Abstract
3DNA dendrimers are uniform three-dimensional DNA structures commercially available from Genisphere, Hatfield, PA. The base unit is made by two strands of DNA that are complementary only in the central region, while the four end regions can be annealed with other base units of different sequences. Thus, dendrimers can grow in layers with finite control. At two layers, the dendrimer has 36 free arms which are available for attaching multiple labels of interest. In our study, eight arm extensions were incorporated into the dendrimer. Each of these arms is capable of annealing to three independent short oligomers labeled with a fluorophore. Using fluorescence correlation spectroscopy, we monitor changes of the dendrimer brightness and calculate the number of the labeled oligonucleotides incorporated into the dendrimers in a titration experiment. We confirmed that the incorporation of the labeled oligomers into the dendrimer is close to the expected value and the fluorescence of the labeled nucleotides is not quenched. Single molecule images of the dendrimers show high homogeneity and multiple bleaching steps. Therefore, 3DNA dendrimers can serve as good scaffolds for advanced fluorescence imaging.
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