One type of topoisomerase, called topoisomerase I, produces a transient sin-gle-strand break; this break in the phosphodiester backbone allows the two sections of DNA helix on either side of the nick to rotate freely relative to each other, using the phosphodiester bond in the strand opposite the nick as a swivel point (Figure 5–21). Any tension in the DNA helix will drive this rotation in the direction that relieves the tension. As a result, DNA replication can occur with the rotation of only a short length of helix—the part just ahead of the fork. Because the covalent linkage that joins the DNA topoisomerase protein to a DNA phosphate retains rotate, torsional stress will build up
Figure 5–19 Strand-directed mismatch repair. (A) The two proteins shown are present in both bacteria and eukaryotic cells: MutS binds specifically to a mismatched base pair, while MutL scans the nearby DNA for a nick. Once MutL finds a nick, it triggers the degradation of the nicked strand all the way back through the mismatch. Because nicks are largely confined to newly replicated strands in eukaryotes, replication errors are selectively removed. In bacteria, an additional protein in the complex (MutH) nicks unmethylated (and therefore newly replicated) GATC sequences, thereby beginning the process illustrated here. In eukaryotes, MutL contains a DNA nicking activity that aids in the removal of the damaged strand.
(B) The structure of the MutS protein bound to a DNA mismatch. This protein is a dimer, which grips the DNA double helix as shown, kinking the DNA at the mismatched base pair. It seems that the MutS protein scans the DNA for mismatches by testing for sites that can be readily kinked, which are those with an abnormal base pair.  (PDB code: 1EWQ.)
Figure 5–20 The “winding problem”  that arises during DNA replication.
(A) For a bacterial replication fork moving at 500 nucleotides per second, the parental DNA helix ahead of the fork must rotate at 50 revolutions per second. (B) If the ends of the DNA double helix remain fixed (or difficult to rotate), tension builds up in front of the replication fork as it becomes overwound. Some of this tension can be taken up by supercoiling, whereby the DNA double helix twists around itself (see Figure 6–19). However, if the tension continues to build up, the replication fork will eventually stop because further unwinding requires more energy than the helicase can provide. Note that in (A), the dotted line represents about 20 turns of DNA.
one end of the DNA double helix cannot rotate relative to the other end topoisomerase with tyrosine at the active site
CH2 OH CH2 OH DNA topoisomerase covalently attaches to a DNA phosphate, thereby breaking a phosphodiester linkage in one DNA strand the two ends of the DNA double helix can now rotate relative to each other, relieving accumulated strain
Figure 5–21 The reversible DNA nicking reaction catalyzed by a eukaryotic DNA topoisomerase I enzyme. As indicated, these enzymes transiently form a single covalent bond with DNA; this allows free rotation of the DNA around the covalent backbone bonds linked to the blue phosphate.
CH2HO the original phosphodiester bond energy is stored in the phosphotyrosine linkage, making the reaction reversible CH2 OH spontaneous re-formation of the phosphodiester bond regenerates both the DNA helix and the DNA topoisomerase the energy of the cleaved phosphodiester bond, resealing is rapid and does not require additional energy input. In this respect, the rejoining mechanism differs from that catalyzed by the enzyme DNA ligase, discussed previously (see Figure 5–12).
A second type of DNA topoisomerase, topoisomerase II, forms a covalent linkage to both strands of the DNA helix at the same time, making a transient