Tight Single-Stranded DNA Knots

Abstract

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.

Synthesising topological links

“…These scaffold arrays may be used to organize guests for X-ray diffraction analysis [24], much as Fujita and his colleagues have done with MOFs [25]. Crystallization of topological targets is particularly chancy, unless they are as tight as possible, a tedious experimental determination [26]. The targets made from double helical DNA are likely to be much tighter than those made from single-strands.…”

Characterization of Novel Functions and Topologies in RNA

“…Yet on a 15% gel, both knRNAs migrate faster than that same 197-mer RNA. This variable mobility is a hallmark of nucleic acids with a higher order topology such as a branch, a lariat, a circle or a covalentlyclosed knot (Coppins & Silverman 2004;Wasserman et al 1985;Wang et al 1993;Wang et al 1996;Vogel et al 1997). To illustrate how extreme the gel mobility shifts can be as a consequence of these higher order topologies, we have included a circular 98-mer (generated by intramolecular ligation of the linear transcript) on the gels in Figure 15.…”

RNA pseudoknots

“…Knotting has also been described for chemically synthesized, single-stranded DNA molecules ( [9], and references therein). The basepairing schemes in these circular molecules of 70, or more, nucleotides are reminiscent of RNA pseudoknots.…”