The construction of a trefoil knot from a DNA branched junction motif

A DNA trefoil (3(1)) knot has been constructed from a 104-nucleotide molecule whose strands form a 3-arm branched junction motif. This construction tests the notion that a node in a DNA knot can be equated with a half-turn of double-helical DNA, and is consistent with that concept. Of five 104-mer sequences tested, only one produces high yields of the target knot. The other molecules produce larger quantities of circular material and of a knot containing more nodes. The key features that differentiate the successful design from the others are (1) the ligation takes place in the linker region between helical domains and (2) only six nucleotide pairs are used for each of the double-helical arms of the junction. The successful design separates the double-helical regions from each other by a spacer containing two deoxythymidine nucleotides at the site of the branched junction.