archaellar motor. The robot is roughly spherical, and embedded in the surface are several 3D-printed computerised motors which drive the rotation of flexible filaments, in order to simulate archaellar motors and their archaella.
The artists were inspired by the knowledge that Sulfolobus acidocaldarius thrives in a hot acid environment, and came up with the notion that theoretically human consciousness could be uploaded to these extremophiles in order to survive the hot acid conditions that may prevail on Earth in the future. Of course, this goes well beyond the confines of the original MARA research, but the artist’s role is to dream and work outside the normal boundaries, and the story draws people in, so they want to find out more about the science.
ArchaeaBot received critical acclaim when it was exhibited at the prestigious Ars Electronica Festival 2018, an annual gathering of of artists, scientists and technologists, intended as a setting for experimentation, evaluation and reinvention. The artwork was also exhibited at the LABoral Centre for Art and Industrial Creativity, following a discussion between Anna Dumitriu, Alex May, Amanda Wilson and Institute director, Karin Ohlenschlaeger to a live audience, and will soon be presented at Art & the Life Sciences: Ethics & Perspectives in Athens, Greece.
ArchaeaBot will be further developed over the next year, with an aim to add a translucent S-layer, refined artificial motors and interactive features. The artists also hope to build a second robot based on the other model organism that is being used for structural electron cryo-microscopy investigations; Haloferax volcanii.
From the MARA perspective, the project is achieving excellent outreach, helping to inform the public about the MARA objectives and the biology of Archaea.
Image credit: Vanessa Graf - Ars Electronica
From Sep, 17th to Sep 19th members of the MARA project participated in the Computational DNA engineering workshop in Plitvice, Croatia. Within this international and highly successful meeting researchers from different computational areas presented their work and discussed possible collaboration opportunities. The diverse research backgrounds and domain knowledge of the workshop participants led to fruitful discussions about relevant research questions, problems and ideas.
The Work Package 2 comprises the development of modified aptamers recognizing several important bacterial pathogens, the design and testing of model
Autonomous Detection Nucleic Acids (AUDENAs) to achieve a pathogen detection tool with exchangeable specificity-determining unit.
The tasks are handled by Austrian Institute of Technology (AIT) and Pure Biologics Inc. (PB, who replaced Apta Biosciences
as the consortium partner in late 2017).
Recently, Pure Biologics has finished the first package of selections directed towards chosen bacterial targets and started another set of selections. The results are currently being analysed using Next Generation Sequencing techniques, which in conjunction with powerful bioinformatical analysis allow to readily identify multiple potential binders of the bacterial targets. Next, identified aptamers will be tested and optimized in order to incorporate them into working AUDENAs.
Parallelly, scientists at AIT have designed various AUDENA concepts and tested the new sensor class with previously published conventional DNA aptamers. With these experiments they could proof that the AUDENA technology can be used for the detection of bacterial antigens. A publication of the results in a scientific journal is planned in 2018 to demonstrate the usability of these cost-effective, stable and point-of-care compatible detection molecules.
The 5th MARA project General Assembly meeting took place in Freibug on May 14th and 15th, 2018.
(Poly)cation-induced protection of conventional and wireframe DNA origami nanostructures.
Yasaman Ahmadi, Elisa De Llanoa, Ivan Barišić. Nanoscale. 2018 Apr 26;10(16):7494-7504.
The Polish company Pure biologics joined the consortium in December 2017, as Apta Biosciences unfortunately left the project.
The MARA project GA meeting took place in Vienna, on December 19th, 2017.
The next meeting will be in Freiburg on May 14th and 15th, 2018.
Multiscale Visualization and Scale-Adaptive Modification of DNA Nanostructures.
Miao H, De Llano E, Sorger J, Ahmadi Y, Kekic T, Isenberg T, Groller ME, Barisic I, Viola I. IEEE Trans Vis Comput Graph. 2018 Jan;24.
The MARA project GA meeting took place in Aarhus, on May 23rd and 24th, 2017.
The MARA project General Assembly meeting took place in London, on June 2nd and 3rd, 2016.
The 2nd MARA project General Assembly meeting took place in Slunj, on Nov 24th and 25th, 2016.
MARA news on "Very Important Business".
MARA is in the news. Please click on the link to read the full press release.
The MARA project kick-off meeting took place in Vienna, Austria, on December 10th and 11th 2015.
Apta Biosciences reports about the newly granted MARA project.