One type of DNA tertiary structure is supercoiling, which takes place when the DNA helix is subjected to strain by being overwound or underwound. B-DNA is in its lowest-energy state when it has approximately 10 bp per turn of its helix. In this relaxed state, a stretch of 100 bp of DNA would assume about 10 complete turns (Figure 8.16a). If energy is used to add or remove any turns, strain is placed on the molecule, causing the helix to supercoil, or twist on itself. Molecules that are overrotated exhibit positive supercoiling (Figure 8.16b). Underrotated molecules exhibit negative supercoiling (Figure 8.16c). Supercoiling is a partial solution to the cell’s DNA packing problem because supercoiled DNA occupies less space than relaxed DNA.

Supercoiling takes place when the strain of overrotating or underrotating cannot be compensated by the turning of the ends of the double helix, which is the case if the DNA is circular—that is, there are no free ends. If the chains can turn freely, their ends will simply turn as extra rotations are added or removed, and the molecule will spontaneously revert to the relaxed state. Both bacterial and eukaryotic DNA usually fold into loops stabilized by proteins (which prevent free rotation of the ends; see Figure 8.17 on the next page), and supercoiling takes place within the loops.

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Supercoiling relies on topoisomerases, enzymes that add or remove rotations from the DNA helix by temporarily breaking the nucleotide strands, rotating the ends around each other, and then rejoining the broken ends. Thus, topoisomerases can both induce and relieve supercoiling, although not all topoisomerases do both.

Most DNA found in cells is negatively supercoiled. This state has two advantages over relaxed DNA. First, negative supercoiling makes the separation of the two strands of DNA easier during replication and transcription. Negatively supercoiled DNA is underrotated, so separation of the two strands during replication and transcription is more rapid and requires less energy. Second, the supercoiled DNA can be packed into a smaller space than can relaxed DNA.