Structural DNA nanotechnology design and self-assembly of two-dimensional and three-dimensional crystalline lattices

Structural DNA nanotechnology aims at the design, construction, and characterization of objects, lattices and devices at the nanometer scale from branched DNA motifs. I have characterized three paranemic crossover DNA molecules: PX 9:5 with 5 and 7 unit tangles in length, and T-PX with three duplex domains. My preliminary results indicate that the inner crossovers in PX 9:5 molecules fit our model well but the outer ones do not fit out model and that six crossovers have been shown to exist in T-PX molecules.; One of the key goals in structural DNA nanotechnology is to build highly-ordered structures self-assembled from individual DNA motifs. The most successful examples of self-assembly are the programmable 2D periodic lattices. I successfully self-assemble two novel DNA motifs, six-helix bundles (6HB) and nine-helix bundles (9HB), into 2D periodic lattices using double cohesion, which is an effective tool to assembly large motifs into lattices. These two motifs are inherently 3D because they contain three vectors that span 3-space. I also self-assemble an eight-helix bundle, an intermediate design between 6HB and 9HB, into 2D periodic lattices.; The deepest challenge in structural DNA nanotechnology is to extend the system of self-assembly from 2D to 3D. A number of designs have been tried to obtain 3D crystalline lattices (crystals): TX in three different systems, 6HB, and 9HB. Double cohesion is used for construction of 3D lattices from 6HB and 9HB. Crystals from 9HB diffract X-rays to 10 A. The unit cell dimensions obtained from X-ray diffraction are not consistent with my design except for the long axis. Nevertheless, the results of 9HB confirm the formation of partially ordered 3D crystalline lattices.; Trouble shooting in 3D crystals is nearly impossible unless they diffract X-rays to 3-4 A resolution. However we can troubleshoot errors in 2D lattices. Errors found in 2D lattices provide instruction for the future design of individual motifs used to construct of 3D crystalline lattices.