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.

Selective G-Quadruplex DNA Recognition by a New Class of Designed Cyanines

“…The synthetic ability to structurally tailor cyanines as well as their many therapeutically favorable features, such as low toxicity, also renders them ideal candidates for their potential development as quadruplex targeting agents. In addition, the fluorescence properties of cyanines have been extensively developed in understanding the structural transitions associated with quadruplex folding/unfolding as well as in developing fluorescence agents for detecting different quadruplex conformers in vitro [ 14 , 15 , 16 , 17 ]. Development of quadruplex-specific fluorescence probes with reduced duplex affinity would significantly aid in targeting and visualization of quadruplex structures in an otherwise duplex-enriched genomic content.…”

A comparative study for recognizing G-quadruplexes using dimeric cyanine dyes with different sizes of aromatic substituents

“…35 In 10 mM Na + or K + , the uorescence intensity of YOYO-1 with the G-quadruplex is even lower than those with a mixture base duplex of comparable length. Other types of probes, such as a BODIPY-based uores-cent sensor (GQR), 36 bind to their specic G-quadruplex accompanied by 30-fold uorescence enhancement, which is less than one seventh compared with AB-P4.…”

Fluorescence imaging using synthetic GFP chromophores

“…In this mini-review we will describe only the applications of the synthetic FP Cros for fluorescence imaging, and some fluorescence studies in solutions which can be potentially applied for imaging. Indeed, numerous classes of various fluorogens are known [7][8][9] which are used for the fluorimetric determination of analytes described in this mini-review.…”