1) They’re usually too big (~30 nm) and thus may not be able to fit in very small morphological regions such as the synaptic cleft, which are usually about 20 nm wide. One possible way to deal with this is to make the QD smaller! This may be possible to do if researchers switch from CdSe to InP as the crystal core. It is a common mistake to assume that QD’s are smaller than conventional fluorescent dyes–they are in fact 10 to 20 times larger than fluorescein isothiocyanate fluorophores.
2) Since QD’s blink, it can be difficult to track multiple molecules bound to them in a given region as they might cross over undetected. Thus sophisticated algorithms must distinguish between various QD’s. However, it is possible for each QD to emit a different fluorescent wavelength if their sizes are varied slightly, due to variations in the effects of quantum confinement. Note also that the material of the outer surface plays a large role in determining the fluorescence emitted by the same crystal core, which could possibly also be exploited to yield more variation in QD emissions.
3) The QD’s often affect the ligand characteristics of the bound antibody. If one is hoping to detect the function of some protein in typical cellular processes it will be difficult to do so if the QD-bound molecule has different activity–for example, less preferential binding to another protein–than non-QD-bound endogenous molecules. The possibility of this needs to be carefully quantified before an experimental design assumes that it is not the case.
Despite these problems, there are some ways that QD’s could be used in vivo to detect action potentials. If they were bound to synaptically-important proteins in multiple adjacent neurons, it might be possible to track the spike trains of each neuron and how they interact after exposure to various chemical manipulations. One of the most important benefits of QD’s to this type of design is their high photostability and long lifetime in the aqueous solution of cells.
Alcor D, et al. 2009 Single-particle tracking methods for the study of membrane receptors dynamics. doi: 10.1111/j.1460-9568.2009.06927.
Cao YW, et al. 1999 Synthesis and Characterization of InAs/InP and InAs/CdSe Core/Shell Nanocrystals. Abstract.
Pathak, et al. 2009 Quantum Dot Labeling and Imaging of Glial Fibrillary Acidic Protein Intermediate Filaments and Gliosis in the Rat Neural Retina and Dissociated Astrocytes. doi:10.1166/jnn.2009.GR08