DNA repair

• Proofreading of DNA during replication
• DNA repair immediately after replication
• DNA damage repair during the rest of the cell cycle

DNA repair is a correction of errors occurring in the structure of the DNA molecule.

Errors in the structure of DNA that can be repaired are often a violation of the sequence of nucleotides that make up each strand of DNA. The DNA molecule consists of two chains or strands complementary to each other. This means that if the damage occurs in one of the chains, then it is possible to restore the damaged part using the second chain as a template. In addition, in eukaryotic cells, each chromosome has a homologous, i.e. containing the same set of genes (but not alleles). In the extreme case, when the site on both strands of the molecule is damaged, it can be copied from the homologous chromosome. Also, after the S-phase of the cell cycle, when replication (self-copying) has occurred, each chromosome consists of two double-stranded identical chromatids, that is, essentially of two identical DNA molecules. This can also be used to restore the original structure of the damaged molecule.

In the course of evolution, many different cellular molecular mechanisms responsible for DNA repair appeared. Basically, these are different enzymes and their complexes. Some of them are also involved in replication. Damage of the genes that encode such enzymes are especially dangerous. This leads to the loss of a repair mechanism. In this case, a faster accumulation of damage and mutations occurs in the cells. Often this is the cause of the emergence of uncontrollably dividing cells, i.e. the appearance of tumors.

On the other hand, if the DNA damage is extremely strong, then the self-destruct mechanism (apoptosis) is triggered in the cells. Thus, such cells are not allowed to divide, so the next generation will not contain significant DNA damage.

Errors in DNA can occur at various stages of its existence (during synthesis, in pre- and post-synthetic periods), for various reasons (accidentally, under the action of chemically active substances, radiation, etc.). Also, the changes are different: the loss of a chemical group of the nucleotide or the addition of an one, the replacement of the nucleotide by another, the establishment of a chemical bond between two neighboring nucleotides, the breaking of the chain, the loss of the site, etc. Because of this diversity, there is a difficulty in classifying repair mechanisms. Often they are divided into those that occur during replication, immediately after it and during the rest of the life cycle of a cell. Below, the most studied causes of structural changes and methods of DNA repair are described.

Note that not all errors have been corrected, relatively small and not critical can be transmitted to the next generation of cells and organisms. They can not be called damages, rather it's mutations. Most mutations are harmful, but those that are neutral or useful in given environmental conditions serve as a material for evolution. Thus, the imperfection of DNA repair mechanisms has ensured the diversity of life on our planet.

Proofreading of DNA during replication

DNA polymerases perform the main work during DNA replication by attaching the nucleotide behind the nucleotide to a new chain. In addition to the basic function, many polymerases are able to remove the incorrectly attached last nucleotide, which is not complementary to the nucleotide of the template chain.

The chemical structure of nucleotides can be slightly modified. Modified nucleotides can be connected by hydrogen bonds not to their complementary partners. For example, cytosine should bind to guanine. But its altered form establishes hydrogen bonds with adenine.

When a new DNA strand is synthesized, firstly the next nucleotide is been linking by hydrogen bonds to the complementary base of matrix. After that, the polymerase binds nucleotide to the end of the growing chain using a covalent bond.

However, if it was a modified nucleotide that illegally associated with the base of the template, then it usually returns quickly to its original form and becomes non-complementary. Hydrogen bonds are breaking, and it turns out that the end of the new chain has a freely hanging nucleotide, covalently bound to the growing chain.

In this case, DNA polymerase cannot attach the next nucleotide. However, the enzyme can remove that erroneous nucleotide.

If the hydrogen bonds do not break, then after the wrong nucleotide the chain will continue to grow further, and the point mutation will remain. It can be fixed after replication.

DNA repair immediately after replication

After a new DNA strand has been synthesized, certain enzyme complexes recognize incorrectly paired bases. In this case, there is a problem to determine the new and old chain of the DNA molecule. The new one is distinguished by the absence of methylated bases, and in eukaryotes there are temporal discontinuities. By these features, enzyme complexes identify the newly synthesized chain. So the nucleotide of the new chain is considered to be an "error" in mis-paired bases.

Once the error is found, other enzymes cut out a whole region of DNA containing an unjustified base, and not just one nucleotide. After that, the polymerase re-builds this site, and the ligase sews it with the rest of the chain. This mechanism, when a patch of DNA is cut and re-synthesized, is called excision repair, it is quite universal and is used in many cases of repair, and not only when DNA is "checked" immediately after replication.

DNA damage repair during the cell cycle

The DNA of an organism can change not only because of replication errors. The cell lives on, unfavorable external factors act on it, its internal biochemical environment can change, provoking the reactions that detrimental to DNA. As a result, the genetic material is damaged in one way or another. Depending on the type of damage and its scale, various reparation mechanisms involving several different sets of enzyme complexes are included.

1. There are enzymes that cancel nucleotide changes in place without removing DNA patches. In other words, if there was a nucleotide in the chain containing the base of guanine (G), which attached the methyl group and turned into methyl guanine, the enzyme would convert it back to guanine. Basically, that type of DNA repair occurs when certain groups of atoms are attached or detached.

2. In case of loss of purine bases, excision repair may occur. In the case of deamination and some other structural changes in the bases, the glycosylase enzymes excise only the damaged base of the nucleotide. Only after this, excision repair occur.

3. The site is cut out also when dimers are formed (two adjacent nucleotides are connected together). Typically, such reactions occur under the influence of ultraviolet rays. The formation of a dimer provokes a divergence of complementary DNA strands in this and nearby regions. A bubble is formed, which is recognized by enzymes. Then the excision repair begins.

4. There are such strong damages of DNA molecules, when the structure of both its chains is broken in the same place. In this case, it is not possible to restore one chain, using the other as a template. One example of such damage can be the rupture of the DNA molecule into two parts under the action of strong radioactive irradiation.

In case of damage to both strands of the DNA molecule, recombinant repair may come to the rescue, when a site from a homologous chromosome or sister chromatid has been inserting in place of the damaged site. Also in the case of rupture, there are enzymes capable of reattaching a torn off piece of DNA. However, some nucleotides can be lost, this can lead to serious mutations.

In the presynthetic period of the cell cycle recombinant repair can occur only between homologous chromosomes, since in this period, each chromosome consists of only one chromatid. In the post-synthetic period, when the chromosomes consist of two identical chromatids, the site can be borrowed from the sister chromatid.

Note that in sister chromatids the set of alleles is initially identical (if there was no crossing-over). In homologous chromosomes, it's not so. Thus, from the point of view of genetics, real recombination occurs only in the case of an exchange between homologous chromosomes. Although here in both cases we are talking about recombination.

Let's consider an example. Suppose a thymine dimer appeared in the DNA and it was not repaired before replication. In the process of replication, the chains of the original DNA molecule diverge and a new complementary chain is built on each. On the matrix chain that contains thymine dimer, the site of the new chain can not be built in this place. In this place just there is no normal template. A gap appears in the daughter strand, and the dimer remains in the parent strand. That is, this DNA molecule "does not know" what is the correct nucleotide sequence of the site.

In this case, the only way of repair is the borrowing the piece of DNA from another chromatid. It is transferred from one of its chains. The gap that arises here is built up according to the pattern of the complementary chain. On the damaged molecule the transferred site is inserted into the gap of the new chain, the template chain will remain to contain the dimer, which can be repaired later.