Abstract
We study DNA target search by type II restriction endonucleases. In our single molecule technique, micron sized beads tethered with single DNAs are imaged using video microscopy. Under diffusion limited conditions, release of individual beads due to cleavage identifies the instant a single protein acquires its DNA target. In our experiments, we study NdeI, an endonuclease that is found in Neisseria denitrificans. In vivo, many other proteins bound on the DNA act as ‘roadblocks’ and prevent DNA binding proteins from sliding on the DNA during target search.
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