Programmable molecular recognition based on the geometry of DNA nanostructures

Fractal assembly of micrometre-scale DNA origami arrays with arbitrary patterns

“…The increasing number of nucleotides makes it difficult to scale up, due to the cost of the strands, the design challenges for controlling the spurious interactions among distinct strands, and the resulting decrease in yield. Using hierarchical approaches, DNA molecules can be annealed in two stages, first self-assembling into smaller structures such as cross-shaped DNA tiles 34 or DNA origami tiles, [11][12][13] and then the individual tiles coming together to form larger structures. In the two-stage approaches, the interior strands can be reused for different tiles, but an increasing number of unique edge strands is still required.…”

Programmable disorder in random DNA tilings

“…S4) were designed with no staple crossovers at the end of each helix row, allowing relaxed edges in which blunt ends are free to adopt normal groove angles and stacking interactions between tiles are encouraged. 1 In contrast, if the edge staples are designed with staple crossovers, the scaffold and staple crossovers will pull the phosphates 180 • away from each other in the blunt ends and result in weakened stacking interactions.…”

“…S4) in every three columns of staples. 1,7 a b Figure S4: Two designs of bridge staples for a square DNA origami tile. a, A "strong-weak" bridge design that uses longer domains on one side of the seams between adjacent triangles and shorter domains on the other.…”

“…As the weakest stacking bond (a T-A and A-T stack) is approximately 10% of the strongest (a G-C and C-G stack), 8 origami tiles with a mix of various stacking bonds between two edges can be misaligned to maximize the binding energy. 1 Sequences of staple strands are listed in Tables S1 and S4. To reduce the binding energy between two edges and increase specificity, we took out 6 edge staples which resulted in a total of 10 stacking bonds when two tiles are perfectly aligned, and a maximum of 6 stacking bonds when they are misaligned. With this tile, arrays of increased sizes on the scale of 1 × 1 μm and with better alignment were self-assembled (Fig.…”

“…Grigory Tikhomirov 1 † , Philip Petersen 2 † and Lulu Qian 1,3 Contents S10 Cadnano diagrams S10.1 Square DNA origami design with strong-weak bridge staples 81 82 82 80 82 80 82 80 82 80 80 8...…”