Interaction of YOYO-1 with guanine-rich DNA

J Biomol Struct Dyn. 2014;32(7):1155-63. doi: 10.1080/07391102.2013.807752. Epub 2013 Jul 5.

Abstract

The oxazole homodimer YOYO-1 has served as a valuable tool for the detection and quantification of nucleic acids. While the base specificity and selectivity of binding of YOYO-1 has been researched to some extent, the effect of unorthodox nucleic acid conformations on dye binding has received relatively less attention. In this work, we attempt to correlate the quadruplex-forming ability of G-rich sequences with binding of YOYO-1. Oligonucleotides differing in the number of tandem G repeats, total length, and length of loop sequence were evaluated for their ability to form quadruplexes in presence of sodium (Na(+)) or potassium (K(+)) ions. The fluorescence behavior of YOYO-1 upon binding such G-rich sequences was also ascertained. A distinct correlation was observed between the strength and propensity of quadruplex formation, and the affinity of YOYO-1 to bind such sequences. Specifically, as exemplified by the oligonucleotides 5'-G4T2G4-3' and 5'-G3TG3TG3-3', sequences possessing longer G-rich regions and shorter loop sequences formed stronger quadruplexes in presence of K(+) which translated to weaker binding of YOYO-1. The dependence of binding of YOYO-1 on sequence and structural features of G-rich DNA has not been explored previously and such studies are expected to aid in more effective interpretation of applications involving the fluorophore.

Keywords: G-quadruplex; G-quartet dependence on monovalent cations; YOYO-1; fluorescence enhancement of intercalating dyes; nucleic acid staining reagents; quadruplex topology.

MeSH terms

  • Benzoxazoles / chemistry*
  • DNA / chemistry*
  • G-Quadruplexes
  • Guanine / chemistry*
  • Intercalating Agents / chemistry*
  • Models, Molecular
  • Oligonucleotides / chemistry
  • Quinolinium Compounds / chemistry*

Substances

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