The goal of the MARA project is to create self-organizing DNA-origami structures that mimic the reactions of proteins, and ultimately, to develop a molecular nano-drill that can specifically identify target bacteria and destroy them by perforating their membranes. Accordingly, these combined actions will introduce irreversible changes into their osmotic systems, bolstering the fight against microbes resistant to conventional antibiotics.
Targeted treatment of infectious diseases and preventing the spread of multidrug resistant pathogens remain to be clinical challenges. In the MARA project, we aim to develop and combine three novel technologies: Autonomous Detection Nucleic Acids (AUDENA), a DNA Scaffold Embedded Protein Emulation Complex (D-SEPEC), and a Molecular Robot (MORO) to create a DNA-based molecular toolkit for rapid pathogen characterization and treatment.
Acting as the detection arm of MORO, AUDENAs will detect pathogenic antigens using DNA-based molecular detection motifs. AUDENAs are single stranded DNA probes comprising a chemically-modified aptamer that recognizes a target and a DNAzyme for a signal reporting. AUDENAs will be designed to target antibiotic resistance factors and bacterial surface antigens. In general, AUDENAs can be used as sensors to detect almost all chemical substances, provided that a specific targeting aptamer is generated.
Whereas the AUDENAs act as the recognition arm of the MORO, D-SEPECs will be the main working component. D-SEPEC refers to the combination of a DNA origami structure, with an enzymatic catalytic center embedded in the scaffold of the nanostructure. The resulting complex emulates reactions of the original enzyme. As proof-of-concept, an ATP-driven archaeal rotary motor is planned to be emulated.
MORO aims to combine AUDENA-based targeting mechanisms and the D-SEPEC rotary motor-driven molecular drill into a single structure, a Molecular Robot. In the presence of a pathogen, the MORO will specifically dock onto the pathogen’s surface and activate its ATP-driven motor, an action that places a drill head into the pathogen’s cell membrane, thereby disrupting its function. Functionality of the MORO is planned to be evaluated using several human pathogens.
PURE BIOLOGICS’ ROLE
Pure Biologics’ role in the MARA project is to develop chemically-modified aptamers, engineered to recognize relevant bacterial antigens and antibiotic resistance proteins (e.g. beta lactamases). These aptamers will comprise the target-detecting nanoprobes, along with a DNAzyme for signal reporting – AUDENAs (Autonomous Detection Nucleic Acids). This will in turn serve as an integral component of the recognition element comprising the DNA-based MORO nanorobots.
Pure Biologics has performed more than a dozen in vitro aptamer selection campaigns for various bacterial protein targets, including surface markers, as well as antibiotic-resistance enzymes. These selections have already succeeded to identify several highly specific aptamers and measured kinetic parameters of the resulting aptamers have demonstrated their utilities in further stages of the project.
PROJECT DATA SHEET
Title: ,Molecular Analytical Robotics Assays
Program: part of Measure “Future and Emerging Technologies Open”, of the Program ,,Horizon 2020-European Union funding for Research & Innovation”
Project value: PLN 2 364 360,00 (the entire consortium: PLN 16 577 388,67)
Contribution of European Funds: PLN 2 364 360,00 (the entire consortium: PLN 16 577 388,67)
Start: 1st December 2015 (Pure Biologics entry date: 19th December 2017 )
End: 31st August 2020
Consortium members: Austrian Institute of Technology (Austria), Albert-Ludwigs-Universität Freiburg (Germany), Aarhus Universitet (Denmark), Imperial College London (United Kingdom), Pure Biologics S.A.