The effects of replication and transcription on DNA supercoiling. Because DNA is a double-helical structure, strand separation leads to added stress and supercoiling if the DNA is constrained (not free to rotate) ahead of the strand separation. (a) The general effect can be illustrated by twisting two strands of a rubber band about each other to form a double helix. If one end is constrained, separating the two strands at the other end will lead to twisting. (b) In a DNA molecule, the progress of a DNA polymerase or RNA polymerase (as shown) along the DNA involves separation of the strands. Chromosomal DNAs are typically complexed with many proteins that inhibit free rotation. As the polymerase moves on a DNA molecule that is rotationally constrained, the DNA becomes overwound ahead of the enzyme (upstream; positive supercoils) and underwound behind it (downstream; negative supercoils). Red arrows indicate the direction of winding.