Cells have developed a number of systems designed to repair DNA damage and correct mutations. Obviously, these mechanisms are not perfectly successful, but as we'll see, without them mutation rates would be much higher.

Repair of Thymine Dimers

Several mechanisms are available for the removal or correction of thymine dimers from DNA. Which mechanism is used depends upon the circumstances of the cell.

• Photoreactivation - It has been observed that a brief exposure to blue light following UV exposure can reverse the effects of the UV radiation. In other words, the blue light can cause a thymine dimer to be corrected. This is due to the function of an enzyme called photolyase or photoreactivation enzyme (PRE), which cleaves the covalent bonds linking the thymine dimers using the energy from a photon of blue light. This is essentially a reversal of the reaction that produced the thymine dimer in the first place.
• Excision Repair - This is a repair system that doesn't require light. Instead of just breaking the bonds of the thymine dimer (as was done by photolyase), the excision repair system removes (excises) the region surrounding the offending nucleotides. Several proteins are involvedin this process (in prokaryotes these are the products of the 'uvr' genes, for 'UV repair'). The steps of excision repair in prokaryotes are as follows:

• The distortion in the DNA (caused by the thymine dimer) is recognized by a protein complex. A pair of endonucleases makes nicks in the DNA strand on either side of the thymine dimer (generally the nicks are 12 nucleotides apart).

• The 12-nucleotide piece of DNA between the nicks is removed, and DNA polymerase I fills in the gap left behind.

• DNA ligase seals the final nick in the DNA.

• Recombination Repair - Sometimes, DNA replication will begin before a thymine dimer can be repaired by one of the other mechanisms. When the replication machinery hits the dimer, replication stops. Occasionally, the replication will reinitiate just beyond the dimer, leaving a gap in the DNA.

This leaves the cell with a curious predicament: if it tries to fix the dimer by excision repair, there is no template to use for resynthesis of the DNA. How, then, does the DNA get repaired? The answer is that the cell uses recombination to provide a template strand for repair synthesis. Here's how:

First, the damaged region undergoes recombination with the complemenary strand on the other DNA molecule. One strand is exchanged between the two DNA molecules.

This essentially transfers the gap to the DNA molecule that doesn't have the dimer.

The gap can now be filled in by DNA polymerase I, and the dimer can be repaired by excision, since a template strand now exists.

A more detailed examination of the actual mechanism of recombination will be presented later in the module.

• SOS Repair - If the UV exposure is sufficiently severe, the DNA damage may overwhelm the other repair mechanisms. In such situations, DNA replication would almost certainly halt, and the cell would die. As a last ditch effort to save itself, a cell activates the SOS repair system. This is a complex system, in which a whole battery of repair mechanisms are used to try to save the cell. One of these mechanisms allows replication to proceed across damaged templates, even though the template can't accurately be read. As a result, random nucleotides get inserted into the newly-synthesized DNA strand. This mechanism is therefore error-prone, and leads to mutations, which could be deleterious. In this case, however, the alternative is death, so mutation is preferable.