Fluorescence lifetime imaging for studying DNA compaction and gene activities

Abstract Optical imaging is a most useful and widespread technique for the investigation of the structure and function of the cellular genomes. However, an analysis of immensely convoluted and irregularly compacted DNA polymer is highly challenging even by modern super-resolution microscopy approach...

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Autores principales:	Svitlana M. Levchenko, Artem Pliss, Xiao Peng, Paras N. Prasad, Junle Qu
Formato:	article
Lenguaje:	EN
Publicado:	Nature Publishing Group 2021
Materias:	Applied optics. Photonics TA1501-1820 Optics. Light QC350-467
Acceso en línea:	https://doaj.org/article/092937b12b384e06a7f8e5a73e07dd60
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spelling	oai:doaj.org-article:092937b12b384e06a7f8e5a73e07dd602021-11-08T10:57:48ZFluorescence lifetime imaging for studying DNA compaction and gene activities10.1038/s41377-021-00664-w2047-7538https://doaj.org/article/092937b12b384e06a7f8e5a73e07dd602021-11-01T00:00:00Zhttps://doi.org/10.1038/s41377-021-00664-whttps://doaj.org/toc/2047-7538Abstract Optical imaging is a most useful and widespread technique for the investigation of the structure and function of the cellular genomes. However, an analysis of immensely convoluted and irregularly compacted DNA polymer is highly challenging even by modern super-resolution microscopy approaches. Here we propose fluorescence lifetime imaging (FLIM) for the advancement of studies of genomic structure including DNA compaction, replication as well as monitoring of gene expression. The proposed FLIM assay employs two independent mechanisms for DNA compaction sensing. One mechanism relies on the inverse quadratic relation between the fluorescence lifetimes of fluorescence probes incorporated into DNA and their local refractive index, variable due to DNA compaction density. Another mechanism is based on the Förster resonance energy transfer (FRET) process between the donor and the acceptor fluorophores, both incorporated into DNA. Both these proposed mechanisms were validated in cultured cells. The obtained data unravel a significant difference in compaction of the gene-rich and gene-poor pools of genomic DNA. We show that the gene-rich DNA is loosely compacted compared to the dense DNA domains devoid of active genes.Svitlana M. LevchenkoArtem PlissXiao PengParas N. PrasadJunle QuNature Publishing GrouparticleApplied optics. PhotonicsTA1501-1820Optics. LightQC350-467ENLight: Science & Applications, Vol 10, Iss 1, Pp 1-11 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Applied optics. Photonics TA1501-1820 Optics. Light QC350-467
spellingShingle	Applied optics. Photonics TA1501-1820 Optics. Light QC350-467 Svitlana M. Levchenko Artem Pliss Xiao Peng Paras N. Prasad Junle Qu Fluorescence lifetime imaging for studying DNA compaction and gene activities
description	Abstract Optical imaging is a most useful and widespread technique for the investigation of the structure and function of the cellular genomes. However, an analysis of immensely convoluted and irregularly compacted DNA polymer is highly challenging even by modern super-resolution microscopy approaches. Here we propose fluorescence lifetime imaging (FLIM) for the advancement of studies of genomic structure including DNA compaction, replication as well as monitoring of gene expression. The proposed FLIM assay employs two independent mechanisms for DNA compaction sensing. One mechanism relies on the inverse quadratic relation between the fluorescence lifetimes of fluorescence probes incorporated into DNA and their local refractive index, variable due to DNA compaction density. Another mechanism is based on the Förster resonance energy transfer (FRET) process between the donor and the acceptor fluorophores, both incorporated into DNA. Both these proposed mechanisms were validated in cultured cells. The obtained data unravel a significant difference in compaction of the gene-rich and gene-poor pools of genomic DNA. We show that the gene-rich DNA is loosely compacted compared to the dense DNA domains devoid of active genes.
format	article
author	Svitlana M. Levchenko Artem Pliss Xiao Peng Paras N. Prasad Junle Qu
author_facet	Svitlana M. Levchenko Artem Pliss Xiao Peng Paras N. Prasad Junle Qu
author_sort	Svitlana M. Levchenko
title	Fluorescence lifetime imaging for studying DNA compaction and gene activities
title_short	Fluorescence lifetime imaging for studying DNA compaction and gene activities
title_full	Fluorescence lifetime imaging for studying DNA compaction and gene activities
title_fullStr	Fluorescence lifetime imaging for studying DNA compaction and gene activities
title_full_unstemmed	Fluorescence lifetime imaging for studying DNA compaction and gene activities
title_sort	fluorescence lifetime imaging for studying dna compaction and gene activities
publisher	Nature Publishing Group
publishDate	2021
url	https://doaj.org/article/092937b12b384e06a7f8e5a73e07dd60
work_keys_str_mv	AT svitlanamlevchenko fluorescencelifetimeimagingforstudyingdnacompactionandgeneactivities AT artempliss fluorescencelifetimeimagingforstudyingdnacompactionandgeneactivities AT xiaopeng fluorescencelifetimeimagingforstudyingdnacompactionandgeneactivities AT parasnprasad fluorescencelifetimeimagingforstudyingdnacompactionandgeneactivities AT junlequ fluorescencelifetimeimagingforstudyingdnacompactionandgeneactivities
_version_	1718442397469245440

Fluorescence lifetime imaging for studying DNA compaction and gene activities

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