I am using reverse micelle method to synthesize silica nanoparticles where in Cy5 -APTES (previously prepared) is covalently linked to the silica network to give fluorescent particles. I want to use Cy5( or alternative for cy5) as a dye. Most of the established protocols use it as well. But I find that Cy5 degrades as soon as I add ammonia in my solution. (the reverse micelle method - triton X 100, hexanol,water, TEOS, NH3 Cy5-APTES ) There is also a paper which describes why this phenomenon happens and apparently, it is because of the hydroxide ions (ammonia+water) which attack the electrophilic sites of the Cy5 dye and disturb the conjugation which results in degradation. The colour of each batch that I synthesized varied from bluish green to light yellow. Attached is the pic of the particles with different batch. Please suggest if using any other alternatives (like atto dyes or alexa dyes might be resistant to this kind of degradation. I have also attached the paper which describes this mechanism.