Build-to-order nanostructures using DNA self-assembly

We aimed at the establishment of methodology that allows construction of freely designable nanostructures made with the DNA double strand, to serve scaffolds of diverse applications. An essential step in utilizing the capability of DNA to self-assemble is the selection of each oligonucleotide sequence, which determines the self-assembly of nanostructures. We have originally developed an algorithm to choose such unique sequences, which consists of two modules. In the first module, GUSP (Generation of Unique Segment Pairs), we select a set of (n, r) unique segment pairs, which is defined as the segment set that satisfies the following conditions: (1) each segment length is n nucleotides, (2) all intended pairs of segments are in perfect match, and (3) the aberrant contiguous matching between any other segments is r bases less than the maximum. In the second module, ELIS (Evaluation of Linked Segments), the best assignment of segment pairs to the designed structure is searched. The assignment is done by looking for the lowest Tm of aberrant contiguous matching. We experimentally confirmed the feasibility of our approach by annealing oligonucleotides designed by the algorithm described above, and observing the self-assembled structures by AFM imaging and agarose gel electrophoresis. By connecting a Y-structure in the specific position of a trimeric hexagon, we showed the addressability in a DNA nanostructure. And we constructed tetrahedron and octahedron as examples of triangle-based nanostructures.