Fluorescent Sensor for Monitoring Structural Changes of G-Quadruplexes and Detection of Potassium Ion

Abstract

G-rich sequences with the potential for quadruplex formation are common in genomic DNA. Considering that the biological functions of G-quadruplexes may well depend on their structures, the development of a sensitive structural probe for distinguishing different types of quadruplexes has received great attention. Crystal violet (CV) is a triphenylmethane dye, which can stack onto the two external G-quartets of a G-quadruplex. The ability of CV to discriminate G-quadruplexes from duplex and single-stranded DNAs has been reported by us. Herein, the ability of CV to discriminate parallel from antiparallel structures of a G-quadruplex was studied. The binding of CV to an antiparallel G-quadruplex can make its fluorescence intensity increase to a high level because of the protection of bound CV from the solvent by quadruplex end loops. The presence of side loops in parallel G-quadruplexes cannot provide bound CV such protection, causing the fluorescence intensity of CV/G-quadruplex mixture to be obviously weaker when the G-quadruplex adopts a parallel structure than that when the G-quadruplex adopts an antiparallel structure. Therefore, CV can be developed as a sensitive fluorescent biosensor for the discrimination of antiparallel G-quadruplexes from parallel G-quadruplexes and for monitoring the structural interconversion of G-quadruplexes. In addition, considering that some G-rich DNA sequences can adopt different G-quadruplex structures under Na(+) or K(+) ion conditions, a novel, cheap and simple K(+) ion detection method was developed. This method displays a high K(+) ion selectivity against Na(+) ion, the change of 200 mM in Na(+) ion concentration only causes a similar fluorescent signal change to 0.3 mM K(+) ion.