DNA barcodes using a double nanopore system

Abstract The potential of a double nanopore system to determine DNA barcodes has been demonstrated experimentally. By carrying out Brownian dynamics simulation on a coarse-grained model DNA with protein tag (barcodes) at known locations along the chain backbone, we demonstrate that due to large vari...

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Autores principales:	Swarnadeep Seth, Aniket Bhattacharya
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/c16ae387f05d4eeeabb235d8f2d7798a
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spelling	oai:doaj.org-article:c16ae387f05d4eeeabb235d8f2d7798a2021-12-02T16:51:31ZDNA barcodes using a double nanopore system10.1038/s41598-021-89017-62045-2322https://doaj.org/article/c16ae387f05d4eeeabb235d8f2d7798a2021-05-01T00:00:00Zhttps://doi.org/10.1038/s41598-021-89017-6https://doaj.org/toc/2045-2322Abstract The potential of a double nanopore system to determine DNA barcodes has been demonstrated experimentally. By carrying out Brownian dynamics simulation on a coarse-grained model DNA with protein tag (barcodes) at known locations along the chain backbone, we demonstrate that due to large variation of velocities of the chain segments between the tags, it is inevitable to under/overestimate the genetic lengths from the experimental current blockade and time of flight data. We demonstrate that it is the tension propagation along the chain’s backbone that governs the motion of the entire chain and is the key element to explain the non uniformity and disparate velocities of the tags and DNA monomers under translocation that introduce errors in measurement of the length segments between protein tags. Using simulation data we further demonstrate that it is important to consider the dynamics of the entire chain and suggest methods to accurately decipher barcodes. We introduce and validate an interpolation scheme using simulation data for a broad distribution of tag separations and suggest how to implement the scheme experimentally.Swarnadeep SethAniket BhattacharyaNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 11, Iss 1, Pp 1-9 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Swarnadeep Seth Aniket Bhattacharya DNA barcodes using a double nanopore system
description	Abstract The potential of a double nanopore system to determine DNA barcodes has been demonstrated experimentally. By carrying out Brownian dynamics simulation on a coarse-grained model DNA with protein tag (barcodes) at known locations along the chain backbone, we demonstrate that due to large variation of velocities of the chain segments between the tags, it is inevitable to under/overestimate the genetic lengths from the experimental current blockade and time of flight data. We demonstrate that it is the tension propagation along the chain’s backbone that governs the motion of the entire chain and is the key element to explain the non uniformity and disparate velocities of the tags and DNA monomers under translocation that introduce errors in measurement of the length segments between protein tags. Using simulation data we further demonstrate that it is important to consider the dynamics of the entire chain and suggest methods to accurately decipher barcodes. We introduce and validate an interpolation scheme using simulation data for a broad distribution of tag separations and suggest how to implement the scheme experimentally.
format	article
author	Swarnadeep Seth Aniket Bhattacharya
author_facet	Swarnadeep Seth Aniket Bhattacharya
author_sort	Swarnadeep Seth
title	DNA barcodes using a double nanopore system
title_short	DNA barcodes using a double nanopore system
title_full	DNA barcodes using a double nanopore system
title_fullStr	DNA barcodes using a double nanopore system
title_full_unstemmed	DNA barcodes using a double nanopore system
title_sort	dna barcodes using a double nanopore system
publisher	Nature Portfolio
publishDate	2021
url	https://doaj.org/article/c16ae387f05d4eeeabb235d8f2d7798a
work_keys_str_mv	AT swarnadeepseth dnabarcodesusingadoublenanoporesystem AT aniketbhattacharya dnabarcodesusingadoublenanoporesystem
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DNA barcodes using a double nanopore system

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