SYNTHETIC DNA KNOTS AND CATENANES

The double helical structure of DNA can be used as the basis for the s ynthesis of specific single-stranded catenanes and knots. It is possib le to construct DNA stick figures, such as a cube, from branched DNA c omponents. The edges of these molecules are double helical DNA, and th e individual strands combine to form complex DNA catenanes. The sequen ces of these molecules are selected by minimizing the sequence symmetr y of the component strands, and they are ligated together by technique s used routinely in biotechnology. Precise catenation is controlled by the use of topological protecting groups, to prevent braiding that is not wanted in the target molecule. Solid-support based assembly techn iques have been developed to facilitate the construction of these obje cts. DNA molecules containing double crossovers form another route to the construction of DNA catenanes. DNA knots can be designed readily, because it is possible to equate a half-turn of double helical DNA wit h a node in a knot. Right-handed B-DNA and left-handed Z-DNA can be us ed to generate nodes of opposite signs. Greater control on the synthes is of DNA knots can be obtained by condensing the individual nodes int o larger structures, such as extended pieces of linear double stranded DNA or branched junctions. Trefoil and figure-8 DNA knots have been c onstructed from the same synthetic DNA molecule, containing two helica l domains. The techniques of DNA catenane synthesis appear to be appli cable to knot synthesis.