A biophysical study of DNA condensation mediated by histones and protamines
Autor(a) principal: | |
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Data de Publicação: | 2022 |
Outros Autores: | , , , , , |
Tipo de documento: | Artigo |
Idioma: | eng |
Título da fonte: | Repositório Institucional da UNIFESP |
Texto Completo: | https://www.sciencedirect.com/science/article/pii/S016773222202284X https://repositorio.unifesp.br/11600/67488 |
Resumo: | The compaction of long DNA strands into confined spaces such as the nuclei of eukaryotic cells is an essential phenomenon towards the emergence of elaborated forms of life. Histones and protamines are the major nucleoproteins involved in this task participating in the formation of chromatin in somatic and germinative cells, respectively. In addition to a fundamental understanding of critical biological processes, DNA condensation also holds strong potential in biotechnology. Herein, we investigate the mesoscale structure of complexes formed between DNA and histones or protamines. A sophisticated set of biophysical methods encompassing steady-state fluorimetry, small-angle X-ray scattering and infrared nano spectroscopy was used to unveil both the self-assembly and molecular interactions of these complexes. We explored the fluorescence of a molecular rotor, thioflavin T, to investigate the accessibility of ligands in the inter-base environment of DNA strands. AFM-based infrared spectroscopy was used for the first time to probe the vibrational signature of individual DNA/nucleoprotein nano assemblies and disclose secondary-structure features. Our results show that protamines form highly compact structures in which DNA folding hinders access to the inter-base spacing. These assemblies exhibit diversified secondary-structure conformations, with the presence of -sheets stabilizing the packing. In contrast, histone-based complexes are characterized by fibrillar nano assemblies exhibiting larger inter strands separations and access to guest molecules that intercalate between bases. The findings presented here may help the understanding of DNA condensation mediated by these two major nucleoproteins and may assist the optimization of gene vehicles based on these promising nano assemblies. |
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Repositório Institucional da UNIFESP |
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3465 |
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da Silva, Emerson Rodrigo [UNIFESP]Souza, Bruna B.S. [UNIFESP]Lourenço, Thiago C. [UNIFESP]Gerbelli, Barbara B.Oseliero Filho, Pedro L.Oliveira, Cristiano L.P. [UNIFESP]Miranda, Antonio [UNIFESP]http://lattes.cnpq.br/78005892064573262023-05-11T14:02:02Z2023-05-11T14:02:02Z2022-12-15https://www.sciencedirect.com/science/article/pii/S016773222202284Xhttps://repositorio.unifesp.br/11600/67488The compaction of long DNA strands into confined spaces such as the nuclei of eukaryotic cells is an essential phenomenon towards the emergence of elaborated forms of life. Histones and protamines are the major nucleoproteins involved in this task participating in the formation of chromatin in somatic and germinative cells, respectively. In addition to a fundamental understanding of critical biological processes, DNA condensation also holds strong potential in biotechnology. Herein, we investigate the mesoscale structure of complexes formed between DNA and histones or protamines. A sophisticated set of biophysical methods encompassing steady-state fluorimetry, small-angle X-ray scattering and infrared nano spectroscopy was used to unveil both the self-assembly and molecular interactions of these complexes. We explored the fluorescence of a molecular rotor, thioflavin T, to investigate the accessibility of ligands in the inter-base environment of DNA strands. AFM-based infrared spectroscopy was used for the first time to probe the vibrational signature of individual DNA/nucleoprotein nano assemblies and disclose secondary-structure features. Our results show that protamines form highly compact structures in which DNA folding hinders access to the inter-base spacing. These assemblies exhibit diversified secondary-structure conformations, with the presence of -sheets stabilizing the packing. In contrast, histone-based complexes are characterized by fibrillar nano assemblies exhibiting larger inter strands separations and access to guest molecules that intercalate between bases. The findings presented here may help the understanding of DNA condensation mediated by these two major nucleoproteins and may assist the optimization of gene vehicles based on these promising nano assemblies.Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)FAPESP, 19/20907-7120745engElsivierJournal of Molecular LiquidsCondensationNucleoproteinMesophaseChromatinDNAA biophysical study of DNA condensation mediated by histones and protaminesinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/article368info:eu-repo/semantics/openAccessreponame:Repositório Institucional da UNIFESPinstname:Universidade Federal de São Paulo (UNIFESP)instacron:UNIFESPEscola Paulista de Medicina (EPM)Ciências Biológicas (Biologia Molecular)BiofísicaBiofísica molecularBiofísicaORIGINALartigo_bruna_revision2.pdfartigo_bruna_revision2.pdfArquivo principalapplication/pdf1263947${dspace.ui.url}/bitstream/11600/67488/3/artigo_bruna_revision2.pdfb95118a3a0838d3ba87f7378efa7d9b1MD53open 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Repositório InstitucionalPUBhttp://www.repositorio.unifesp.br/oai/requestopendoar:34652023-10-05T04:02:24Repositório Institucional da UNIFESP - Universidade Federal de São Paulo (UNIFESP)false |
