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

Molecules. 2021 Jun 19;26(12):3748. doi: 10.3390/molecules26123748.

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.

Keywords: DNA; YOYO-1; brightness method; equilibrium constant; intercalation.

MeSH terms

  • Benzoxazoles / chemistry*
  • DNA / chemistry*
  • Dimerization
  • Fluorescent Dyes / chemistry
  • Intercalating Agents / chemistry*
  • Quinolines / chemistry*
  • Quinolinium Compounds / chemistry*

Substances

  • Benzoxazoles
  • Fluorescent Dyes
  • Intercalating Agents
  • Quinolines
  • Quinolinium Compounds
  • oxazole yellow
  • 1,1'-((4,4,7,7-tetramethyl)-4,7-diazaundecamethylene)bis-4-(3-methyl-2,3-dihydro(benzo-1,3-oxazole)-2-methylidene)quinolinium
  • DNA