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Ionic Current-Based Mapping of Short Sequence Motifs in Single DNA Molecules Using Solid-State Nanopores
[Image: see text] Nanopore sensors show great potential for rapid, single-molecule determination of DNA sequence information. Here, we develop an ionic current-based method for determining the positions of short sequence motifs in double-stranded DNA molecules with solid-state nanopores. Using the D...
Autores principales: | , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
American Chemical Society
2017
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Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5599873/ https://www.ncbi.nlm.nih.gov/pubmed/28829136 http://dx.doi.org/10.1021/acs.nanolett.7b01009 |
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author | Chen, Kaikai Juhasz, Matyas Gularek, Felix Weinhold, Elmar Tian, Yu Keyser, Ulrich F. Bell, Nicholas A. W. |
author_facet | Chen, Kaikai Juhasz, Matyas Gularek, Felix Weinhold, Elmar Tian, Yu Keyser, Ulrich F. Bell, Nicholas A. W. |
author_sort | Chen, Kaikai |
collection | PubMed |
description | [Image: see text] Nanopore sensors show great potential for rapid, single-molecule determination of DNA sequence information. Here, we develop an ionic current-based method for determining the positions of short sequence motifs in double-stranded DNA molecules with solid-state nanopores. Using the DNA-methyltransferase M.TaqI and a biotinylated S-adenosyl-l-methionine cofactor analogue we create covalently attached biotin labels at 5′-TCGA-3′ sequence motifs. Monovalent streptavidin is then added to bind to the biotinylated sites giving rise to additional current blockade signals when the DNA passes through a conical quartz nanopore. We determine the relationship between translocation time and position along the DNA contour and find a minimum resolvable distance between two labeled sites of ∼200 bp. We then characterize a variety of DNA molecules by determining the positions of bound streptavidin and show that two short genomes can be simultaneously detected in a mixture. Our method provides a simple, generic single-molecule detection platform enabling DNA characterization in an electrical format suited for portable devices for potential diagnostic applications. |
format | Online Article Text |
id | pubmed-5599873 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2017 |
publisher | American Chemical Society |
record_format | MEDLINE/PubMed |
spelling | pubmed-55998732017-09-18 Ionic Current-Based Mapping of Short Sequence Motifs in Single DNA Molecules Using Solid-State Nanopores Chen, Kaikai Juhasz, Matyas Gularek, Felix Weinhold, Elmar Tian, Yu Keyser, Ulrich F. Bell, Nicholas A. W. Nano Lett [Image: see text] Nanopore sensors show great potential for rapid, single-molecule determination of DNA sequence information. Here, we develop an ionic current-based method for determining the positions of short sequence motifs in double-stranded DNA molecules with solid-state nanopores. Using the DNA-methyltransferase M.TaqI and a biotinylated S-adenosyl-l-methionine cofactor analogue we create covalently attached biotin labels at 5′-TCGA-3′ sequence motifs. Monovalent streptavidin is then added to bind to the biotinylated sites giving rise to additional current blockade signals when the DNA passes through a conical quartz nanopore. We determine the relationship between translocation time and position along the DNA contour and find a minimum resolvable distance between two labeled sites of ∼200 bp. We then characterize a variety of DNA molecules by determining the positions of bound streptavidin and show that two short genomes can be simultaneously detected in a mixture. Our method provides a simple, generic single-molecule detection platform enabling DNA characterization in an electrical format suited for portable devices for potential diagnostic applications. American Chemical Society 2017-08-22 2017-09-13 /pmc/articles/PMC5599873/ /pubmed/28829136 http://dx.doi.org/10.1021/acs.nanolett.7b01009 Text en Copyright © 2017 American Chemical Society This is an open access article published under an ACS AuthorChoice License (http://pubs.acs.org/page/policy/authorchoice_termsofuse.html) , which permits copying and redistribution of the article or any adaptations for non-commercial purposes. |
spellingShingle | Chen, Kaikai Juhasz, Matyas Gularek, Felix Weinhold, Elmar Tian, Yu Keyser, Ulrich F. Bell, Nicholas A. W. Ionic Current-Based Mapping of Short Sequence Motifs in Single DNA Molecules Using Solid-State Nanopores |
title | Ionic Current-Based Mapping of Short Sequence Motifs
in Single DNA Molecules Using Solid-State Nanopores |
title_full | Ionic Current-Based Mapping of Short Sequence Motifs
in Single DNA Molecules Using Solid-State Nanopores |
title_fullStr | Ionic Current-Based Mapping of Short Sequence Motifs
in Single DNA Molecules Using Solid-State Nanopores |
title_full_unstemmed | Ionic Current-Based Mapping of Short Sequence Motifs
in Single DNA Molecules Using Solid-State Nanopores |
title_short | Ionic Current-Based Mapping of Short Sequence Motifs
in Single DNA Molecules Using Solid-State Nanopores |
title_sort | ionic current-based mapping of short sequence motifs
in single dna molecules using solid-state nanopores |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5599873/ https://www.ncbi.nlm.nih.gov/pubmed/28829136 http://dx.doi.org/10.1021/acs.nanolett.7b01009 |
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