Multiple crossover molecules in DNA nanotechnology

The goals of DNA nanotechnology include the construction of nanoscale objects and devices from DNA, as well as the self-assembly of periodic arrays; DNA nanotechnology would benefit from a greater diversity of DNA motifs, particularly those based on branched molecules. In the first part of this thesis, I report the construction, analysis, ligation and self-assembly of DNA triple crossover complexes. A triple crossover molecule (TX) consists of four oligonucleotides hybridized to form three double-stranded DNA helices lying in a plane and linked by strand exchange at four immobile crossover points. The complexes were analyzed by nondenaturing gel electrophoresis and heat-induced unfolding. Ferguson analysis and hydroxyl radical autofootprinting provide strong evidence for the assembly of the strands to the targeted TX structure. Ligation of reporter strands has been demonstrated with this motif, as well as the self-assembly of hydrogen-bonded two-dimensional crystals in two different arrangements.; In the second part of this thesis, a robust sequence-dependent rotary DNA device is described. Sequence-dependent devices can produce a large variety of states, because each device can be controlled individually. This device is based on a new DNA topological motif, paranemic crossover (PX) DNA, and its conversion to a related motif (JX₂ DNA) in which one end is rotated relative to the other end by 180°. The device operating in a four-step cycle is demonstrated by atomic force microscopy (AFM).; DNA nanotechnology and some of the approaches to DNA-based computing are dependent on unusual motifs of DNA. Sticky-ended association has been used extensively to direct the assembly of the unusual DNA motifs to useful objects and arrays. In the third part of the thesis, I report the use of edge-sharing to design and construct unusual motifs from DNA triangles by lashing DNA triangles together with DNA double crossover molecules. The constructions of the edge-shared two-triangle and three-triangle motifs are demonstrated by analyzing the ligated products with restriction enzymes. One-dimensional DNA arrays have been obtained using the edge-shared two-triangle motif and are demonstrated by AFM.