1. DNA Repair

2. The human genome contains 3 billion base pairs
The human genome contains 3 billion base pairs . If we have an error one in a million this mean we will have 3000 errors during each replication cycle of the genome.

3. The genome of a typical mammalian cell accumulates many thousands of lesions during a 24-hour period. However, as a result of DNA repair, fewer than 1 in 1,000 becomes a mutation. DNA is a relatively stable molecule, but in the absence of repair systems, the cumulative effect of many infrequent but damaging reactions would make life impossible.

4. After synthesis, the DNA may undergo some damages during the cell life-span, but naturally there are certain repair systems present inside the body that can provide protections against DNA damages. The rate of DNA repair is dependent on many factors, including the cell type, the age of the cell, and the extracellular environment.

5. A cell that has accumulated a large amount of DNA damage, or one that no longer effectively repairs damage incurred to its DNA, can enter one of three possible states:
an irreversible state of dormancy, known as senescence ( getting old )
cell suicide, also known as apoptosis or programmed cell death
unregulated cell division, which can lead to the formation of a tumor that is cancerous

6. The 2015 Nobel Prize in Chemistry was awarded to Tomas Lindahl, Paul Modrich, and Aziz Sancar (Turkish-American in the field of genetics, was born in Mardin in 1946 ), for their work on the molecular mechanisms of DNA repair processes. There are two types: nucleotide excision repair and base excision repair

7. I. Mismatch Repair System during DNA replication
1.Exonucleolytic proofreading of DNA polymerase usually occurring simultaneously with DNA replication. In these processes DNA molecules with single mismatched 3’ OH ends do not become effective templates because polymerase cannot extend when 3’ OH is not base paired. DNA polymerase has a separate exonuclease catalytic site that removes unpaired residues at the terminus and replace them by the correct base pair.

8. 2. An alternative DNA mismatch repair is a system which recognizes and repairs major insertion, deletion and mis-incorporation of bases. During DNA synthesis the newly synthesized (daughter) strand often includes errors and such defective copy of the mismatch repair gene could have serious consequences on human health.

9. The mismatch repair system carries out the following corrections:
 Removes replication errors which are not
recognized by the replication machine.
 Detects structural changes in the DNA helix.
The newly synthesized strand is preferentially nicked to be distinguished from the parental strand. Next step is the binding of mismatch proofreading complex at the defective base pair of the new strand, followed by removal of segment from this strand to be correctly replaced using the parental strand as a template.

10. II. Repair of DNA damage after DNA maturation
Main Causes of DNA damage that occur after DNA synthesis:
1. Chemical pollutants
2. Radiation
Industrial chemicals such as vinyl chloride or hydrogen peroxide, and environmental chemicals such as polycyclic hydrocarbons found in smoke and tar create a large chemical modifications in DNA leading to the formation of oxidized bases, alkylated bases such as methyl bases or conversion of one base into another type (conversion of cytidine into uridine).

11. Thermal disruption at elevated temperature increases the rate of depurination (loss of purine bases from the DNA backbone) and single strand breaks. For example, hydrolytic depurination is seen in the thermophilic bacteria, which grow in hot springs above 80 °C.

12. The main types of DNA damage caused by these environmental factors are:
base loss
base modification
strands breakage.

13. Thymine oxidation
Repair of DNA damages Despite the exposure of DNA to large damaging environmental factors each day, very few damages actually have serious effects on human chromosomal DNA due to highly efficient repair mechanisms. An inactivation or loss of functions in these DNA repair systems may cause errors in replication and lead to genetic diseases such as :

15. Fanconi anaemia (FA)
It is a rare genetic disease. Among those affected the majority develop cancer, most often acute myelogenous leukemia, and 90% develop bone marrow failure (the inability to produce blood cells) by age 40. About 60–75% of people have congenital defects, commonly short stature, abnormalities of the skin, arms, head, eyes, kidneys, and ears, and developmental disabilities.

16. Lynch syndrome (HNPCC or hereditary nonpolyposis colorectal cancer)
It is an autosomal dominant genetic condition that has a high risk of colon cancer as well as other cancers including endometrial cancer (second most common), ovary, stomach, small intestine, hepatobiliary tract, upper urinary tract, brain, and skin. The increased risk for these cancers is due to inherited mutations that impair DNA mismatch repair. It is a type of cancer syndrome.

17. Werner syndrome (WS)
It is also known as "adult progeria", is a rare, autosomal recessive progeroid syndrome (PS), which is characterized by the appearance of premature aging. The median and mean ages of death are 47–48 and 54 years, respectively. The main cause of death is cardiovascular disease or cancer.

18. Types of DNA repair systems
Base Excision Repair (BER) BER is a cellular mechanism that repairs damaged DNA throughout the cell cycle. It is primarily responsible for removing small, non-helix distorting base lesions from the genome. BER is important for removing damaged bases that could otherwise cause mutations by mispairing or lead to breaks in DNA during replication. The repair system containing the following system:

19. First, a glycosylase enzyme recognizes a specific type of incorrect base., which then cleaves the N-glycosyl bond to remove the defective nitrogen base and generating an apurinicor apyrimidinic (AP) site. Different DNA glycosylasesrecognize different types of defective bases.
Each DNA glycosylase is generally specific for one
type of lesion. Uracil DNA glycosylases, for example, found in most cells, specifically remove from DNA the uracil that results from spontaneous deamination of cytosine. Mutant cells that lack this enzyme have a high rate of G≡ C to A=T mutations.

