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Reporting Stage 1

Periodic Activity Report 1 - Executive Summary

This Executive Summary is designed to summarise the data presented at the 2nd BioNano-Switch Workshop, held at INSEC-MN in Lisbon on 3rd September 2007.  Due to concerns about protection of Intellectual Property developed during Year 1 of the Project this publishable Summary is necessarily brief on scientific detail.

This Project was designed to provide an engineering approach to the construction of a generic biosensing system, using unique components such as molecular motors to move magnetic beads attached to DNA (as a single‑molecule transducer) – and including a molecular amplifier to improve signal to noise ratio – that could be incorporated into a modular biosensor.  The biological components of the modules were to be constructed with a cassette‑like approach; in order to simplify production, ease the introduction of future variability and thus to adopt a Synthetic Biology approach to the construction of the device.

At the end of the first Reporting Period of this Project, we can report significant progress in all aspects of the work and much of this has involved significant and successful collaborations between the Partners within the Consortium.  UoP and IMIC have collaborated on production of molecular motor variants (of the EcoR124I motor), which have been well characterised in both bulk solution experiments and at the single molecule level (in collaboration with TUDelft, through Dr Ralph Seidel – now at Dresden and Dr Mark Szczelkun at Bristol).  We have produced a number of new recombinant fusion proteins that are required for the Project and some additional protein fusions that provide further useful variations to those suggested in the original proposal.  While we await confirmation of some of the constructs, using DNA sequence analysis, and also production of a few further recombinants involving protease genes and the molecular motor FtsK, this work is progressing significantly.  UoP and IMIC will discuss a strategy for the next stage of the work, which will take place during year 2 and will mainly involve work with the molecular motor FtsK.

A significant collaboration is also taking place between NPLML and EMPA, who are looking at the use of Hall Effect sensors for the Project.  Fabrication of sensors has been carried out by EMPA, and NPLML have used their instrumentation and “know-how” to calibrate the output from these sensors and demonstrate their capability for the next stage of the Project.  This next stage will entail precise positioning of the sensors and localisation of biomaterial above the sensors, which will necessitate detailed discussions between the Coordinator, INESC-MN and EMPA.

Collaboration has also occurred between NPLML and UoP; with NPLML visiting Portsmouth to discuss a model system that can be used to develop a strategy for the required metrology.  It was decided, from the outcomes of the Meeting, that NPL would investigate the accuracy of various positioning strategies using the biotin and streptavidin system.  This system can also be used to study protein‑protein interactions on a surface – and Portsmouth would provide biotinylated DNA for surface attachment and characterisation of motor binding.  This work is progressing well and is already accompanied by studies on surface attachment of the EcoR124I motor.  The University of Portsmouth has provided an additional PhD studentship who is carrying out this analysis and whose work in this area is supporting the BioNano‑Switch Project.

Another significant collaboration is taking place between INESC-MN and ENS/CNRS; where INESC-MN have demonstrated an early version of the proposed device without, at this stage, associated microfluidics.  This setup has demonstrated the expected output and shown the system can be used with an existing Magnetic Tweezer setup for orthogonal detection of motor activity.  This provides a useful device, around which a prototype device can be designed.  Magnetic beads have been sent by UoP to INESC-MN for characterisation, using the magnetoresistive technology and the resulting data has been exchanged with UoP for analysis and possible publication.

TUDelft and ENS/CNRS have characterised a number of molecular motors (in addition to EcoR124I and FtsK that were characterised during the previous Mol Switch Project – IST-2001-38036) and other DNA manipulating enzymes, studies of which have demonstrated significant opportunity for application of the proposed device in a range of uses, from environmental sensing, to healthcare biosensing and drug screening (Koster et al., 2007).

The Consortium has, therefore, demonstrated considerable integration of their activities, thus indicating a healthy Project, which should make significant progress toward the final objectives.  At least one new capability has been described, with a potential for Commercialisation, suggesting that the Project will provide future funding capabilities via a Commercial route.  All Partners have now signed a Consortium Agreement, which includes a Preliminary Agreement concerning IP and a mechanism that will allow UoP to lead the Commercialisation.  Current discussions regarding IPR and IP Management are underway.