The Interaction Of Triphenylmethane Dyes With G-quadruplexes And Their Corresponding Applications

Triphenylmethane (TPM) dyes normally render rather weak fluorescence due to easy vibrational deexcitation. However, when they stack onto the two external G-quartets of a G-quadruplex (especially intramolecular G-quadruplex), such vibrations will be restricted, resulting in greatly enhanced fluorescence intensities. Thus, TPM dyes may be developed as sensitive G-quadruplex fluorescent probes. Here, fluorescence spectra and energy transfer spectra of five TPM dyes in the presence of G-quadruplexes, single-or double-stranded DNAs were compared. The results show that the fluorescence spectra of four TPM dyes can be used to discriminate intramolecular G-quadruplexes from intermolecular G-quadruplexes, single-and double-stranded DNAs. The energy transfer fluorescence spectra and energy transfer fluorescence titration can be used to distinguish G-quadruplexes (including intramolecular and intermolecular G-quadruplexes) from single-and double-stranded DNAs. Positive charges and substituent size in TPM dyes may be two important factors in influencing the binding stability of the dyes and G-quadruplexes.In addition, a novel K+ detection method was reported using a label-free G-quadruplex-forming oligonucleotide and a triphenylmethane fluorescent dye crystal violet (CV). This method is based on the fluorescence difference of some CV/G-quadruplex complexes in the presence of K+ or Na+, and the fluorescence change with the variation of K+ concentration. According to the nature of the fluorescence change of C V as a function of ionic conditions, two K+ detection modes can be developed. One is a fluorescence-decreasing mode, in which T3TT3 (5'-GGGTTTGGGTGGGTTTGGG) is used, and the fluorescence of CV decreases with an increased concentration of K+. The other is a fluorescence-increasing mode, in which Hum21 (5'-GGGTTAGGGTTAGGGTTAGGG) is used, and the fluorescence of CV increases with an increased concentration of K+. Compared with some published K+ detection methods, this method has some important characteristics, such as lower cost of the test, higher concentrations of Na+ that can be tolerated, adjustable linear detection range and longer excitation and emission wavelengths. Preliminary results demonstrated that the method might be used in biological systems, for example in urine.In this paper, a DNA IMPLICATION logic gate was also constructed based on triphenylmethane (TPM) dye/G-quadruplex complexes, using Ag+ and Cys as two inputs and fluorescence intensity of TPM dye as the output signal. The formation of the TPM dye/G-quadruplex complexes rendered the dye greatly enhanced fluorescence signal and the output signal of the gate was 1. The addition of Cys had no effect on the fluorescence signal and the output still was 1. However, the addition of Ag+ instead of Cys could greatly disrupt the G-quadruplex structure, accompanied by the fluorescence decrease of the dye, rendering an output signal of 0. The addition of Cys into Ag+-quenched fluorescence system led to the recovery of the fluorescence due to the release of Ag+ from DNA by Cys, giving an output signal of 1. Compared with previously published DNA logic gates, the gate operation is rapid and reversible with reliable, nondestructive readout and excellent digital behavior. In addition, the modulation of the fluorescence of the TPM dye/G-quadruplex complexes by Ag+ or/and Cys can also be used to develop highly selective homogenous sensing methods of Ag+ and Cys.