Tight single-stranded DNA knots.

Trefoil (3(1)) and figure-8 (4(1)) knots have been synthesized from DNA molecules containing two single-turn helical domains, linked by four oligodeoxythymidine linkers. Both topologies are derived from the same DNA molecule. The tightest knots are fashioned by minimizing the lengths of the linkers. The shortest equal-length linkers from which a trefoil knot can be made readily are seven nucleotides long, in a 74-nucleotide molecule, whereas those in the shortest figure-8 knot are six nucleotides long, in a 70-nucleotide molecule. In addition to these limiting knots, other knots containing 80, 88, 96 and 104 nucleotides have been constructed. The mobilities of these molecules on denaturing gels show the conventional logarithmic dependence on length. Ferguson analysis of their mobilities indicates a linear dependence of surface area on length. The 80-mer trefoil knot is the tightest molecule that can be restricted in both domains.