The universal fluorescent staining property of thiazole orange (TO) dye with most nucleic acids is regulated being specific for G-quadruplexes DNA structures distinctively by molecular modification to introduce a styrene-like substituent at ortho-position of TO scaffold. The investigation shows amazing outcomes because both experimental and molecular docking study realize how such a small piece of substituent leads to remarkable fluorescent signal discrimination with respect to different types of nucleic acids. The results reveal that the modified dye is also same as TO binding with nucleic acids but the distinctive interaction signal, either enhanced or quenched, determined by the spatial length and orientation of the substituent on TO has never been known. The new fluorescent dye modified with a p-(dimethylamino)styryl substituent offers 10-fold more selective towards telomeric G-quadruplexes than double stranded DNA substrates. In addition, native PAGE experiments, FRET, CD analysis, and live cell imaging were also studied and demonstrated the potential applications of this class of thiazole orange based fluorescent probes in bioassays and cell imaging. Copyright © 2016 American Chemical Society.