Commercially available CdSe-ZnS Quantum Dots (QDs) have been modified by exchanging the hydrophobic surface ligands with (2-mercaptoethyl)-trimethylammonium chloride. The resulting water soluble conjugate was titrated with solutions of adenosine triphosphate (ATP), adenosine diphosphate, adenosine monophosphate, guanosine triphosphate (GTP), guanosine diphosphate and guanosine monophosphate in 0.01 M 4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid buffer (pH 7.4). A strong fluorescence quench of about 80% was observed for ATP, a quench of 25% was observed for GTP while the others had virtually no effect. The quenching effect of ATP and GTP was attributed to the high negative charge density associated with these substrate's resulting in a strong attraction to the QD surface enabling them to engage in electron transfer with the excited QD. The lack of fluorescence quenching associated with the other nucleotides was most likely due to their reduced charge density resulting in a lower affinity for the QD surface.