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Submicrometer elasticity of double-stranded DNA revealed by precision force-extension measurements with magnetic tweezers

Submicrometer elasticity of double-stranded DNA (dsDNA) governs nanoscale bending of DNA segments and their interactions with proteins. Single-molecule force spectroscopy, including magnetic tweezers (MTs), is an important tool for studying DNA mechanics. However, its application to short DNAs under...

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Autores principales: Shon, Min Ju, Rah, Sang-Hyun, Yoon, Tae-Young
Formato: Online Artículo Texto
Lenguaje:English
Publicado: American Association for the Advancement of Science 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6561745/
https://www.ncbi.nlm.nih.gov/pubmed/31206015
http://dx.doi.org/10.1126/sciadv.aav1697
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author Shon, Min Ju
Rah, Sang-Hyun
Yoon, Tae-Young
author_facet Shon, Min Ju
Rah, Sang-Hyun
Yoon, Tae-Young
author_sort Shon, Min Ju
collection PubMed
description Submicrometer elasticity of double-stranded DNA (dsDNA) governs nanoscale bending of DNA segments and their interactions with proteins. Single-molecule force spectroscopy, including magnetic tweezers (MTs), is an important tool for studying DNA mechanics. However, its application to short DNAs under 1 μm is limited. We developed an MT-based method for precise force-extension measurements in the 100-nm regime that enables in situ correction of the error in DNA extension measurement, and normalizes the force variability across beads by exploiting DNA hairpins. The method reduces the lower limit of tractable dsDNA length down to 198 base pairs (bp) (67 nm), an order-of-magnitude improvement compared to conventional tweezing experiments. Applying this method and the finite worm-like chain model we observed an essentially constant persistence length across the chain lengths studied (198 bp to 10 kbp), which steeply depended on GC content and methylation. This finding suggests a potential sequence-dependent mechanism for short-DNA elasticity.
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spelling pubmed-65617452019-06-14 Submicrometer elasticity of double-stranded DNA revealed by precision force-extension measurements with magnetic tweezers Shon, Min Ju Rah, Sang-Hyun Yoon, Tae-Young Sci Adv Research Articles Submicrometer elasticity of double-stranded DNA (dsDNA) governs nanoscale bending of DNA segments and their interactions with proteins. Single-molecule force spectroscopy, including magnetic tweezers (MTs), is an important tool for studying DNA mechanics. However, its application to short DNAs under 1 μm is limited. We developed an MT-based method for precise force-extension measurements in the 100-nm regime that enables in situ correction of the error in DNA extension measurement, and normalizes the force variability across beads by exploiting DNA hairpins. The method reduces the lower limit of tractable dsDNA length down to 198 base pairs (bp) (67 nm), an order-of-magnitude improvement compared to conventional tweezing experiments. Applying this method and the finite worm-like chain model we observed an essentially constant persistence length across the chain lengths studied (198 bp to 10 kbp), which steeply depended on GC content and methylation. This finding suggests a potential sequence-dependent mechanism for short-DNA elasticity. American Association for the Advancement of Science 2019-06-12 /pmc/articles/PMC6561745/ /pubmed/31206015 http://dx.doi.org/10.1126/sciadv.aav1697 Text en Copyright © 2019 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works. Distributed under a Creative Commons Attribution NonCommercial License 4.0 (CC BY-NC). http://creativecommons.org/licenses/by-nc/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution-NonCommercial license (http://creativecommons.org/licenses/by-nc/4.0/) , which permits use, distribution, and reproduction in any medium, so long as the resultant use is not for commercial advantage and provided the original work is properly cited.
spellingShingle Research Articles
Shon, Min Ju
Rah, Sang-Hyun
Yoon, Tae-Young
Submicrometer elasticity of double-stranded DNA revealed by precision force-extension measurements with magnetic tweezers
title Submicrometer elasticity of double-stranded DNA revealed by precision force-extension measurements with magnetic tweezers
title_full Submicrometer elasticity of double-stranded DNA revealed by precision force-extension measurements with magnetic tweezers
title_fullStr Submicrometer elasticity of double-stranded DNA revealed by precision force-extension measurements with magnetic tweezers
title_full_unstemmed Submicrometer elasticity of double-stranded DNA revealed by precision force-extension measurements with magnetic tweezers
title_short Submicrometer elasticity of double-stranded DNA revealed by precision force-extension measurements with magnetic tweezers
title_sort submicrometer elasticity of double-stranded dna revealed by precision force-extension measurements with magnetic tweezers
topic Research Articles
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6561745/
https://www.ncbi.nlm.nih.gov/pubmed/31206015
http://dx.doi.org/10.1126/sciadv.aav1697
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