DNA looping by FokI: the impact of twisting and bending rigidity on protein-induced looping dynamics

Niels Laurens, David A. Rusling, Christian Pernstich, Ineke Brouwer, Stephen E. Halford, Gijs J. L. Wuite

Research output: Contribution to journalArticlepeer-review


Protein-induced DNA looping is crucial for many genetic processes such as transcription, gene regulation and DNA replication. Here, we use tethered-particle motion to examine the impact of DNA bending and twisting rigidity on loop capture and release, using the restriction endonuclease FokI as a test system. To cleave DNA efficiently, FokI bridges two copies of an asymmetric sequence, invariably aligning the sites in parallel. On account of the fixed alignment, the topology of the DNA loop is set by the orientation of the sites along the DNA. We show that both the separation of the FokI sites and their orientation, altering, respectively, the twisting and the bending of the DNA needed to juxtapose the sites, have profound effects on the dynamics of the looping interaction. Surprisingly, the presence of a nick within the loop does not affect the observed rigidity of the DNA. In contrast, the introduction of a 4-nt gap fully relaxes all of the torque present in the system but does not necessarily enhance loop stability. FokI therefore employs torque to stabilise its DNA-looping interaction by acting as a 'torsional' catch bond.

Original languageEnglish
Pages (from-to)4988-4997
Number of pages10
JournalNucleic Acids Research
Issue number11
Early online date28 Feb 2012
Publication statusPublished - 1 Jun 2012


  • DNA/chemistry
  • DNA Cleavage
  • Deoxyribonucleases, Type II Site-Specific/chemistry
  • Motion
  • Nucleic Acid Conformation
  • Protein Conformation
  • Torque


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