1. DNA Repair
DNA repair is a system used to correct DNA damage caused by either:
A- Errors during DNA replication including incorrect base-pairing (mismatching e.g. G may be paired with T not with C)
B- Environmental damaging agents that cause the alteration or removal of nucleotide bases. These damaging agents can be either:
i- chemicals, for example, nitrous acid
ii- radiation e.g. UV light which can join two adjacent pyrimidines
iii- high-energy ionizing radiation, which can cause double-strand breaks.
C- Bases can be also lost or changed spontaneously (without cause)

2. Types of DNA damage:
1- Mismatches of the normal bases because of an errors during DNA replication.
2- Thymine dimer (binding of two adjacent thymine) which prevent replication. This damage is caused by UV light.
3-Double strand break caused by high energy radiation or free radicals.
4-DNA bases alterations caused by chemicals such as nitrous acid, or spontaneously or deaminating agents that convert cytosine into uracil.

3. Double strand break (on the right)

4. If the damage is not repaired, a permanent mutation may be introduced that can result in number of deleterious effects leading to cancer. Luckily, cells are remarkably efficient at repairing damage done to DNA.
Most of repair systems involve:
1- recognition of the of damage on DNA,
2-removal or excision of the damage,
3-replacement or filling the produced gap with new DNA and ligation

5. A- Mismatch repair:
Mismatch repair is mediated by a group of proteins known as the Mut proteins. Analogous proteins are present in humans.
Steps of repair:
Identification of the mismatched strand:
When mismatch occurs, the Mut proteins that identify the mis-paired base (s) must be able to differentiate between the correct strand and the strand with the mismatch.
For example: in mis-paired G-T, Mut proteins should recognize whether G or T is the false base added in the new strand.

6. Differentian is based on the presence of GATC sequence in which adenine base is methylated, this unique sequence is found approximately once every thousand nucleotides. Methylation of adenine is not done immediately after replication, so the newly synthesized DNA is hemi-methylated i.e parent strand is methylated, but the daughter new strand is not. The methylated parent strand is assumed to be correct, and the daughter strand that will be repaired.

8. . Repair of damaged DNA: Figure handout
When the mismatch is identified, an specific nuclease nicks (cuts) the daughter strand and the mismatched nucleotide(s) is/are removed by another nuclease. Extra nucleotides at the 5' and 3' ends of the mismatch are also removed. The gap left after removal of the nucleotides is filled by DNA synthesized by DNA polymerase I using the parent strand as a template. The nick is sealed by ligase.

11. B- Repair of damage caused by ultraviolet (UV) light:
Exposure of a cell to UV light can result in the covalent joining of two adjacent pyrimidines (usually thymines), producing a dimer. These thymine dimers prevent DNA polymerase from replicating the DNA strand beyond the site of dimer formation.

13. The UV-damage repair includes: See Figure also
Recognition and excision of dimers by UV-specific nuclease (exinuclease): This enzyme recognizes the dimer and cleaves the damaged strand on both 5'- side and 3' side of the dimer. A short oligonucleotide containing the dimer is released leaving a gap that is then filled by DNA polymerase and the nick is sealed by ligase.