The partial exchange of surface passivating trioctylphosphine oxide (TOPO) on CdSe and ZnS coated CdSe (CdSe/ZnS) quantum dots (QDs), with primary amines, was utilized to grow ultra-thin films of these QDs under non-aqueous conditions. This was achieved using 1,12-diaminododecane in a layer-by-layer assembly format, where one of the amino groups binds with the QD surface and the other regenerates the interface for further binding of nanocrystals. The nature of the growth is dependent on the relative surface affinity between the TOPO and primary amine, towards the zinc or cadmium sites on the quantum dots. Using this technique, high quality luminescent films of these quantum dots can be built with well-defined thicknesses. Charge transport characteristics of these films were measured and electroluminescent devices have been fabricated using this methodology as well. These amine-assisted QD assemblies were expanded to polymeric amines and water-soluble poly(allylamine) was utilized to encapsulate bare CdSe QDs that are surface exchanged with 3-amino-1-propanol. The internal structure of the resulting polymer-QD nanoclusters were characterized with the combination of static and dynamic light scattering techniques. Denser internal structures were more efficient in preserving photoluminescent (PL) properties of the quantum dots due to less penetration of water in the vicinity. Initial red-shift exhibited by the polymer-QD nanoclusters were modeled using effective mass approximation and perturbation theory. The CdSe/ZnS QDs were also encapsulated with poly(ethylene glycol) functionalized phospholipids and conjugated to circular plasmid deoxyribonuleic acid (DNA) using peptide nucleic acid - N-suceinimidyl-3-(2-pyridylthio)propionate (PNA-SPDP) linker. Cellular uptake of the fluorescent QD-DNA conjugates were tracked in vitro in CHO-K1 cells using confocal microscopy. Nuclear uptake was also studied using a nuclear staining organic dye, TO-PRO-3.