The goal of this work was to produce water-soluble fluorescent semiconductor nanocrystals suitable to interact specifically with biomolecules and thereby creating hybrid supramolecular structures composed of nanocrystals and proteins. Hydrophobic TOPO-coated cadmium selenide (CdSe) nanocrystals (NCs) were synthesized using published protocols (TOP/TOPO method). The challenge was to find a novel procedure to solubilize and functionalize the NCs in water for further specific interactions with biomolecules. We therefore coated the NCs with a lipid mono-layer (lipid-NCs) in a one-step process. The lipid monolayer made the NCs water soluble and simultaneously allowed to decorate the NCs surface with different functional groups. The resulting lipid-NCs are functionalized, fluorescent and stable; they can thus be used for further interaction with biomolecules. The ability of the functionalized lipid-NCs to bind specifically to biomolecules was demonstrated for His6-NCs, biotin-NCs and NTA-NCs (hexahistidine, biotin and nitrilotriacetic acid NCs) using fluorescence resonance energy transfer (FRET). Multifunctional NCs were also produced by decorating the NCs with biotin and NTA simultaneously; these NCs showed specific interactions toward to the complementary partner molecules. The properties of the lipid monolayer coat on the NCs surface were characterized by investigating its interaction with the peripheral membrane protein cytochrome c. This protein bound to the lipid-NCs only in the presence of negatively charged lipids, very similarly as in the case of lipid vesicles and mitochondrial membranes. The functionalized-NCs could also be immobilized on micro-patterned surfaces for creation of a photostable, fluorescent patterned surface for biosensor applications. We could observe via FRET the specific binding of a fluorescent protein on the NCs patterns.