Topology, motion, and periodic lattices in DNA nanotechnology

Working at the nanometer scale is very attractive: not only because of its promise in future technology, also because of our curiosity. DNA, the molecule that the Nature has chosen for storing genetic information, is particularly suited for this purpose. Branched motifs of DNA constitute a system for the tractable assembly of objects, links and arrays on the nanometer scale. This strategy has been extended in three aspects in this dissertation. First is the synthesis of Borromean rings, in which, although linked together, removal of any individual circle unlinks the remaining rings. Molecules with the Borromean property present a formidable synthetic task, because their assembly entails placing nodes with equal numbers of positive and negative signs specifically about a link. The half-turn of double helical DNA provides nodes for topological construction, whose signs can be imposed by choosing B-DNA (negative) or Z-DNA (positive). Besides static species, it is desirable to assemble nanomechanical devices from the same material. This is the second part of the work. The simplest device is a rigid object that responds to an external stimulus by changing structure in a predictable fashion. A molecular device was constructed that consists of two rigid DNA double crossover (DX) molecules connected by 4.5 double helical turns. Twenty nucleotide pairs of this helix can be converted to Z-DNA. In conditions that promote B-DNA, the two unconnected domains of the DX molecules lie on the same side of the central helix; however, in Z-promoting conditions, the unconnected domains lie on opposite sides of the central helix. This relative repositioning is detected by fluorescence resonance energy transfer (FRET), because the separation of two dyes attached to the device changes as a consequence of the transition. In the last part, a two-dimensional DNA crystal has been designed and constructed from Holliday junction analogs that are not inherently rigid. Wishing less flexibility, four junctions have been fused into a rhombus-like molecule. The rhombuses can be directed to self-assemble by hydrogen bonding into a 1- or 2-dimensional periodic array. The expected spacing is seen when the array is observed by atomic force microscopy (AFM).