title: Type III restriction enzymes cleave DNA by long-range interaction between sites in both head-to-head and tail-to-tail inverted repeat.
abstract: Cleavage of viral DNA by the bacterial Type III Restriction-Modification enzymes requires the ATP-dependent long-range communication between a distant pair of DNA recognition sequences. The classical view is that Type III endonuclease activity is only activated by a pair of asymmetric sites in a specific head-to-head inverted repeat. Based on this assumption and due to the presence of helicase domains in Type III enzymes, various motor-driven DNA translocation models for communication have been suggested. Using both single-molecule and ensemble assays we demonstrate that Type III enzymes can also cleave DNA with sites in tail-to-tail repeat with high efficiency. The ability to distinguish both inverted repeat substrates from direct repeat substrates in a manner independent of DNA topology or accessory proteins can only be reconciled with an alternative sliding mode of communication.
authors.affiliation: DNA-Protein Interactions Unit, Department of Biochemistry, School of Medical Sciences, University of Bristol, Bristol, BS8 1TD, United Kingdom.
authors.forename: Kara
authors.initials: K
authors.lastname: van Aelst
authors.forename: Júlia
authors.initials: J
authors.lastname: Tóth
authors.forename: Subramanian P
authors.initials: SP
authors.lastname: Ramanathan
authors.forename: Friedrich W
authors.initials: FW
authors.lastname: Schwarz
authors.forename: Ralf
authors.initials: R
authors.lastname: Seidel
authors.forename: Mark D
authors.initials: MD
authors.lastname: Szczelkun
mesh_terms: D001665:Binding Sites / Q000235:genetics / Q000502:physiology; D004279:DNA, Viral / Q000378:metabolism*; D015263:Deoxyribonucleases, Type III Site-Specific / Q000378:metabolism*; D055029:Inverted Repeat Sequences; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D009841:Oligonucleotides; D013379:Substrate Specificity
chemical_list: D004279:DNA, Viral; D009841:Oligonucleotides; D015263:Deoxyribonucleases, Type III Site-Specific