Two Intercalation Mechanisms of Oxazole Yellow Dimer (YOYO-1) into DNA

The oxazole yellow dye, YOYO-1 (a symmetric homodimer), is a commonly used molecule for staining DNA. We applied the brightness analysis to study the intercalation of YOYO-1 into the DNA. We distinguished two binding modes of the dye to dsDNA: mono-intercalation and bis-intercalation. Bis-intercalat...

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Autores principales: Kucharska, Karolina, Pilz, Marta, Bielec, Krzysztof, Kalwarczyk, Tomasz, Kuźma, Patrycja, Hołyst, Robert
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2021
Materias:
Article
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8234192/
https://www.ncbi.nlm.nih.gov/pubmed/34205435
http://dx.doi.org/10.3390/molecules26123748
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author Kucharska, Karolina
Pilz, Marta
Bielec, Krzysztof
Kalwarczyk, Tomasz
Kuźma, Patrycja
Hołyst, Robert
author_facet Kucharska, Karolina
Pilz, Marta
Bielec, Krzysztof
Kalwarczyk, Tomasz
Kuźma, Patrycja
Hołyst, Robert
author_sort Kucharska, Karolina
collection PubMed
description The oxazole yellow dye, YOYO-1 (a symmetric homodimer), is a commonly used molecule for staining DNA. We applied the brightness analysis to study the intercalation of YOYO-1 into the DNA. We distinguished two binding modes of the dye to dsDNA: mono-intercalation and bis-intercalation. Bis-intercalation consists of two consecutive mono-intercalation steps, characterised by two distinct equilibrium constants (with the average number of base pair per binding site equals 3.5): [Formula: see text] and [Formula: see text] , respectively. Mono-intercalation dominates at high concentrations of YOYO-1. Bis-intercalation occurs at low concentrations.
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spelling pubmed-82341922021-06-27 Two Intercalation Mechanisms of Oxazole Yellow Dimer (YOYO-1) into DNA Kucharska, Karolina Pilz, Marta Bielec, Krzysztof Kalwarczyk, Tomasz Kuźma, Patrycja Hołyst, Robert Molecules Article The oxazole yellow dye, YOYO-1 (a symmetric homodimer), is a commonly used molecule for staining DNA. We applied the brightness analysis to study the intercalation of YOYO-1 into the DNA. We distinguished two binding modes of the dye to dsDNA: mono-intercalation and bis-intercalation. Bis-intercalation consists of two consecutive mono-intercalation steps, characterised by two distinct equilibrium constants (with the average number of base pair per binding site equals 3.5): [Formula: see text] and [Formula: see text] , respectively. Mono-intercalation dominates at high concentrations of YOYO-1. Bis-intercalation occurs at low concentrations. MDPI 2021-06-19 /pmc/articles/PMC8234192/ /pubmed/34205435 http://dx.doi.org/10.3390/molecules26123748 Text en © 2021 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Kucharska, Karolina
Pilz, Marta
Bielec, Krzysztof
Kalwarczyk, Tomasz
Kuźma, Patrycja
Hołyst, Robert
Two Intercalation Mechanisms of Oxazole Yellow Dimer (YOYO-1) into DNA
title Two Intercalation Mechanisms of Oxazole Yellow Dimer (YOYO-1) into DNA
title_full Two Intercalation Mechanisms of Oxazole Yellow Dimer (YOYO-1) into DNA
title_fullStr Two Intercalation Mechanisms of Oxazole Yellow Dimer (YOYO-1) into DNA
title_full_unstemmed Two Intercalation Mechanisms of Oxazole Yellow Dimer (YOYO-1) into DNA
title_short Two Intercalation Mechanisms of Oxazole Yellow Dimer (YOYO-1) into DNA
title_sort two intercalation mechanisms of oxazole yellow dimer (yoyo-1) into dna
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8234192/
https://www.ncbi.nlm.nih.gov/pubmed/34205435
http://dx.doi.org/10.3390/molecules26123748
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