Cargando…
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...
Autores principales: | , , , |
---|---|
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 |
_version_ | 1782361548086312960 |
---|---|
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. |
format | Online Article Text |
id | pubmed-4360479 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2015 |
publisher | Nature Publishing Group |
record_format | MEDLINE/PubMed |
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 |
work_keys_str_mv | AT zhangtianbiao determinationofbasebindingstrengthandbasestackinginteractionofdnaduplexusingatomicforcemicroscope AT zhangchanglin determinationofbasebindingstrengthandbasestackinginteractionofdnaduplexusingatomicforcemicroscope AT dongzaili determinationofbasebindingstrengthandbasestackinginteractionofdnaduplexusingatomicforcemicroscope AT guanyifu determinationofbasebindingstrengthandbasestackinginteractionofdnaduplexusingatomicforcemicroscope |