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

ABSTRACT: 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.

SUBMITTER: Kucharska K

PROVIDER: S-EPMC8234192 | biostudies-literature | 2021 Jun

REPOSITORIES: biostudies-literature

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

Kucharska Karolina K Pilz Marta M Bielec Krzysztof K Kalwarczyk Tomasz T Kuźma Patrycja P Hołyst Robert R

Molecules (Basel, Switzerland) 20210619 12

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 an ...[more]

PMID: 34205435

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