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Initial state of DNA-Dye complex sets the stage for protein induced fluorescence modulation

Protein-induced fluorescence enhancement (PIFE) is a popular tool for characterizing protein-DNA interactions. PIFE has been explained by an increase in local viscosity due to the presence of the protein residues. This explanation, however, denies the opposite effect of fluorescence quenching. This...

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Autores principales: Rashid, Fahad, Raducanu, Vlad-Stefan, Zaher, Manal S., Tehseen, Muhammad, Habuchi, Satoshi, Hamdan, Samir M.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group UK 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6506533/
https://www.ncbi.nlm.nih.gov/pubmed/31068591
http://dx.doi.org/10.1038/s41467-019-10137-9
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author Rashid, Fahad
Raducanu, Vlad-Stefan
Zaher, Manal S.
Tehseen, Muhammad
Habuchi, Satoshi
Hamdan, Samir M.
author_facet Rashid, Fahad
Raducanu, Vlad-Stefan
Zaher, Manal S.
Tehseen, Muhammad
Habuchi, Satoshi
Hamdan, Samir M.
author_sort Rashid, Fahad
collection PubMed
description Protein-induced fluorescence enhancement (PIFE) is a popular tool for characterizing protein-DNA interactions. PIFE has been explained by an increase in local viscosity due to the presence of the protein residues. This explanation, however, denies the opposite effect of fluorescence quenching. This work offers a perspective for understanding PIFE mechanism and reports the observation of a phenomenon that we name protein-induced fluorescence quenching (PIFQ), which exhibits an opposite effect to PIFE. A detailed characterization of these two fluorescence modulations reveals that the initial fluorescence state of the labeled mediator (DNA) determines whether this mediator-conjugated dye undergoes PIFE or PIFQ upon protein binding. This key role of the mediator DNA provides a protocol for the experimental design to obtain either PIFQ or PIFE, on-demand. This makes the arbitrary nature of the current experimental design obsolete, allowing for proper integration of both PIFE and PIFQ with existing bulk and single-molecule fluorescence techniques.
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spelling pubmed-65065332019-05-10 Initial state of DNA-Dye complex sets the stage for protein induced fluorescence modulation Rashid, Fahad Raducanu, Vlad-Stefan Zaher, Manal S. Tehseen, Muhammad Habuchi, Satoshi Hamdan, Samir M. Nat Commun Article Protein-induced fluorescence enhancement (PIFE) is a popular tool for characterizing protein-DNA interactions. PIFE has been explained by an increase in local viscosity due to the presence of the protein residues. This explanation, however, denies the opposite effect of fluorescence quenching. This work offers a perspective for understanding PIFE mechanism and reports the observation of a phenomenon that we name protein-induced fluorescence quenching (PIFQ), which exhibits an opposite effect to PIFE. A detailed characterization of these two fluorescence modulations reveals that the initial fluorescence state of the labeled mediator (DNA) determines whether this mediator-conjugated dye undergoes PIFE or PIFQ upon protein binding. This key role of the mediator DNA provides a protocol for the experimental design to obtain either PIFQ or PIFE, on-demand. This makes the arbitrary nature of the current experimental design obsolete, allowing for proper integration of both PIFE and PIFQ with existing bulk and single-molecule fluorescence techniques. Nature Publishing Group UK 2019-05-08 /pmc/articles/PMC6506533/ /pubmed/31068591 http://dx.doi.org/10.1038/s41467-019-10137-9 Text en © The Author(s) 2019 Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.
spellingShingle Article
Rashid, Fahad
Raducanu, Vlad-Stefan
Zaher, Manal S.
Tehseen, Muhammad
Habuchi, Satoshi
Hamdan, Samir M.
Initial state of DNA-Dye complex sets the stage for protein induced fluorescence modulation
title Initial state of DNA-Dye complex sets the stage for protein induced fluorescence modulation
title_full Initial state of DNA-Dye complex sets the stage for protein induced fluorescence modulation
title_fullStr Initial state of DNA-Dye complex sets the stage for protein induced fluorescence modulation
title_full_unstemmed Initial state of DNA-Dye complex sets the stage for protein induced fluorescence modulation
title_short Initial state of DNA-Dye complex sets the stage for protein induced fluorescence modulation
title_sort initial state of dna-dye complex sets the stage for protein induced fluorescence modulation
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6506533/
https://www.ncbi.nlm.nih.gov/pubmed/31068591
http://dx.doi.org/10.1038/s41467-019-10137-9
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