title: Type III restriction enzymes communicate in 1D without looping between their target sites.
abstract: To cleave DNA, Type III restriction enzymes must communicate the relative orientation of two asymmetric recognition sites over hundreds of base pairs. The basis of this long-distance communication, for which ATP hydrolysis by their helicase domains is required, is poorly understood. Several conflicting DNA-looping mechanisms have been proposed, driven either by active DNA translocation or passive 3D diffusion. Using single-molecule DNA stretching in combination with bulk-solution assays, we provide evidence that looping is both highly unlikely and unnecessary, and that communication is strictly confined to a 1D route. Integrating our results with previous data, a simple communication scheme is concluded based on 1D diffusion along DNA.
authors.affiliation: BIOTEChnology Center Dresden, Dresden University of Technology, 01062 Dresden, Germany.
authors.forename: Subramanian P
authors.initials: SP
authors.lastname: Ramanathan
authors.forename: Kara
authors.initials: K
authors.lastname: van Aelst
authors.forename: Alice
authors.initials: A
authors.lastname: Sears
authors.forename: Luke J
authors.initials: LJ
authors.lastname: Peakman
authors.forename: Fiona M
authors.initials: FM
authors.lastname: Diffin
authors.forename: Mark D
authors.initials: MD
authors.lastname: Szczelkun
authors.forename: Ralf
authors.initials: R
authors.lastname: Seidel
mesh_terms: D001665:Binding Sites; D004247:DNA / Q000737:chemistry / Q000378:metabolism*; D015263:Deoxyribonucleases, Type III Site-Specific / Q000378:metabolism*; D004058:Diffusion; D006868:Hydrolysis; D008956:Models, Chemical; D009690:Nucleic Acid Conformation; D052898:Optical Tweezers; D013379:Substrate Specificity
chemical_list: D004247:DNA; D015263:Deoxyribonucleases, Type III Site-Specific