Kucharska K, Pilz M, Bielec K, Kalwarczyk T, Kuźma P, Hołyst R. Two Intercalation Mechanisms of Oxazole Yellow Dimer (YOYO-1) into DNA.
Molecules 2021;
26:molecules26123748. [PMID:
34205435 PMCID:
PMC8234192 DOI:
10.3390/molecules26123748]
[Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 06/14/2021] [Accepted: 06/15/2021] [Indexed: 11/16/2022] Open
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.
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