THE CONSTRUCTION OF A TREFOIL KNOT FROM A DNA BRANCHED JUNCTION MOTIF

A DNA trefoil (31) knot has been constructed from a 104-nucleotide mol ecule whose strands form a 3-arm branched junction motif This construc tion 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 circula r material and of a knot containing more nodes. The key features that differentiate the successful design from the others are (1) the ligati on takes place in the linker region between helical domains and (2) on ly six nucleotide pairs are used for each of the double-helical arms o f the junction. The successful design separates the double-helical reg ions from each other by a spacer containing two deoxythymidine nucleot ides at the site of the branched junction. (C) 1994 John Wiley & Sons, Inc.