DNA bridges: A novel platform for single-molecule sequencing and other DNA-protein interaction applications.

DNA molecular combing is a technique that stretches thousands of long individual DNA molecules (up to 10 Mbp) into a parallel configuration on surface. It has previously been proposed to sequence these molecules by synthesis. However, this approach poses two critical challenges: 1-Combed DNA molecul...

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Autores principales:	Maurizio Righini, Justin Costa, Wei Zhou
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/2e89354eb00d41cea5ae0b127ebab549
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spelling	oai:doaj.org-article:2e89354eb00d41cea5ae0b127ebab5492021-12-02T20:16:18ZDNA bridges: A novel platform for single-molecule sequencing and other DNA-protein interaction applications.1932-620310.1371/journal.pone.0260428https://doaj.org/article/2e89354eb00d41cea5ae0b127ebab5492021-01-01T00:00:00Zhttps://doi.org/10.1371/journal.pone.0260428https://doaj.org/toc/1932-6203DNA molecular combing is a technique that stretches thousands of long individual DNA molecules (up to 10 Mbp) into a parallel configuration on surface. It has previously been proposed to sequence these molecules by synthesis. However, this approach poses two critical challenges: 1-Combed DNA molecules are overstretched and therefore a nonoptimal substrate for polymerase extension. 2-The combing surface sterically impedes full enzymatic access to the DNA backbone. Here, we introduce a novel approach that attaches thousands of molecules to a removable surface, with a tunable stretching factor. Next, we dissolve portions of the surface, leaving the DNA molecules suspended as 'bridges'. We demonstrate that the suspended molecules are enzymatically accessible, and we have used an enzyme to incorporate labeled nucleotides, as predicted by the specific molecular sequence. Our results suggest that this novel platform is a promising candidate to achieve high-throughput sequencing of Mbp-long molecules, which could have additional genomic applications, such as the study of other protein-DNA interactions.Maurizio RighiniJustin CostaWei ZhouPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 16, Iss 11, p e0260428 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Maurizio Righini Justin Costa Wei Zhou DNA bridges: A novel platform for single-molecule sequencing and other DNA-protein interaction applications.
description	DNA molecular combing is a technique that stretches thousands of long individual DNA molecules (up to 10 Mbp) into a parallel configuration on surface. It has previously been proposed to sequence these molecules by synthesis. However, this approach poses two critical challenges: 1-Combed DNA molecules are overstretched and therefore a nonoptimal substrate for polymerase extension. 2-The combing surface sterically impedes full enzymatic access to the DNA backbone. Here, we introduce a novel approach that attaches thousands of molecules to a removable surface, with a tunable stretching factor. Next, we dissolve portions of the surface, leaving the DNA molecules suspended as 'bridges'. We demonstrate that the suspended molecules are enzymatically accessible, and we have used an enzyme to incorporate labeled nucleotides, as predicted by the specific molecular sequence. Our results suggest that this novel platform is a promising candidate to achieve high-throughput sequencing of Mbp-long molecules, which could have additional genomic applications, such as the study of other protein-DNA interactions.
format	article
author	Maurizio Righini Justin Costa Wei Zhou
author_facet	Maurizio Righini Justin Costa Wei Zhou
author_sort	Maurizio Righini
title	DNA bridges: A novel platform for single-molecule sequencing and other DNA-protein interaction applications.
title_short	DNA bridges: A novel platform for single-molecule sequencing and other DNA-protein interaction applications.
title_full	DNA bridges: A novel platform for single-molecule sequencing and other DNA-protein interaction applications.
title_fullStr	DNA bridges: A novel platform for single-molecule sequencing and other DNA-protein interaction applications.
title_full_unstemmed	DNA bridges: A novel platform for single-molecule sequencing and other DNA-protein interaction applications.
title_sort	dna bridges: a novel platform for single-molecule sequencing and other dna-protein interaction applications.
publisher	Public Library of Science (PLoS)
publishDate	2021
url	https://doaj.org/article/2e89354eb00d41cea5ae0b127ebab549
work_keys_str_mv	AT mauriziorighini dnabridgesanovelplatformforsinglemoleculesequencingandotherdnaproteininteractionapplications AT justincosta dnabridgesanovelplatformforsinglemoleculesequencingandotherdnaproteininteractionapplications AT weizhou dnabridgesanovelplatformforsinglemoleculesequencingandotherdnaproteininteractionapplications
_version_	1718374515976699904

DNA bridges: A novel platform for single-molecule sequencing and other DNA-protein interaction applications.

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