title: Stretching of DNA confined in nanochannels with charged walls.
abstract: There is currently a growing interest in control of stretching of DNA inside nanoconfined regions due to the possibility to analyze and manipulate single biomolecules for applications such as DNA mapping and barcoding, which are based on stretching the DNA in a linear fashion. In the present work, we couple Finite Element Methods and Monte Carlo simulations in order to study the conformation of DNA molecules confined in nanofluidic channels with neutral and charged walls. We find that the electrostatic forces become more and more important when lowering the ionic strength of the solution. The influence of the nanochannel cross section geometry is also studied by evaluating the DNA elongation in square, rectangular, and triangular channels. We demonstrate that coupling electrostatically interacting walls with a triangular geometry is an efficient way to stretch DNA molecules at the scale of hundreds of nanometers. The paper reports experimental observations of λ-DNA molecules in poly(dimethylsiloxane) nanochannels filled with solutions of different ionic strength. The results are in good agreement with the theoretical predictions, confirming the crucial role of the electrostatic repulsion of the constraining walls on the molecule stretching.
authors.forename: Chiara
authors.initials: C
authors.lastname: Manneschi
authors.affiliation: Nanomed Labs, Department of Physics, University of Genova , via Dodecaneso 33, 16146 Genova, Italy.
authors.forename: Paola
authors.initials: P
authors.lastname: Fanzio
authors.affiliation: Department of Applied Physics and COMP Center of Excellence, Aalto University School of Science , P.O. Box 11100, FIN-00076 Aalto, Espoo, Finland and Department of Physics, Brown University , Providence, Rhode Island 02912-1843, USA.
authors.forename: Tapio
authors.identifier: 0000-0002-3210-3181
authors.initials: T
authors.lastname: Ala-Nissila
authors.affiliation: Nanomed Labs, Department of Physics, University of Genova , via Dodecaneso 33, 16146 Genova, Italy.
authors.forename: Elena
authors.initials: E
authors.lastname: Angeli
authors.affiliation: Nanomed Labs, Department of Physics, University of Genova , via Dodecaneso 33, 16146 Genova, Italy.
authors.forename: Luca
authors.initials: L
authors.lastname: Repetto
authors.affiliation: Nanomed Labs, Department of Physics, University of Genova , via Dodecaneso 33, 16146 Genova, Italy.
authors.forename: Giuseppe
authors.identifier: 0000-0002-4028-6555
authors.initials: G
authors.lastname: Firpo
authors.affiliation: Nanomed Labs, Department of Physics, University of Genova , via Dodecaneso 33, 16146 Genova, Italy.
authors.forename: Ugo
authors.initials: U
authors.lastname: Valbusa