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Probing the elastic limit of DNA bending
Sharp bending of double-stranded DNA (dsDNA) plays an essential role in genome structure and function. However, the elastic limit of dsDNA bending remains controversial. Here, we measured the opening rates of small dsDNA loops with contour lengths ranging between 40 and 200 bp using single-molecule...
Autores principales: | , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2014
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4176374/ https://www.ncbi.nlm.nih.gov/pubmed/25122748 http://dx.doi.org/10.1093/nar/gku735 |
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author | Le, Tung T. Kim, Harold D. |
author_facet | Le, Tung T. Kim, Harold D. |
author_sort | Le, Tung T. |
collection | PubMed |
description | Sharp bending of double-stranded DNA (dsDNA) plays an essential role in genome structure and function. However, the elastic limit of dsDNA bending remains controversial. Here, we measured the opening rates of small dsDNA loops with contour lengths ranging between 40 and 200 bp using single-molecule Fluorescence Resonance Energy Transfer. The relationship of loop lifetime to loop size revealed a critical transition in bending stress. Above the critical loop size, the loop lifetime changed with loop size in a manner consistent with elastic bending stress, but below it, became less sensitive to loop size, indicative of softened dsDNA. The critical loop size increased from ∼60 bp to ∼100 bp with the addition of 5 mM magnesium. We show that our result is in quantitative agreement with the kinkable worm-like chain model, and furthermore, can reproduce previously reported looping probabilities of dsDNA over the range between 50 and 200 bp. Our findings shed new light on the energetics of sharply bent dsDNA. |
format | Online Article Text |
id | pubmed-4176374 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2014 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-41763742014-12-01 Probing the elastic limit of DNA bending Le, Tung T. Kim, Harold D. Nucleic Acids Res Structural Biology Sharp bending of double-stranded DNA (dsDNA) plays an essential role in genome structure and function. However, the elastic limit of dsDNA bending remains controversial. Here, we measured the opening rates of small dsDNA loops with contour lengths ranging between 40 and 200 bp using single-molecule Fluorescence Resonance Energy Transfer. The relationship of loop lifetime to loop size revealed a critical transition in bending stress. Above the critical loop size, the loop lifetime changed with loop size in a manner consistent with elastic bending stress, but below it, became less sensitive to loop size, indicative of softened dsDNA. The critical loop size increased from ∼60 bp to ∼100 bp with the addition of 5 mM magnesium. We show that our result is in quantitative agreement with the kinkable worm-like chain model, and furthermore, can reproduce previously reported looping probabilities of dsDNA over the range between 50 and 200 bp. Our findings shed new light on the energetics of sharply bent dsDNA. Oxford University Press 2014-09-15 2014-08-13 /pmc/articles/PMC4176374/ /pubmed/25122748 http://dx.doi.org/10.1093/nar/gku735 Text en © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research. http://creativecommons.org/licenses/by/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Structural Biology Le, Tung T. Kim, Harold D. Probing the elastic limit of DNA bending |
title | Probing the elastic limit of DNA bending |
title_full | Probing the elastic limit of DNA bending |
title_fullStr | Probing the elastic limit of DNA bending |
title_full_unstemmed | Probing the elastic limit of DNA bending |
title_short | Probing the elastic limit of DNA bending |
title_sort | probing the elastic limit of dna bending |
topic | Structural Biology |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4176374/ https://www.ncbi.nlm.nih.gov/pubmed/25122748 http://dx.doi.org/10.1093/nar/gku735 |
work_keys_str_mv | AT letungt probingtheelasticlimitofdnabending AT kimharoldd probingtheelasticlimitofdnabending |