A bio-hybrid rotaxane catalyst

In processive catalysis, a catalyst binds to a substrate and remains bound while performing 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. We used this DNA-binding clamp to construct a bio-hybrid rotaxane catalyst. To this end, the clamp was conjugated to a chemical catalyst with sequence-specific oxidation behaviour. The resulting catalytic clamp could be loaded onto a DNA plasmid, and its catalytic activity was visualised using an AFM-based method that detects and spatially locates oxidised sites in DNA. It was found that both the catalytic processivity and the sliding direction of the rotaxane catalyst can be influenced by varying experimental conditions. Toroidal processive enzymes, i.e. enzymes that are able to thread onto biopolymers and to perform stepwise reactions along the polymer chain, are among the most fascinating tools involved in the clockwork machinery of life. Processive catalysis is ubiquitous in Nature and contrasts the nontemplated distributive catalysis, which is the most common mode of operation for both