Structural DNA nanotechnology is derived from naturally occurring structures and phenomena in cellular biochemistry. Motifs based on branched DNA molecules are linked together by sticky ends to produce objects, periodic arrays, and nanomechanical devices. The motifs include Holliday junction analogues, double and triple crossover molecules, knots, and parallelograms. Polyhedral catenanes, such as a cube or a truncated octahedron, have been assembled from branched junctions. Stiff motifs have been used to produce periodic arrays, containing topographic features visible in atomic force microscopy; these include deliberately striped patterns and cavities whose sizes can be tuned by design. Deliberately knotted molecules have been assembled. Aperiodic arrangements of DNA tiles can be used to produce assemblies corresponding to logical computation. Both DNA structural transitions and branch migration have been used as the basis for the operation of DNA nanomechanical devices. Structural DNA nanotechnology has been used in a number of applications in biochemistry. An RNA knot has been used to establish the existence of RNA topoisomerase activity. The sequence dependence of crossover isomerization and branch migration at symmetric sites has been established through the use of symmetric immobile junctions. DNA parallelogram arrays have been used to determine the interhelical angles for a variety of DNA branched junctions. The relationship between biochemistry and structural DNA nanotechnology continues to grow.
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