Improving the signal sensitivity and photostability of DNA hybridizations on microarrays by using dye-doped core-shell silica nanoparticles

The development of new highly sensitive and selective methods for microarray-based analysis is a great challenge because, for many bioassays, the amount of genetic material available for analysis is extremely limited. Currently, imaging and detection of DNA microarrays are based primarily on the use of organic dyes. To overcome the problems of photobleaching and low signal intensities of organic dyes, we developed a new class of silica core-shell nanoparticles that encapsulated with cyanine dyes and applied the dye-doped nanoparticles as labeling in the DNA microarray-based bioanalysis. The developed nanoparticles have core-shell structure containing 15-nm Au colloidal cores with 95 dye-alkanethiol (dT)20 oligomers chemisorbed on the each Au particle surface and 10-15-nm silica coatings bearing thiol functional groups. To be utilized for microarray detection, the dye-doped nanoparticles were conjugated with DNA signaling probes by using heterobifunctional cross-linker. The prepared nanoparticle conjugates are stable in both aqueous electrolytes and organic solvents. Two-color DNA microarray-based detection was demonstrated in this work by using Cy3- and Cy5-doped nanoparticles in sandwich hybridization. The use of the fluorophore-doped nanoparticles in high-throughput microarray detection reveals higher sensitivity with a detection limit of 1 pM for target DNA in sandwich hybridization and greater photostable signals than the direct use of organic fluorophore as labeling. A wide dynamic range of approximately 4 orders of magnitude was also found when the dye-doped nanoparticles were applied in microarray-based DNA bioanalysis. In addition, the use of these dye-doped nanoparticles as the labeling in hybridization also improved the differentiation of single-nucleotide polymorphisms. This work offers promising prospects for applying dye-doped nanoparticles as labeling for gene profiling based on DNA microarray technology.