Datta, Shohini GhoshShohini GhoshDattaReynolds, ChristopherChristopherReynoldsGoud, Yugender K.Yugender K.GoudDatta, BhaskarBhaskarDatta2025-08-302025-08-302014-07-0310.1080/07391102.2013.8077522-s2.0-84899905620http://repository.iitgn.ac.in/handle/IITG2025/2124423829319The 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. © 2013 © 2013 Taylor & Francis.falsefluorescence enhancement of intercalating dyes | G-quadruplex | G-quartet dependence on monovalent cations | nucleic acid staining reagents | quadruplex topology | YOYO-1Article153802541155-11633 July 201445WOS:000335117100012