title: A clamp-like biohybrid catalyst for DNA oxidation.
abstract: In processive catalysis, a catalyst binds to a substrate and remains bound as it performs several consecutive reactions, as exemplified by DNA polymerases. Processivity is essential in nature and is often mediated by a clamp-like structure that physically tethers the catalyst to its (polymeric) template. In the case of the bacteriophage T4 replisome, a dedicated clamp protein acts as a processivity mediator by encircling DNA and subsequently recruiting its polymerase. Here we use this DNA-binding protein to construct a biohybrid catalyst. Conjugation of the clamp protein to a chemical catalyst with sequence-specific oxidation behaviour formed a catalytic clamp that can be loaded onto a DNA plasmid. The catalytic activity of the biohybrid catalyst was visualized using a procedure based on an atomic force microscopy method that detects and spatially locates oxidized sites in DNA. Varying the experimental conditions enabled switching between processive and distributive catalysis and influencing the sliding direction of this rotaxane-like catalyst.
authors.affiliation: 1] Institute for Molecules and Materials, Radboud University Nijmegen, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands [2].
authors.forename: Stijn F M
authors.initials: SF
authors.lastname: van Dongen
authors.forename: Joost
authors.initials: J
authors.lastname: Clerx
authors.forename: Kasper
authors.initials: K
authors.lastname: Nørgaard
authors.forename: Tom G
authors.initials: TG
authors.lastname: Bloemberg
authors.forename: Jeroen J L M
authors.initials: JJ
authors.lastname: Cornelissen
authors.forename: Michael A
authors.initials: MA
authors.lastname: Trakselis
authors.forename: Scott W
authors.initials: SW
authors.lastname: Nelson
authors.forename: Stephen J
authors.initials: SJ
authors.lastname: Benkovic
authors.forename: Alan E
authors.initials: AE
authors.lastname: Rowan
authors.forename: Roeland J M
authors.initials: RJ
authors.lastname: Nolte
mesh_terms: D001483:Base Sequence; D002384:Catalysis; D056831:Coordination Complexes / Q000737:chemistry*; D004247:DNA / Q000737:chemistry*; D004249:DNA Damage; D018625:Microscopy, Atomic Force; D008958:Models, Molecular; D009842:Oligopeptides / Q000737:chemistry*; D010084:Oxidation-Reduction
chemical_list: D056831:Coordination Complexes; D009842:Oligopeptides; D004247:DNA