The fluorescence resonance energy transfer (FRET) from the donor 6,7-dimethoxy-2,4[1H,3H]-quinazolinedione (Q) to the acceptor lumichrome (L) exhibits strong pH dependency and in aqueous solution at pH 9 it is used to sense Hg+2 or Ag+ ions, selectively. QL hybrid forms organic nanoparticles through self-assembly at pH 9 as evident from TEM micrographs. The QL system can sense Hg+2 or Ag+ ion in aqueous medium at pH9 at a nanomolar concentration range using FRET pathway via complexation and nanoparticle formation, respectively. In the QL system, the ions can be easily distinguished with the help of UV-vis spectroscopic study or through the naked eye. We have successfully utilized the above metal ions for the fabrication of NOR and INHIBIT molecular logic gates using FRET of QL system as a signal transducer and Hg+2, Ag+ ion and pH as chemical activators. © 2013 Elsevier B.V. All rights reserved.