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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Bibliographic Details
Published in:Molecules (Basel, Switzerland) Switzerland), 2021-06, Vol.26 (12), p.3748
Main Authors: Kucharska, Karolina, Pilz, Marta, Bielec, Krzysztof, Kalwarczyk, Tomasz, Kuźma, Patrycja, Hołyst, Robert
Format: Article
Language:English
Subjects:
brightness method
Chemical equilibrium
Deoxyribonucleic acid
DNA
Dyes
Equilibrium
equilibrium constant
Experiments
Intercalation
Lasers
Low concentrations
Methods
Microscopy
Oxazole
Spectrum analysis
Surfactants
YOYO-1
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Summary: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): K1=3.36±0.43×107M−1 and K2=1.90±0.61×105M−1, respectively. Mono-intercalation dominates at high concentrations of YOYO-1. Bis-intercalation occurs at low concentrations.
ISSN:1420-3049
1420-3049
DOI:10.3390/molecules26123748