Creating complex molecular topologies by configuring DNA four-way junctions

Nat Chem. 2016 Oct;8(10):907-14. doi: 10.1038/nchem.2564. Epub 2016 Jul 4.


The realization of complex topologies at the molecular level represents a grand challenge in chemistry. This necessitates the manipulation of molecular interactions with high precision. Here we show that single-stranded DNA (ssDNA) knots and links can be created by utilizing the inherent topological properties that pertain to the DNA four-way junction, at which the two helical strands form a node and can be configured conveniently and connected for complex topological construction. Using this strategy, we produced series of ssDNA topoisomers with the same sequences. By finely designing the curvature and torsion, double-stranded DNA knots were accessed by hybridizing and ligating the complementary strands with the knotted ssDNA templates. Furthermore, we demonstrate the use of a constructed ssDNA knot both to probe the topological conversion catalysed by DNA topoisomerase and to study the DNA replication under topological constraint.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • DNA / chemistry
  • DNA Replication
  • DNA Topoisomerases, Type I / chemistry
  • DNA, Single-Stranded / chemistry*
  • Nucleic Acid Conformation
  • Nucleic Acid Hybridization


  • DNA, Single-Stranded
  • DNA
  • DNA Topoisomerases, Type I