CdSe semiconductor nonocrystal quantum dots are assembled into nanowire-like arrays employing microtubule fibers is nanoscale molecular "scaffolds" Spectrally and time-resolved energy-transfer analysis is used to assess the assembly of the nanoparticles into the hybrid, Inorganic biomolecular structure. Specifically, we demonstrate that a comprehensive study of energy transfer between quantum dot pairs on the biotemplate and alternatively, between quantum dots and molecular dyes embedded In the microtubule scaffold comprises a powerful spectroscopic tool for evaluating the assembly,process, In addition to revealing the extent to which assembly has occurred, the approach allows determination of particle-to-particle (and particle-to-dye) distances within the biomediated array Significantly the characterization is realized in situ, without need for further sample workup or risk of disturbing the solution phase constructs. Furthermore, we find that the assemblies prepared in-this way exhibit efficient quantum dot quantum dot and quantum dot dye energy transfer that affords faster energy-transfer rates compared to densely packed quantum dot arrays on planar, substrates and to small-molecule-mediated quantum dot dye couples, respectively.