Blue shift of CdSe/ZnS nanocrystal-labels upon DNA-hybridization

Fluorescence is a widely used tool in biology to study the complexity and dynamics of biological processes. Compared to conventional organic dye molecules, fluorescent semiconductor nanocrystals (QDs) have several promising advantages. They can be excited by a broad range of wavelengths from UV up to their individual absorption edge, and they have narrow, tuneable emission spectra, which can be well resolved over the same spectral range. Moreover, in contrast to most organic fluorophores they are highly resistant to chemical and metabolic degradation and have a higher photobleaching threshold [1-5]. The challenges for using QDs in biological studies include designing hydrophilic QDs with surface chemistry well adapted to different biological applications. Surface modified QDs should be luminescent with optical properties not differing from the unmodified QDs [6-10].Here we report the preparation of water-soluble CdSe/ZnS QDs, which have been surface modified for versatile and selective coupling of biological probes and subsequent specific labeling of cells. Because of the wide emission range, narrow spectral linewidth, brightness, and the adjustable, size dependent emission wavelengths of these QDs, they are expected to be a good choice for multiplex-imaging. Theoretically our CdSe/ZnS QDs should allow labeling of several different probes and imaging of up to eight different biological molecules in the visible range of the spectrum [11,12]. We demonstrate that synthetic oligonucleotides can be efficiently covalently linked to these QDs. We further show that they can be used for subsequent analysis of expressed genes by in situ hybridisation experiments. The technique was successfully applied to detect transcripts in the plant Arabidopsis thaliana, a fully sequenced model organism [13].CdSe/ZnS core/shell QDs were prepared according to a method published previously [14]. Briefly, cadmium stearate and trioctylphosohine-selenid (TOP-Se) were reacted at temperatures abo