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Determination of Base Binding Strength and Base Stacking Interaction of DNA Duplex Using Atomic Force Microscope

As one of the most crucial properties of DNA, the structural stability and the mechanical strength are attracting a great attention. Here, we take advantage of high force resolution and high special resolution of Atom Force Microscope and investigate the mechanical force of DNA duplexes. To evaluate...

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Detalles Bibliográficos
Autores principales: Zhang, Tian-biao, Zhang, Chang-lin, Dong, Zai-li, Guan, Yi-fu
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group 2015
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4360479/
https://www.ncbi.nlm.nih.gov/pubmed/25772017
http://dx.doi.org/10.1038/srep09143
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author Zhang, Tian-biao
Zhang, Chang-lin
Dong, Zai-li
Guan, Yi-fu
author_facet Zhang, Tian-biao
Zhang, Chang-lin
Dong, Zai-li
Guan, Yi-fu
author_sort Zhang, Tian-biao
collection PubMed
description As one of the most crucial properties of DNA, the structural stability and the mechanical strength are attracting a great attention. Here, we take advantage of high force resolution and high special resolution of Atom Force Microscope and investigate the mechanical force of DNA duplexes. To evaluate the base pair hydrogen bond strength and base stacking force in DNA strands, we designed two modes (unzipping and stretching) for the measurement rupture forces. Employing k-means clustering algorithm, the ruptured force are clustered and the mean values are estimated. We assessed the influence of experimental parameters and performed the force evaluation for DNA duplexes of pure dG/dC and dA/dT base pairs. The base binding strength of single dG/dC and single dA/dT were estimated to be 20.0 ± 0.2 pN and 14.0 ± 0.3 pN, respectively, and the base stacking interaction was estimated to be 2.0 ± 0.1 pN. Our results provide valuable information about the quantitative evaluation of the mechanical properties of the DNA duplexes.
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spelling pubmed-43604792015-03-19 Determination of Base Binding Strength and Base Stacking Interaction of DNA Duplex Using Atomic Force Microscope Zhang, Tian-biao Zhang, Chang-lin Dong, Zai-li Guan, Yi-fu Sci Rep Article As one of the most crucial properties of DNA, the structural stability and the mechanical strength are attracting a great attention. Here, we take advantage of high force resolution and high special resolution of Atom Force Microscope and investigate the mechanical force of DNA duplexes. To evaluate the base pair hydrogen bond strength and base stacking force in DNA strands, we designed two modes (unzipping and stretching) for the measurement rupture forces. Employing k-means clustering algorithm, the ruptured force are clustered and the mean values are estimated. We assessed the influence of experimental parameters and performed the force evaluation for DNA duplexes of pure dG/dC and dA/dT base pairs. The base binding strength of single dG/dC and single dA/dT were estimated to be 20.0 ± 0.2 pN and 14.0 ± 0.3 pN, respectively, and the base stacking interaction was estimated to be 2.0 ± 0.1 pN. Our results provide valuable information about the quantitative evaluation of the mechanical properties of the DNA duplexes. Nature Publishing Group 2015-03-16 /pmc/articles/PMC4360479/ /pubmed/25772017 http://dx.doi.org/10.1038/srep09143 Text en Copyright © 2015, Macmillan Publishers Limited. All rights reserved http://creativecommons.org/licenses/by/4.0/ This work is licensed under a Creative Commons Attribution 4.0 International License. The images or other third party material in this article are included in the article's Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder in order to reproduce the material. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/
spellingShingle Article
Zhang, Tian-biao
Zhang, Chang-lin
Dong, Zai-li
Guan, Yi-fu
Determination of Base Binding Strength and Base Stacking Interaction of DNA Duplex Using Atomic Force Microscope
title Determination of Base Binding Strength and Base Stacking Interaction of DNA Duplex Using Atomic Force Microscope
title_full Determination of Base Binding Strength and Base Stacking Interaction of DNA Duplex Using Atomic Force Microscope
title_fullStr Determination of Base Binding Strength and Base Stacking Interaction of DNA Duplex Using Atomic Force Microscope
title_full_unstemmed Determination of Base Binding Strength and Base Stacking Interaction of DNA Duplex Using Atomic Force Microscope
title_short Determination of Base Binding Strength and Base Stacking Interaction of DNA Duplex Using Atomic Force Microscope
title_sort determination of base binding strength and base stacking interaction of dna duplex using atomic force microscope
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4360479/
https://www.ncbi.nlm.nih.gov/pubmed/25772017
http://dx.doi.org/10.1038/srep09143
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