dc.title.en.fl_str_mv |
A biophysical study of DNA condensation mediated by histones and protamines |
title |
A biophysical study of DNA condensation mediated by histones and protamines |
spellingShingle |
A biophysical study of DNA condensation mediated by histones and protamines da Silva, Emerson Rodrigo [UNIFESP] Condensation Nucleoprotein Mesophase Chromatin DNA |
title_short |
A biophysical study of DNA condensation mediated by histones and protamines |
title_full |
A biophysical study of DNA condensation mediated by histones and protamines |
title_fullStr |
A biophysical study of DNA condensation mediated by histones and protamines |
title_full_unstemmed |
A biophysical study of DNA condensation mediated by histones and protamines |
title_sort |
A biophysical study of DNA condensation mediated by histones and protamines |
author |
da Silva, Emerson Rodrigo [UNIFESP] |
author_facet |
da Silva, Emerson Rodrigo [UNIFESP] Souza, Bruna B.S. [UNIFESP] Lourenço, Thiago C. [UNIFESP] Gerbelli, Barbara B. Oseliero Filho, Pedro L. Oliveira, Cristiano L.P. [UNIFESP] Miranda, Antonio [UNIFESP] |
author_role |
author |
author2 |
Souza, Bruna B.S. [UNIFESP] Lourenço, Thiago C. [UNIFESP] Gerbelli, Barbara B. Oseliero Filho, Pedro L. Oliveira, Cristiano L.P. [UNIFESP] Miranda, Antonio [UNIFESP] |
author2_role |
author author author author author author |
dc.contributor.authorLattes.pt_BR.fl_str_mv |
http://lattes.cnpq.br/7800589206457326 |
dc.contributor.author.fl_str_mv |
da Silva, Emerson Rodrigo [UNIFESP] Souza, Bruna B.S. [UNIFESP] Lourenço, Thiago C. [UNIFESP] Gerbelli, Barbara B. Oseliero Filho, Pedro L. Oliveira, Cristiano L.P. [UNIFESP] Miranda, Antonio [UNIFESP] |
dc.subject.eng.fl_str_mv |
Condensation Nucleoprotein Mesophase Chromatin |
topic |
Condensation Nucleoprotein Mesophase Chromatin DNA |
dc.subject.por.fl_str_mv |
DNA |
description |
The compaction of long DNA strands into confined spaces such as the nuclei of eukaryotic cells is an essential phenomenon towards the emergence of elaborated forms of life. Histones and protamines are the major nucleoproteins involved in this task participating in the formation of chromatin in somatic and germinative cells, respectively. In addition to a fundamental understanding of critical biological processes, DNA condensation also holds strong potential in biotechnology. Herein, we investigate the mesoscale structure of complexes formed between DNA and histones or protamines. A sophisticated set of biophysical methods encompassing steady-state fluorimetry, small-angle X-ray scattering and infrared nano spectroscopy was used to unveil both the self-assembly and molecular interactions of these complexes. We explored the fluorescence of a molecular rotor, thioflavin T, to investigate the accessibility of ligands in the inter-base environment of DNA strands. AFM-based infrared spectroscopy was used for the first time to probe the vibrational signature of individual DNA/nucleoprotein nano assemblies and disclose secondary-structure features. Our results show that protamines form highly compact structures in which DNA folding hinders access to the inter-base spacing. These assemblies exhibit diversified secondary-structure conformations, with the presence of -sheets stabilizing the packing. In contrast, histone-based complexes are characterized by fibrillar nano assemblies exhibiting larger inter strands separations and access to guest molecules that intercalate between bases. The findings presented here may help the understanding of DNA condensation mediated by these two major nucleoproteins and may assist the optimization of gene vehicles based on these promising nano assemblies. |
publishDate |
2022 |
dc.date.issued.fl_str_mv |
2022-12-15 |
dc.date.accessioned.fl_str_mv |
2023-05-11T14:02:02Z |
dc.date.available.fl_str_mv |
2023-05-11T14:02:02Z |
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.pt_BR.fl_str_mv |
https://www.sciencedirect.com/science/article/pii/S016773222202284X |
dc.identifier.uri.fl_str_mv |
https://repositorio.unifesp.br/11600/67488 |
url |
https://www.sciencedirect.com/science/article/pii/S016773222202284X https://repositorio.unifesp.br/11600/67488 |
dc.language.iso.fl_str_mv |
eng |
language |
eng |
dc.relation.ispartof.en.fl_str_mv |
Journal of Molecular Liquids |
dc.rights.driver.fl_str_mv |
info:eu-repo/semantics/openAccess |
eu_rights_str_mv |
openAccess |
dc.format.none.fl_str_mv |
120745 |
dc.publisher.none.fl_str_mv |
Elsivier |
publisher.none.fl_str_mv |
Elsivier |
dc.source.none.fl_str_mv |
reponame:Repositório Institucional da UNIFESP instname:Universidade Federal de São Paulo (UNIFESP) instacron:UNIFESP |
instname_str |
Universidade Federal de São Paulo (UNIFESP) |
instacron_str |
UNIFESP |
institution |
UNIFESP |
reponame_str |
Repositório Institucional da UNIFESP |
collection |
Repositório Institucional da UNIFESP |
bitstream.url.fl_str_mv |
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MD5 MD5 MD5 MD5 |
repository.name.fl_str_mv |
Repositório Institucional da UNIFESP - Universidade Federal de São Paulo (UNIFESP) |
repository.mail.fl_str_mv |
|
_version_ |
1783460227752919040 |