To completely separate the DNA strands, the DNA must be unwound. Eukaryotic DNA is linear and naturally unwinds itself as its strands separate. Since the prokaryotic DNA is circular and the strands aren’t free to rotate about each other, they twist as they unwind. The strands are forced to coil tighter and tighter until the entire circular DNA begins to twist around itself. This process is called supercoiling. The figure at left shows a practical example of supercoiling.

If supercoiling isn't alleviated, pressure can build up in front of the replication fork (the exact point where the strands separate) until the helicase can longer move forward. Prevention of supercoil build-up is the job of another DNA binding protein; topoisomerase. The topoisomerase binds to both strands of the dsDNA at a point in front of the helicase. The topoisomerase then nicks or breaks one of the strands and swivels it around to release the built-up strain. Afterward, the topoisomerase repairs the broken strand and the helicase can freely move forward again. See Topoisomerase web term paper

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