Long-range communication of Type III restriction enzymes between their cleavage sites based on ATP-triggered 1D diffusion

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Restriction enzymes are the main defence mechanism of bacteria against invading viruses. They recog-nize viral DNA upon the methylation state of their target sequence and destroy it by cleaving it into pieces. Among the known restriction systems, the Type I and III restriction enzymes use both ATP hy-drolysis in order to carry out DNA cleavage. For Type I restriction enzymes it is meanwhile very well es-tablished that they use ATP hydrolysis to actively translocate DNA, i.e. to act as molecular motors. Whereas a similar mode of action is also proposed for Type III systems, DNA translocation has not been demonstrated so far. Based on indirect measurements we have recently proposed an alternative model in which these enzymes use 1D diffusion rather than translocation to randomly scan large distances on DNA. By combining two single-molecule techniques, in particular magnetic tweezers and fluorescence imaging, we now can directly visualize the diffusion of these enzymes on DNA. This enables us to ad-dress major questions about the mechanisms of these enzymes, such as the role of ATP hydrolysis, con-formational changes that trigger the sliding process as well as the direct communication between en-zymes originating from different target site to collectively cut DNA.