title: Interaction of YOYO-1 with guanine-rich DNA.
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.
authors.affiliation: a Department of Chemistry , Indian Institute of Technology Gandhinagar , VGEC Complex Chandkheda, Ahmedabad , 382424 , India .
authors.forename: Shohini Ghosh
authors.initials: SG
authors.lastname: Datta
authors.forename: Christopher
authors.initials: C
authors.lastname: Reynolds
authors.forename: Yugender K
authors.initials: YK
authors.lastname: Goud
authors.forename: Bhaskar
authors.initials: B
authors.lastname: Datta
mesh_terms: D001583:Benzoxazoles / Q000737:chemistry*; D004247:DNA / Q000737:chemistry*; D054856:G-Quadruplexes; D006147:Guanine / Q000737:chemistry*; D007364:Intercalating Agents / Q000737:chemistry*; D008958:Models, Molecular; D009841:Oligonucleotides / Q000737:chemistry; D011806:Quinolinium Compounds / Q000737:chemistry*
chemical_list: D001583:Benzoxazoles; D007364:Intercalating Agents; D009841:Oligonucleotides; D011806:Quinolinium Compounds; C075296:1,1'-((4,4,7,7-tetramethyl)-4,7-diazaundecamethylene)bis-4-(3-methyl-2,3-dihydro(benzo-1,3-oxazole)-2-methylidene)quinolinium; D006147:Guanine; D004247:DNA
keywords: G-quadruplex; G-quartet dependence on monovalent cations; YOYO-1; fluorescence enhancement of intercalating dyes; nucleic acid staining reagents; quadruplex topology