title: DNA looping by FokI: the impact of twisting and bending rigidity on protein-induced looping dynamics.
abstract: 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.
authors.affiliation: Department of Physics and Astronomy, VU University, De Boelelaan 1081, 1081 HV Amsterdam, The Netherlands.
authors.forename: Niels
authors.initials: N
authors.lastname: Laurens
authors.forename: David A
authors.initials: DA
authors.lastname: Rusling
authors.forename: Christian
authors.initials: C
authors.lastname: Pernstich
authors.forename: Ineke
authors.initials: I
authors.lastname: Brouwer
authors.forename: Stephen E
authors.initials: SE
authors.lastname: Halford
authors.forename: Gijs J L
authors.initials: GJ
authors.lastname: Wuite
mesh_terms: D004247:DNA / Q000737:chemistry* / Q000378:metabolism; D053837:DNA Cleavage; D015252:Deoxyribonucleases, Type II Site-Specific / Q000737:chemistry / Q000378:metabolism*; D009038:Motion; D009690:Nucleic Acid Conformation; D011487:Protein Conformation; D019415:Torque
chemical_list: D004247:DNA; C035042:endodeoxyribonuclease FokI; D015252:Deoxyribonucleases, Type II Site-Specific