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Symmetric curvature descriptors for label-free analysis of DNA
High-resolution microscopy techniques such as electron microscopy, scanning tunnelling microscopy and atomic force microscopy represent well-established, powerful tools for the structural characterization of adsorbed DNA molecules at the nanoscale. Notably, the analysis of DNA contours allows mappin...
Autores principales: | , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Nature Publishing Group
2014
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5377314/ https://www.ncbi.nlm.nih.gov/pubmed/25248631 http://dx.doi.org/10.1038/srep06459 |
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author | Buzio, Renato Repetto, Luca Giacopelli, Francesca Ravazzolo, Roberto Valbusa, Ugo |
author_facet | Buzio, Renato Repetto, Luca Giacopelli, Francesca Ravazzolo, Roberto Valbusa, Ugo |
author_sort | Buzio, Renato |
collection | PubMed |
description | High-resolution microscopy techniques such as electron microscopy, scanning tunnelling microscopy and atomic force microscopy represent well-established, powerful tools for the structural characterization of adsorbed DNA molecules at the nanoscale. Notably, the analysis of DNA contours allows mapping intrinsic curvature and flexibility along the molecular backbone. This is particularly suited to address the impact of the base-pairs sequence on the local conformation of the strands and plays a pivotal role for investigations relating the inherent DNA shape and flexibility to other functional properties. Here, we introduce novel chain descriptors aimed to characterize the local intrinsic curvature and flexibility of adsorbed DNA molecules with unknown orientation. They consist of stochastic functions that couple the curvatures of two nanosized segments, symmetrically placed on the DNA contour. We show that the fine mapping of the ensemble-averaged functions along the molecular backbone generates characteristic patterns of variation that highlight all pairs of tracts with large intrinsic curvature or enhanced flexibility. We demonstrate the practical applicability of the method for DNA chains imaged by atomic force microscopy. Our approach paves the way for the label-free comparative analysis of duplexes, aimed to detect nanoscale conformational changes of physical or biological relevance in large sample numbers. |
format | Online Article Text |
id | pubmed-5377314 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2014 |
publisher | Nature Publishing Group |
record_format | MEDLINE/PubMed |
spelling | pubmed-53773142017-04-05 Symmetric curvature descriptors for label-free analysis of DNA Buzio, Renato Repetto, Luca Giacopelli, Francesca Ravazzolo, Roberto Valbusa, Ugo Sci Rep Article High-resolution microscopy techniques such as electron microscopy, scanning tunnelling microscopy and atomic force microscopy represent well-established, powerful tools for the structural characterization of adsorbed DNA molecules at the nanoscale. Notably, the analysis of DNA contours allows mapping intrinsic curvature and flexibility along the molecular backbone. This is particularly suited to address the impact of the base-pairs sequence on the local conformation of the strands and plays a pivotal role for investigations relating the inherent DNA shape and flexibility to other functional properties. Here, we introduce novel chain descriptors aimed to characterize the local intrinsic curvature and flexibility of adsorbed DNA molecules with unknown orientation. They consist of stochastic functions that couple the curvatures of two nanosized segments, symmetrically placed on the DNA contour. We show that the fine mapping of the ensemble-averaged functions along the molecular backbone generates characteristic patterns of variation that highlight all pairs of tracts with large intrinsic curvature or enhanced flexibility. We demonstrate the practical applicability of the method for DNA chains imaged by atomic force microscopy. Our approach paves the way for the label-free comparative analysis of duplexes, aimed to detect nanoscale conformational changes of physical or biological relevance in large sample numbers. Nature Publishing Group 2014-09-24 /pmc/articles/PMC5377314/ /pubmed/25248631 http://dx.doi.org/10.1038/srep06459 Text en Copyright © 2014, Macmillan Publishers Limited. All rights reserved http://creativecommons.org/licenses/by-nc-sa/4.0/ This work is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 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-nc-sa/4.0/ |
spellingShingle | Article Buzio, Renato Repetto, Luca Giacopelli, Francesca Ravazzolo, Roberto Valbusa, Ugo Symmetric curvature descriptors for label-free analysis of DNA |
title | Symmetric curvature descriptors for label-free analysis of DNA |
title_full | Symmetric curvature descriptors for label-free analysis of DNA |
title_fullStr | Symmetric curvature descriptors for label-free analysis of DNA |
title_full_unstemmed | Symmetric curvature descriptors for label-free analysis of DNA |
title_short | Symmetric curvature descriptors for label-free analysis of DNA |
title_sort | symmetric curvature descriptors for label-free analysis of dna |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5377314/ https://www.ncbi.nlm.nih.gov/pubmed/25248631 http://dx.doi.org/10.1038/srep06459 |
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