title: Convex lens-induced nanoscale templating.
abstract: We demonstrate a new platform, convex lens-induced nanoscale templating (CLINT), for dynamic manipulation and trapping of single DNA molecules. In the CLINT technique, the curved surface of a convex lens is used to deform a flexible coverslip above a substrate containing embedded nanotopography, creating a nanoscale gap that can be adjusted during an experiment to confine molecules within the embedded nanostructures. Critically, CLINT has the capability of transforming a macroscale flow cell into a nanofluidic device without the need for permanent direct bonding, thus simplifying sample loading, providing greater accessibility of the surface for functionalization, and enabling dynamic manipulation of confinement during device operation. Moreover, as DNA molecules present in the gap are driven into the embedded topography from above, CLINT eliminates the need for the high pressures or electric fields required to load DNA into direct-bonded nanofluidic devices. To demonstrate the versatility of CLINT, we confine DNA to nanogroove and nanopit structures, demonstrating DNA nanochannel-based stretching, denaturation mapping, and partitioning/trapping of single molecules in multiple embedded cavities. In particular, using ionic strengths that are in line with typical biological buffers, we have successfully extended DNA in sub-30-nm nanochannels, achieving high stretching (90%) that is in good agreement with Odijk deflection theory, and we have mapped genomic features using denaturation analysis.
authors.affiliation: Department of Physics, McGill University, Montreal, QC, Canada H3A 2T8; and.
authors.forename: Daniel J
authors.initials: DJ
authors.lastname: Berard
authors.affiliation: Department of Physics, McGill University, Montreal, QC, Canada H3A 2T8; and.
authors.forename: François
authors.initials: F
authors.lastname: Michaud
authors.affiliation: Department of Physics, McGill University, Montreal, QC, Canada H3A 2T8; and Department of Human Genetics, McGill University, Montreal, Canada H3A 0G1.
authors.forename: Sara
authors.initials: S
authors.lastname: Mahshid
authors.affiliation: Department of Physics, McGill University, Montreal, QC, Canada H3A 2T8; and.
authors.forename: Mohammed Jalal
authors.initials: MJ
authors.lastname: Ahamed
authors.affiliation: Department of Physics, McGill University, Montreal, QC, Canada H3A 2T8; and.
authors.forename: Christopher M J
authors.initials: CM
authors.lastname: McFaul
authors.affiliation: Department of Physics, McGill University, Montreal, QC, Canada H3A 2T8; and.
authors.forename: Jason S
authors.initials: JS
authors.lastname: Leith
authors.affiliation: Department of Human Genetics, McGill University, Montreal, Canada H3A 0G1.
authors.forename: Pierre
authors.initials: P
authors.lastname: Bérubé
authors.affiliation: Department of Human Genetics, McGill University, Montreal, Canada H3A 0G1.
authors.forename: Rob
authors.initials: R
authors.lastname: Sladek
authors.affiliation: Department of Physics, McGill University, Montreal, QC, Canada H3A 2T8; and sabrina.leslie@mcgill.ca reisner@physics.mcgill.ca.
authors.forename: Walter
authors.initials: W
authors.lastname: Reisner
authors.affiliation: Department of Physics, McGill University, Montreal, QC, Canada H3A 2T8; and sabrina.leslie@mcgill.ca reisner@physics.mcgill.ca.
authors.forename: Sabrina R
authors.initials: SR
authors.lastname: Leslie
mesh_terms: D004247:DNA / Q000737:chemistry; D021621:Imaging, Three-Dimensional; D007909:Lenses; D049329:Nanostructures / Q000737:chemistry*; D036103:Nanotechnology / Q000379:methods*; D009691:Nucleic Acid Denaturation
chemical_list: D004247:DNA
keywords: CLIC imaging; genomic mapping; nanotechnology; polymer confinement; single-molecule manipulation
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