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Analysis of scanning force microscopy images of protein-induced DNA bending using simulations
Bending of DNA is a feature essential to the function of many DNA-binding proteins. Bending angles can be estimated with a variety of techniques, but most directly from images obtained using scanning force microscopy (SFM). Direct measurement of the bending angle using a tangent method often produce...
Autores principales: | , , , , , , , , |
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Formato: | Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2005
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1083423/ https://www.ncbi.nlm.nih.gov/pubmed/15843682 http://dx.doi.org/10.1093/nar/gni073 |
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author | Dame, Remus T. van Mameren, Joost Luijsterburg, Martijn S. Mysiak, Monika E. Janićijević, Ana Pazdzior, Grzegorz van der Vliet, Peter C. Wyman, Claire Wuite, Gijs J.L. |
author_facet | Dame, Remus T. van Mameren, Joost Luijsterburg, Martijn S. Mysiak, Monika E. Janićijević, Ana Pazdzior, Grzegorz van der Vliet, Peter C. Wyman, Claire Wuite, Gijs J.L. |
author_sort | Dame, Remus T. |
collection | PubMed |
description | Bending of DNA is a feature essential to the function of many DNA-binding proteins. Bending angles can be estimated with a variety of techniques, but most directly from images obtained using scanning force microscopy (SFM). Direct measurement of the bending angle using a tangent method often produces angles that deviate significantly from values obtained using other techniques. Here, we describe the application of SFM in combination with simulations of DNA as a means to estimate protein-induced bending angles in a reliable and unbiased fashion. In this manner, we were able to obtain accurate estimates for the bending angles induced by nuclear factor I, octamer-binding transcription factor 1, the human XPC-Rad23B complex. |
format | Text |
id | pubmed-1083423 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2005 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-10834232005-04-20 Analysis of scanning force microscopy images of protein-induced DNA bending using simulations Dame, Remus T. van Mameren, Joost Luijsterburg, Martijn S. Mysiak, Monika E. Janićijević, Ana Pazdzior, Grzegorz van der Vliet, Peter C. Wyman, Claire Wuite, Gijs J.L. Nucleic Acids Res Methods Online Bending of DNA is a feature essential to the function of many DNA-binding proteins. Bending angles can be estimated with a variety of techniques, but most directly from images obtained using scanning force microscopy (SFM). Direct measurement of the bending angle using a tangent method often produces angles that deviate significantly from values obtained using other techniques. Here, we describe the application of SFM in combination with simulations of DNA as a means to estimate protein-induced bending angles in a reliable and unbiased fashion. In this manner, we were able to obtain accurate estimates for the bending angles induced by nuclear factor I, octamer-binding transcription factor 1, the human XPC-Rad23B complex. Oxford University Press 2005 2005-04-20 /pmc/articles/PMC1083423/ /pubmed/15843682 http://dx.doi.org/10.1093/nar/gni073 Text en © The Author 2005. Published by Oxford University Press. All rights reserved |
spellingShingle | Methods Online Dame, Remus T. van Mameren, Joost Luijsterburg, Martijn S. Mysiak, Monika E. Janićijević, Ana Pazdzior, Grzegorz van der Vliet, Peter C. Wyman, Claire Wuite, Gijs J.L. Analysis of scanning force microscopy images of protein-induced DNA bending using simulations |
title | Analysis of scanning force microscopy images of protein-induced DNA bending using simulations |
title_full | Analysis of scanning force microscopy images of protein-induced DNA bending using simulations |
title_fullStr | Analysis of scanning force microscopy images of protein-induced DNA bending using simulations |
title_full_unstemmed | Analysis of scanning force microscopy images of protein-induced DNA bending using simulations |
title_short | Analysis of scanning force microscopy images of protein-induced DNA bending using simulations |
title_sort | analysis of scanning force microscopy images of protein-induced dna bending using simulations |
topic | Methods Online |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1083423/ https://www.ncbi.nlm.nih.gov/pubmed/15843682 http://dx.doi.org/10.1093/nar/gni073 |
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