Synthesis of a DNA Knot Containing Both Positive and Negative Nodes

Shou Ming Du, Nadrian C. Seeman

Research output: Contribution to journalArticlepeer-review


A figure-eight (41) knot, containing two positive and two negative nodes, has been synthesized by ligating a single-stranded DNA molecule into a closed cycle. The molecule consists of two single-turn double-helical domains connected by four dT14 or dT15 linkers. One of the domains contains the sequence (dCpdGp)6, which is capable of forming left-handed Z-DNA. Ligation yields a trefoil (31) knot or a 41 knot, depending upon the conditions in solution. A 41 knot results if Co(NH3)63+ is present in the solution to promote the formation of Z-DNA; a 31 knot is the product in the absence of Co(NH3)63+. Both domains of the 31 knot are susceptible to restriction endonuclease digestion, but only the domain of the 41 knot expected to be right-handed can be digested by a restriction endonuclease. The 41 knot has both a higher gel-electrophoretic mobility at low polyacrylamide concentrations and a higher friction constant than the 31 knot, when analyzed by Ferguson plots under denaturing conditions.

Original languageEnglish (US)
Pages (from-to)9652-9655
Number of pages4
JournalJournal of the American Chemical Society
Issue number24
StatePublished - Nov 1 1992

ASJC Scopus subject areas

  • Catalysis
  • General Chemistry
  • Biochemistry
  • Colloid and Surface Chemistry


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