Interaction of YOYO-1 with guanine-rich DNA
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.
fluorescence enhancement of intercalating dyes, G-quadruplex, G-quartet dependence on monovalent cations, nucleic acid staining reagents, quadruplex topology, YOYO-1
Datta, Shohini Ghosh, Christopher Reynolds, Yugender K. Goud, and Bhaskar Datta. "Interaction of YOYO-1 with guanine-rich DNA." Journal of Biomolecular Structure and Dynamics 32, no. 7 (2014): 1155-1163.
Journal of Biomolecular Structure and Dynamics