The design of single-stranded nucleic acid knots

Nadrian C. Seeman

Research output: Contribution to journalArticlepeer-review


A general strategy is described for the synthesis of single-stranded nucleic acid knots. Control of nucleic acid sequence is used to direct the formation of secondary structures that produce the target topology. The key feature of the strategy is the equation of a half-turn of double helical DNA or RNA with a node in a knot. By forming nodes from complementary DNA sequences, it appears possible to direct the assembly of any simple knot. Stabilization of individual nodes may be achieved by constructing them from long regions containing both B-DNA and Z-DNA. Control over the braiding of DNA that acts as a link between node-forming domains can be realized by condensing the nodes into well-defined DNA structures, such as extended domains of linear duplex, branched junctions, antijunctions or mesojunctions. Further topological control may be derived from the pairing of linker regions to complementary single-stranded molecules, thereby preventing them from braiding in an undesirable fashion.

Original languageEnglish (US)
Pages (from-to)297-307
Number of pages11
JournalMolecular Engineering
Issue number3
StatePublished - Sep 1992


  • DNA
  • DNA branched junction
  • Knots
  • RNA
  • Z-DNA
  • braiding
  • design
  • ligation
  • nodes
  • topological protection

ASJC Scopus subject areas

  • Biochemistry


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