title: Nanopore-Based Target Sequence Detection.
abstract: The promise of portable diagnostic devices relies on three basic requirements: comparable sensitivity to established platforms, inexpensive manufacturing and cost of operations, and the ability to survive rugged field conditions. Solid state nanopores can meet all these requirements, but to achieve high manufacturing yields at low costs, assays must be tolerant to fabrication imperfections and to nanopore enlargement during operation. This paper presents a model for molecular engineering techniques that meets these goals with the aim of detecting target sequences within DNA. In contrast to methods that require precise geometries, we demonstrate detection using a range of pore geometries. As a result, our assay model tolerates any pore-forming method and in-situ pore enlargement. Using peptide nucleic acid (PNA) probes modified for conjugation with synthetic bulk-adding molecules, pores ranging 15-50 nm in diameter are shown to detect individual PNA-bound DNA. Detection of the CFTRΔF508 gene mutation, a codon deletion responsible for ∼66% of all cystic fibrosis chromosomes, is demonstrated with a 26-36 nm pore size range by using a size-enhanced PNA probe. A mathematical framework for assessing the statistical significance of detection is also presented.
authors.affiliation: Two Pore Guys Inc., Santa Cruz, CA, United States of America.
authors.forename: Trevor J
authors.initials: TJ
authors.lastname: Morin
authors.affiliation: Two Pore Guys Inc., Santa Cruz, CA, United States of America.
authors.forename: Tyler
authors.initials: T
authors.lastname: Shropshire
authors.affiliation: Two Pore Guys Inc., Santa Cruz, CA, United States of America.
authors.forename: Xu
authors.initials: X
authors.lastname: Liu
authors.affiliation: Department of Physics, University of Ottawa, Ontario, Canada.
authors.forename: Kyle
authors.initials: K
authors.lastname: Briggs
authors.affiliation: Two Pore Guys Inc., Santa Cruz, CA, United States of America.
authors.forename: Cindy
authors.initials: C
authors.lastname: Huynh
authors.affiliation: Department of Physics, University of Ottawa, Ontario, Canada.
authors.forename: Vincent
authors.initials: V
authors.lastname: Tabard-Cossa
authors.affiliation: Two Pore Guys Inc., Santa Cruz, CA, United States of America.|Baskin School of Engineering, University of California Santa Cruz, Santa Cruz, CA, United States of America.
authors.forename: Hongyun
authors.initials: H
authors.lastname: Wang
authors.affiliation: Two Pore Guys Inc., Santa Cruz, CA, United States of America.|Baskin School of Engineering, University of California Santa Cruz, Santa Cruz, CA, United States of America.
authors.forename: William B
authors.initials: WB
authors.lastname: Dunbar
mesh_terms: D004247:DNA / Q000737:chemistry*; D004591:Electrophoresis, Polyacrylamide Gel; D024202:Electrophoretic Mobility Shift Assay; D058608:Nanopores; D020135:Peptide Nucleic Acids / Q000737:chemistry; D017422:Sequence Analysis, DNA / Q000379:methods*
chemical_list: D020135:Peptide Nucleic Acids; D004247:DNA