Provided are compositions comprising water-soluble, functionalized nanocrystals. The water-soluble functionalized nanocrystals comprise quantum dots capped with a layer of a capping compound, and further comprise, by operably linking and in a successive manner, one or more additional compounds. The one or more additional compounds is comprised of at least a diaminocarboxylic acid which is operatively linked to the capping compound, and may further comprise an amino acid, an affinity ligand, or a combination thereof. Also provided are methods of using the functionalized nanocrystals having an affinity ligand to detect the presence or absence of a target substrate in a sample. The method comprises contacting the functionalized nanocrystals with the sample so that complexes are formed between the functionalized nanocrystals and substrate, if the substrate is present; exposing the complexes in the detection system to a wavelength of light suitable for exciting the functionalized nanocrystals of the complexes to emit a luminescence peak; and detecting the emitted luminescence peak.