Nanopore-Based Target Sequence Detection

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...

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Main Authors:	Morin, Trevor J., Shropshire, Tyler, Liu, Xu, Briggs, Kyle, Huynh, Cindy, Tabard-Cossa, Vincent, Wang, Hongyun, Dunbar, William B.
Format:	Online
Language:	English
Published:	Public Library of Science 2016
Online Access:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4858282/

id	pubmed-4858282
recordtype	oai_dc
spelling	pubmed-48582822016-05-13 Nanopore-Based Target Sequence Detection Morin, Trevor J. Shropshire, Tyler Liu, Xu Briggs, Kyle Huynh, Cindy Tabard-Cossa, Vincent Wang, Hongyun Dunbar, William B. Research Article 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. Public Library of Science 2016-05-05 /pmc/articles/PMC4858282/ /pubmed/27149679 http://dx.doi.org/10.1371/journal.pone.0154426 Text en © 2016 Morin et al http://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
repository_type	Open Access Journal
institution_category	Foreign Institution
institution	US National Center for Biotechnology Information
building	NCBI PubMed
collection	Online Access
language	English
format	Online
author	Morin, Trevor J. Shropshire, Tyler Liu, Xu Briggs, Kyle Huynh, Cindy Tabard-Cossa, Vincent Wang, Hongyun Dunbar, William B.
spellingShingle	Morin, Trevor J. Shropshire, Tyler Liu, Xu Briggs, Kyle Huynh, Cindy Tabard-Cossa, Vincent Wang, Hongyun Dunbar, William B. Nanopore-Based Target Sequence Detection
author_facet	Morin, Trevor J. Shropshire, Tyler Liu, Xu Briggs, Kyle Huynh, Cindy Tabard-Cossa, Vincent Wang, Hongyun Dunbar, William B.
author_sort	Morin, Trevor J.
title	Nanopore-Based Target Sequence Detection
title_short	Nanopore-Based Target Sequence Detection
title_full	Nanopore-Based Target Sequence Detection
title_fullStr	Nanopore-Based Target Sequence Detection
title_full_unstemmed	Nanopore-Based Target Sequence Detection
title_sort	nanopore-based target sequence detection
description	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.
publisher	Public Library of Science
publishDate	2016
url	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4858282/
_version_	1613576104747991040

Nanopore-Based Target Sequence Detection

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