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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...

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Autores principales: Chen, Kaikai, Juhasz, Matyas, Gularek, Felix, Weinhold, Elmar, Tian, Yu, Keyser, Ulrich F., Bell, Nicholas A. W.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: American Chemical Society 2017
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.
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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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