Addressable functionalization of the nano structure
To demonstrate the usability of the dodecahedron as a scaffolding device we assembled dodeca-hedra employing one to six trisoligonucleotides in which one arm was extended to bear an over-hang sequence. These objects were then exposed to solutions containing one to six complementary 5'-fluorescein-labeled oligonucleotides. Figure 34c shows the native agarose gel of the assembled objects. As expected, fluorescence intensity increases with the number of labels bound to the scaffold while the concomitant decrease of electrophoretic mobility is barely detectable. Similar experiments were carried out with newly developed gold clusters [46] as labels (Figure 34d).
Figure 34 (a) AFM image of the self-assembly product of v1 - v20 showing discrete objects having a size of about 20 nm when adsorbed on mica surface (tapping mode, liquid phase). (b) Cryo-EM measurements of the DNA dodecahedra. Scale bar (light blue): 18 nm. (c) Native agarose gel of the dodecahedral assemblies containing different numbers of overhang sequences hybridized with fluorescein-labeled complementary oligo-nucleotides (F-a'- F-e'), imaged (A) before and (B) after treatment with SYBR gold nucleic acid stain. (d) Native agarose gel of dodecahedral assemblies without (lane 1), with one (v17x, lane 2) and two (v17x and v19x, lane 3) overhang sequences, combined with the respective complementary RUBIgold-labeled oligo-nucleotides (R-c' and R-e'). Lane M: 100bp DNA ladder. (A) The agarose gel was prepared with Gel Star nucleic acid stain (in-gel) and was imaged under UV light after electrophoresis. (B) In order to discriminate gold-labeled from non gold-labeled species, the same agarose gel was treated with diluted acetic acid, then with chloro auric acid and finally with an aqueous hydroxylamine solution (gold staining), resulting in a selective staining of gold-labeled species.