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J. Biol. Chem., Vol. 260, Issue 9, 5720-5728, 05, 1985

The DNA restriction endonuclease of Escherichia coli B. I. Studies of the DNA translocation and the ATPase activities

B Endlich and S Linn

Electron microscopic examination of DNA intermediates formed by the restriction endonuclease of Escherichia coli B revealed supercoiled loops that are presumably formed during an ATP-dependent DNA translocation process in which the enzyme remains bound to the recognition site while tracking along the DNA helix to a cleavage site. The rate of DNA translocation during this process is at least 5000 base pairs/min at 37 degrees C. Even after all cleavages have been completed, complexes are seen that contain terminal loops or loop plus tail structures. During this later phase of the reaction, ATP is hydrolyzed at a rate which is dependent upon the size of the largest possible loop (or loop plus tail); this ATP hydrolysis can be terminated by one double-strand cleavage within the loop region between the recognition site and the terminus. To explain these results, it is hypothesized that after cleavage the enzyme cycles between a tracking (and possibly back-tracking) mode which is fueled by ATP hydrolysis and a relatively long static period in which ATP hydrolysis does not occur. While tracking, the enzyme would be bound both to the recognition site and to a distal site but, while static, the enzyme would be bound only at the recognition site of nonlooped molecules. This post-nuclease phase of the reaction is hypothesized to reflect a reaction whereby the enzyme initially scans DNA molecules before making a strand cleavage.
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