title: DNA Origami-Graphene Hybrid Nanopore for DNA Detection.
abstract: DNA origami nanostructures can be used to functionalize solid-state nanopores for single molecule studies. In this study, we characterized a nanopore in a DNA origami-graphene heterostructure for DNA detection. The DNA origami nanopore is functionalized with a specific nucleotide type at the edge of the pore. Using extensive molecular dynamics (MD) simulations, we computed and analyzed the ionic conductivity of nanopores in heterostructures carpeted with one or two layers of DNA origami on graphene. We demonstrate that a nanopore in DNA origami-graphene gives rise to distinguishable dwell times for the four DNA base types, whereas for a nanopore in bare graphene, the dwell time is almost the same for all types of bases. The specific interactions (hydrogen bonds) between DNA origami and the translocating DNA strand yield different residence times and ionic currents. We also conclude that the speed of DNA translocation decreases due to the friction between the dangling bases at the pore mouth and the sequencing DNA strands.
authors.affiliation: Department of Mechanical Science and Engineering, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States.
authors.forename: Amir
authors.identifier: 0000-0002-2952-8576
authors.initials: A
authors.lastname: Barati Farimani
authors.affiliation: Department of Mechanical Science and Engineering, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States.
authors.forename: Payam
authors.initials: P
authors.lastname: Dibaeinia
authors.affiliation: Department of Mechanical Science and Engineering, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States.
authors.forename: Narayana R
authors.initials: NR
authors.lastname: Aluru
mesh_terms: D004247:DNA / Q000737:chemistry; D006108:Graphite / Q000737:chemistry*; D056004:Molecular Dynamics Simulation; D058608:Nanopores; D017422:Sequence Analysis, DNA
chemical_list: D006108:Graphite; D004247:DNA
keywords: DNA detection; DNA origami; dwell time; graphene; hybrid nanopore; multiplex signal; pore functionalization