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BioGraph'n

Silicon Nitride and Graphene Nanopores for Biotechnology and Biology
Funder: French National Research Agency (ANR)Project code: ANR-12-NANO-0012
Funder Contribution: 716,575 EUR

BioGraph'n

Description

Numerous chemical or biological processes involve the transport of macromolecules through tiny channels of nanometric size. We have been the firsts in France to study these processes (as early as 2003) using natural channels and artificial channels obtained by drilling nanopores in ultra-thin SiC and Si3N4 solid-state membranes with a Focused Ions Beam Apparatus (FIB). The molecules passing through a pore are detected by a simple electrical method. We would like to pursue this research by developing their different aspects : fabrication, detection and applications. We first propose to drill nanopores in single sheets of graphene by using an optimized system of focused Gallium or Helium ions beam, and then to study its use as an ultra-fast DNA and proteins sequencing tool. This domain, which we explore since two years is growing explosively. For what concerns detection, we wish to develop the optical and mechanical detection of the translocation of a macromolecule through a nanopore. The optical detection requires the use of fluorescent or luminescent macromolecules. Spurious light created while illuminating a pore is eliminated by absorting it or by hindering its propagation (condition of zero mode waveguide). This is obtained by coating the surface of the pore and of the silicon nitride membrane by silicon or gold.The mechanical detection of the forces exerted on a macromolecule confined in a nanopore is obtained when the molecule is attached to the tip of an atomic force microscope or to a bead trapped in optical tweezers. We propose to measure the work exerted on a translocating (out of equilibrium) macromolecule and to use the recent Jarzynski’s relation for studying the energetic lanscape explored by the molecule. Our experience in drilling nanopores by focused ions beam enables us to make nanopores in various materials, controlling their size, their position, their organization We are also able to produce a large amount of nanopore which may serve the needs of research laboratories and future applications. We have constructed our project in order to propose valuable applications of nanopores in the fields of Biology and Biotechnoly, avoiding the well-know application to DNA sequencing, which is outside our scope. We have made a association with a small spin-off company created by a partner laboratory of this consortium in order to study the production of DNA vectors for gene tranfer and gene therapy by molecular extrusion through a nanopore. An electric field or a pressure force the passage of a DNA plasmid through a Silicon Nitride Nanopore and put the molecule in contact with a solution of cationic polyelectrolyte at the exit of the pore. An electrostatic complex is formed with a controlled size and composition, with a single DNA molecule per nanoparticle. We propose to use the same principle of molecular extrusion for studying the synthesis of polymers through a nanopore coated with a suitable catalyst and for controlling the folding and unfolding of proteins buy nanopores. We will use a new experimental prtein model, the Luciferase protein, which allows an optical detection of its transport and functionnal foldind after translocation through a nanopore. We thus hope to create new biomimetic objects enabling the analysis and manipulation of macromolecules with a never achieved spatial and temporal resolution

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