What are you going to learn?
- What is DNA repair?
- What are the basic steps of DNA repair?
- What is a mismatch and how does mismatch repair work?
- What is excision repair?
- How can the organism repair damage to both DNA strands?
- What is the difference between nonhomologous end joining and homologous recombination?
- terms: a mismatch, mismatch repair, base excision repair, nucleotide excision repair, double-strand break repair, nonhomologous end joining, homologous recombination
In DNA replication, we mentioned that DNA polymerase is capable of proofreading – in other words, it checks whether a correct nucleotide has been added and if not, it can repair the DNA damage immediately. However, the organism has other mechanisms that can repair DNA damage. Although the exact mechanisms differ, the basic steps of DNA repair are similar. First, the damaged DNA must be recognized and removed. This is usually done by enzymes called nucleases, which cleave the phosphodiester bonds (between the sugar and the phosphate group) so that the damaged nucleotide(s) can be removed. DNA polymerase then fills the gap by synthesizing new complementary nucleotides using the other undamaged strand as a template. Finally, DNA ligase joins the newly synthesized part of the strand with the original one.
1) a nuclease recognizes and removes the damaged DNA
2) DNA polymerase synthesizes new complementary nucleotides
3) DNA ligase joins the new nucleotides with the rest of the strand
One of the mechanisms the organism uses to repair damaged DNA is called mismatch repair. A mismatch is a mispaired nucleotide (for example A may be mispaired with G) that was created in DNA replication. The function of mismatch repair is to repair such errors by recognizing the mismatch using mismatch-repair enzymes, removing a short part of the DNA containing the error and synthesizing new nucleotides with the original DNA strand as a template.
1) mismatch-repair enzymes recognize the mismatch
2) short part of DNA is removed
3) new nucleotides are added
Another important mechanism is called excision repair. There are two types of excision repair: 1) base excision repair, 2) nucleotide excision repair. In base excision repair an incorrect base is removed from the DNA using the general steps of DNA repair described above. Nucleotide excision repair is used to repair more serious damage to the DNA, such as thymine dimers that distort the double helix. It uses a complex of enzymes that finds the distorted part of the DNA and separates its two strands. The damaged part of the strand is removed, and the gap is filled in by DNA polymerase. DNA ligase then again joins the newly synthesized nucleotides with the undamaged DNA strand.
1) enzymes find and separate the DNA strands with the distortion
2) the damaged part of the strand is removed
3) DNA polymerase synthesizes new nucleotides
4) DNA ligase joins the new nucleotides with the rest of the strand
So far, we’ve only mentioned DNA repair mechanisms that can repair damage to one of the DNA strands, using the second as a template. However, if both DNA strands are damaged, the organism can use the double-strand break repair. To be more precise, it can use one of its two subtypes: 1) nonhomologous end joining, 2) homologous recombination. In nonhomologous end joining, the broken DNA ends are just sticked together. As you can imagine, this is not precise, but it is fast.
The homologous recombination, on the other hand, is very precise and can be used after DNA replication when there are two double-helixes, and one gets damaged. First, a nuclease removes the 5'-ends of the two broken strands at the break. Then, one of the broken 3'-ends pairs with the unbroken DNA double-helix to use it as a complementary strand. The DNA polymerase elongates the strand, and the strand then rejoins the second broken strand. Finally, the rest of the missing DNA is synthesized and then joined by DNA ligase. The reason we call homologous recombination homologous is because it uses a homologous template – a template that contains the same genetic information as the one that is in the damaged strand (homologous means the same or similar). Nonhomologous end joining does not use such a template and that is why we call it nonhomologous.
1) a nuclease removes the 5'-ends of the two broken strands
2) one of the broken 3'-ends pairs with the unbroken DNA double-helix
3) DNA polymerase elongates the strand
4) the strand rejoins the second broken strand
5) DNA polymerase synthesizes the rest of the missing DNA
6) DNA ligase joins the new nucleotides with the rest of the strand
References:
Alberts, B. (2014). Essential Cell Biology. Garland Science.
Pierce, B. A. (2019). Genetics: A Conceptual Approach (Seventh ed.). W. H. Freeman.
Snustad, D. P., & Simmons, M. J. (2012). Principles of Genetics. Wiley.