Revisiting the neighbor exclusion model and its applications
Autor(a) principal: | |
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Data de Publicação: | 2009 |
Tipo de documento: | Artigo |
Idioma: | eng |
Título da fonte: | LOCUS Repositório Institucional da UFV |
Texto Completo: | https://doi.org/10.1002/bip.21296 http://www.locus.ufv.br/handle/123456789/13846 |
Resumo: | We review the neighbor exclusion model and some of its applications to analyze the binding data of DNA-ligand complexes. We revisit the closed form of the model developed by McGhee and von Hippel in 1974, showing that this classic model can be used to help studying the behavior of DNA contour and persistence lengths when interacting with intercalating ligands. We present methods to quantitatively analyze the variation of these two quantities, allowing one to determine important parameters of the interaction such as the intrinsic binding constant and the exclusion number of the ligand. |
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Rocha, Marcio S.2017-11-28T09:40:06Z2017-11-28T09:40:06Z2009-08-2010970282https://doi.org/10.1002/bip.21296http://www.locus.ufv.br/handle/123456789/13846We review the neighbor exclusion model and some of its applications to analyze the binding data of DNA-ligand complexes. We revisit the closed form of the model developed by McGhee and von Hippel in 1974, showing that this classic model can be used to help studying the behavior of DNA contour and persistence lengths when interacting with intercalating ligands. We present methods to quantitatively analyze the variation of these two quantities, allowing one to determine important parameters of the interaction such as the intrinsic binding constant and the exclusion number of the ligand.engBiopolymersVolume 93, Issue 1, Pages 1–7, January 2010Neighbor exclusion modelDNAPersistence lengthIntercalationRevisiting the neighbor exclusion model and its applicationsinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articleapplication/pdfinfo:eu-repo/semantics/openAccessreponame:LOCUS Repositório Institucional da UFVinstname:Universidade Federal de Viçosa (UFV)instacron:UFVORIGINALRocha-2010-Biopolymers.pdfRocha-2010-Biopolymers.pdfTexto completoapplication/pdf169552https://locus.ufv.br//bitstream/123456789/13846/1/Rocha-2010-Biopolymers.pdf143c377bb569d1332c7d5724792a2b9eMD51LICENSElicense.txtlicense.txttext/plain; charset=utf-81748https://locus.ufv.br//bitstream/123456789/13846/2/license.txt8a4605be74aa9ea9d79846c1fba20a33MD52THUMBNAILRocha-2010-Biopolymers.pdf.jpgRocha-2010-Biopolymers.pdf.jpgIM Thumbnailimage/jpeg4912https://locus.ufv.br//bitstream/123456789/13846/3/Rocha-2010-Biopolymers.pdf.jpgcf222184b4227b8178b7d5d28fe75dfdMD53123456789/138462017-11-28 22:00:36.646oai:locus.ufv.br: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Repositório InstitucionalPUBhttps://www.locus.ufv.br/oai/requestfabiojreis@ufv.bropendoar:21452017-11-29T01:00:36LOCUS Repositório Institucional da UFV - Universidade Federal de Viçosa (UFV)false |
dc.title.en.fl_str_mv |
Revisiting the neighbor exclusion model and its applications |
title |
Revisiting the neighbor exclusion model and its applications |
spellingShingle |
Revisiting the neighbor exclusion model and its applications Rocha, Marcio S. Neighbor exclusion model DNA Persistence length Intercalation |
title_short |
Revisiting the neighbor exclusion model and its applications |
title_full |
Revisiting the neighbor exclusion model and its applications |
title_fullStr |
Revisiting the neighbor exclusion model and its applications |
title_full_unstemmed |
Revisiting the neighbor exclusion model and its applications |
title_sort |
Revisiting the neighbor exclusion model and its applications |
author |
Rocha, Marcio S. |
author_facet |
Rocha, Marcio S. |
author_role |
author |
dc.contributor.author.fl_str_mv |
Rocha, Marcio S. |
dc.subject.pt-BR.fl_str_mv |
Neighbor exclusion model DNA Persistence length Intercalation |
topic |
Neighbor exclusion model DNA Persistence length Intercalation |
description |
We review the neighbor exclusion model and some of its applications to analyze the binding data of DNA-ligand complexes. We revisit the closed form of the model developed by McGhee and von Hippel in 1974, showing that this classic model can be used to help studying the behavior of DNA contour and persistence lengths when interacting with intercalating ligands. We present methods to quantitatively analyze the variation of these two quantities, allowing one to determine important parameters of the interaction such as the intrinsic binding constant and the exclusion number of the ligand. |
publishDate |
2009 |
dc.date.issued.fl_str_mv |
2009-08-20 |
dc.date.accessioned.fl_str_mv |
2017-11-28T09:40:06Z |
dc.date.available.fl_str_mv |
2017-11-28T09:40:06Z |
dc.type.status.fl_str_mv |
info:eu-repo/semantics/publishedVersion |
dc.type.driver.fl_str_mv |
info:eu-repo/semantics/article |
format |
article |
status_str |
publishedVersion |
dc.identifier.uri.fl_str_mv |
https://doi.org/10.1002/bip.21296 http://www.locus.ufv.br/handle/123456789/13846 |
dc.identifier.issn.none.fl_str_mv |
10970282 |
identifier_str_mv |
10970282 |
url |
https://doi.org/10.1002/bip.21296 http://www.locus.ufv.br/handle/123456789/13846 |
dc.language.iso.fl_str_mv |
eng |
language |
eng |
dc.relation.ispartofseries.pt-BR.fl_str_mv |
Volume 93, Issue 1, Pages 1–7, January 2010 |
dc.rights.driver.fl_str_mv |
info:eu-repo/semantics/openAccess |
eu_rights_str_mv |
openAccess |
dc.format.none.fl_str_mv |
application/pdf |
dc.publisher.none.fl_str_mv |
Biopolymers |
publisher.none.fl_str_mv |
Biopolymers |
dc.source.none.fl_str_mv |
reponame:LOCUS Repositório Institucional da UFV instname:Universidade Federal de Viçosa (UFV) instacron:UFV |
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Universidade Federal de Viçosa (UFV) |
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UFV |
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UFV |
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LOCUS Repositório Institucional da UFV |
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LOCUS Repositório Institucional da UFV |
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