20. 2. The AP sites generated by glycosylase action are then recognized by AP endonuclease, which cleaves the phosphodiester backbone immediately 5' to the AP site, leaving a 3'-OH and 5'-deoxyribose-phosphate terminus (incision step).

21. 3. The 5' deoxyribose phosphate is then removed by specific exonuclease called DNA deoxyribo-phosphodiesterase (dRpase), leaving a nick (gap).
4. The second strand is used as a template to fill in the gap. This process is carried out by a DNA polymerase and a DNA ligase.

23. UV-B light causes covalent cross-linking between adjacent thymine bases creating cyclobutane thymine dimmers. Ionizing radiation such as that created by radioactive or x-rays causes breaks in DNA strands. When thymine dimers are present, the double helix is distorted (bent), as the thymines are pulled toward each other. Hydrogen bonding to adenines on the opposite strand is weakened .The distortion causes a loss of template information. In addition, it can prevent the advancing replication fork or inhibiting the process of RNA transcription.

24. UV irradiation causes dimerization of adjacent thymine bases
FIGURE UV irradiation causes dimerization of adjacent thymine bases. A cyclobutyl ring is formed between carbons 5 and 6 of the pyrimidine rings. Normal base pairing is disrupted by the presence of such dimers.
Fig , p.252

25. Oxidation damage ( oxygen radicals in the presence of metal ions such as Fe2+ can destroy sugar rings in DNA, breaking the strand.)
FIGURE Oxygen radicals, in the presence of metal ions such as Fe2+, can destroy sugar rings in DNA, breaking the strand.
Fig , p.252

26. Missmatch repair in E.coli
FIGURE Mismatch repair in E.coli. (a) The newly synthesized DNA (shown in red) has a mismatch (G–T). (b) MutH, MutS, and MutL link the mismatch with the nearest methylation site, which identifies the blue strand as the parental (correct) strand. (c) An exonuclease removes DNA from the red strand between the proteins. (d) DNA polymerases replace the removed DNA with the correct sequence. (Adapted from Lehninger, Principles of Biochemistry, Third Edition, by David L. Nelson and Michael M. Cox. © 1982, 1992, 2000 by Worth Publishers. Used with permission of W. H. Freeman and Company.)
Fig , p.253

27. BB Base –excition repair Fig. 10-16, p.254
FIGURE Base-excision repair. A damaged base () is excised from the sugar–phosphate backbone by DNA glycosylase, creating an AP site. Then, an apurinic/apyrimidinic endonuclease severs the DNA strand, and an excision nuclease removes the AP site and several nucleotides. DNA polymerase I and DNA ligase then repair the gap.
Fig , p.254

28. Nucleotide Excision Repair (NER)
The related nucleotide excision repair pathway repairs bulky helix-distorting lesions
1. Specific endonuclease cleaves damaged DNA
on either side of a lesion thereby producing a
short gap.
2. Highly processive DNA polymerase fills in the
gap and DNA ligase completes the repair
process.

29. Nucleotide-excision repair
FIGURE Nucleotide-excision repair. When a serious lesion, such as a pyrimidine dimer, is detected, ABC exinuclease binds to the region and cuts out a large piece of DNA, including the lesion. DNA polymerase I and DNA ligase then resynthesize and seal the DNA. (Adapted from Lehninger, Principles of Biochemistry, Third Edition, by David L. Nelson and Michael M. Cox. © 1982, 1992, 2000 by Worth Publishers. Used with permission of W. H. Freeman and Company.)
Fig , p.254

31. Recombination can be used to repair infrequent lesions
Recombination can be used to repair infrequent lesions. (a) The parental DNA (blue) has a lesion on the bottom strand. The newly synthesized top strand (light blue) has the correct sequence. Through recombination, the top blue strand can cross over and pair with the bottom blue strand that has the lesion. The top light blue strand can then be replicated to give the product shown in (b). In (c), the lesions are too numerous for this system to work. Instead, error-prone replication using DNA polymerase II patches over the lesion as best it can. Many mistakes are made in the process. (Adapted from Lehninger, Principles of Biochemistry, Third Edition, by David L. Nelson and Michael M. Cox. © 1982, 1992, 2000 by Worth Publishers. Used with permission of W. H. Freeman and Company.)
p.255

32. Thymine dimer excision repair system
A photo-reactivating enzyme system that can recognizes the thymine dimer and in response to visible light this enzyme system is stimulated to cleave the thymine rings. The system contains UV endonuclease that cleaves the damaged DNA on either side of the dimer to produce a short gap (about 100 nucleotides) on a single strand that can be filled by DNA polymerase using opposite strand as a template. Then the DNA ligase is used to complete the repair process.

34. Xeroderma pigmentosum  It is a rare autosomal recessive genetic disorder of DNA repair in which the ability to repair damage caused by ultraviolet (UV) light is deficient.

35. Nearly 90% of these individuals develop skin carcinomas Most XP individuals also suffer from neurologic disorders including mental retardation. XP individuals are extremely sensitive to sunlight (UV light) and are unable to efficiently repair thymine dimers and other types of DNA damages

36. END