Figure 1.

DNA-nanotubes design.

a, Schematic illustration of six-helix bundle DNA-nanotube folding. In red, single-stranded M13-based vector p7308 “scaffold”. In grey, single-stranded “staple” oligonucleotides of length 42 bases, programmed with complementarity of the scaffold. Right, scaffold-plus-staples schematic view of the six-helix bundle DNA-nanotube folded and cross-sectional view of the DNA-nanotube. b, 3D cartoon view of 800 nm-long six-helix bundle heterodimer, (not-to-scale). Left, six-helix bundle front monomer with core module in grey, capped head module in blue and connector tail module for heterodimerization in orange. Right, six-helix bundle rear monomer with core module in grey, connector head module for heterodimerization in orange and capped tail module in green. c, Scaffold-plus-staples schematic view of the heterodimer junction of front and rear monomer. One strand of each double helix is contributed by the scaffold shown in blue, and the other strand is contributed by a staple. Base pairs are depicted as short vertical lines. Helices 1–6 are labeled on the left. In the orientation displayed, the outside surface of the nanotube is facing the viewer. (i) Front monomer head module. Three staple strands serve to cap the front monomer head (shown in cyan). (ii, v) Core module. There are 28 repeats of 42 bp modules for each monomer. A scaffold crossover connecting helix 2 to 3 occurs in the fifteenth repeat and one connecting helix 4 to 5 occurs in the fourteenth repeat (not shown). (iii) Front monomer tail module. Three staple strands with a total of 26 unpaired bases decorate the tail. The scaffold strand is unpaired for 36 bases. (iv) Rear monomer head module. Three staple strands with a total of 36 unpaired bases decorate the head. These unpaired regions are complementary to the corresponding 36 unpaired bases of the front monomer tail scaffold strand. The 26 unpaired bases in the rear monomer head scaffold strand are complementary to the 26 unpaired bases of the three staple strands that decorate the front monomer tail. In the DNA-nanotube heterodimer, these unpaired regions match up to form the complete intermonomer junction. (vi) Rear monomer tail module. Four staple strands serve to cap the rear monomer tail (shown in green).