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Errors in DNA Replication

The low overall rate of mutation during DNA replication (1 base pair change in one billion base pairs per replication cycle) does not reflect the true number of errors that take place during the replication process. The number is kept so low by a proof-reading system that checks newly synthesized DNA for errors and corrects them when they are found. Errors in DNA replication can take different forms, but usually revolve around the addition of a nucleotide with the incorrect base, meaning the pairing between the parent and daughter strand bases is not complementary. The addition of an incorrect base can take place by a process called tautomerization. A tautomer of a base group is a slight rearrangement of its electrons that allows for different bonding patterns between bases. This can lead to the incorrect pairing of C with A instead of G, for example.

Figure %: Tautomerization of Cytosine

DNA retains its high level of accuracy is with its proof-reading function.

The 3' to 5' Proof-Reading Exonuclease

The 3' to 5' proof-reading exonuclease works by scanning along directly behind as the DNA polymerase adds new nucleotides to the growing strand. If the last nucleotide added is mismatched, then the entire replication holoenzyme backs up, removes the last incorrect base, and attempts to add the correct base again. The enzyme is "3' to 5'" because it scans in the opposite direction of DNA replication, which we learned must always be 5' to 3'. The mechanism of the proof-reading system offers an explanation as to why DNA replication must occur in this direction.

Keeping in mind the chemical mechanism we learned for the addition of nucleotides to the growing DNA strand, imagine what happens when the proof- reading system removes an incorrectly paired base. The exonuclease removes the base by cleaving the phosphodiester bond that had just been formed. In 5' to 3' synthesis, this leaves the 3' -OH still attached to the terminal end of the growing strand ready to attack another nucleotide.

Figure %: 3' to 5' Exonuclease Action
If synthesis occurred in the opposite direction, the terminal end of a growing chain would contain a triphosphate group instead of an -OH group. This triphosphate would become the target of the proof-reading exonuclease and its removal would halt DNA replication.
Figure %: Incorrect 3' to 5' Synthesis

Types of DNA Damage

After DNA has been completely replicated, the daughter strand is often not a perfect copy of the parent strand it came from. Mutations during replication and damage after replication make it necessary for there to be a repair system to fix any errors in newly synthesized DNA. There are three main sources of damage to DNA.

  1. Attack by water which can lead to the removal of an amine group from the base group of a nucleotide or the loss of the entire base group.
  2. Chemical damage that permanently alters the structure of the DNA.
  3. Radiation damage which can lead to nicks in the backbone of DNA or the formation of thymine dimers, which will be discussed later.

These different sources of damage lead to different categories of DNA damage. The damage that is caused by water attack can lead to unnatural bases. Chemical and radiation damage leads to the formation of bulky adducts to, or breaks in, the growing DNA strand. In the previous section we discussed the 3' to 5' proof-reading exonuclease that is responsible for fixing mismatches. Because it is not a perfect system, it can miss mismatched bases. As a result, a third category of DNA damage is mismatched bases.