The ability to selectively control DNA conformation using light as an external stimulus offers unique opportunities to control specific DNA sequences in biological settings and to develop nucleotide-based nanodevices. We describe a duplex/G-quadruplex (G4) junction-binding chemotype derived from a cyclic azobenzene core that reversibly photoswitches between and isomers, mediated exclusively by visible light under physiological conditions. We demonstrate the selective binding of the elongated conformation, with over 50-fold higher affinity, toward LTR-III G4 (an important HIV-1 sequence), and show that binding and dissociation from the LTR-III G4 can be controlled reversibly by alternate irradiation with low-intensity blue and green light. NMR and MD simulations indicate that the different isomers exhibit very distinct binding modes. While the elongated ligand preferentially binds at the G4/duplex junction of the LTR-III sequence, a DNA motif which is gaining increasing attention as a potential drug target, the bent isomer favors the duplex region.