TIGHT SINGLE-STRANDED-DNA KNOTS

Trefoil (3(1)) and figure-8 (4(1)) knots have been synthesized from DN A molecules containing two single-turn helical domains, linked by four oligodeoxythymidine linkers. Both topologies are derived from the sam e DNA molecule. The tightest knots are fashioned by minimizing the len gths of the linkers. The shortest equal-length linkers from which a tr efoil knot can be made readily are seven nucleotides long, in a 74-nuc leotide molecule, whereas those in the shortest figure-8 knot are six nucleotides long- in a 70-nucleotide molecule. In addition to these li miting knots, other knots containing 80, 88,96 and 104 nucleotides hav e been constructed. The mobilities of these molecules on denaturing ge ls show the conventional logarithmic dependence on length. Ferguson an alysis of their mobilities indicates a linear dependence of surface ar ea on length. The 80-mer trefoil knot is the tightest molecule that ca n be restricted in both domains.