Dna repair mechanism

contains two repair mechanisms
1)DIRECT REVERSAL REPAIR
2)EXICION REPAIR

1. DNA REPAIR MECHANISMS Vishnu prasad nair.R.U 100716517001 M.Sc genetics Osmania university

2. In the most DIRECT of these systems (representing true repair ), a repair enzyme simply reverses (undoes) the damage . A more elaborate system is EXCISION REPAIR , in which the damaged nucleotide is not repaired but removed from the DNA . In excision repair systems, the other, undamaged , strand serves as a template for reincorporation of the correct nucleotide by DNA polymerase . two kinds of excision repair systems exist, 1)involving the removal of only the damaged nucleotide . 2)involving the removal of a short stretch of single-stranded DNA that contains the lesion.

3. Direct Reversal of DNA Damage Example- PHOTOREACTIVATION Photoreactivation directly reverses the formation of pyrimidine dimers that result from ultraviolet irradiation. In Photoreactivation , the enzyme DNA Photolyase captures energy from light and uses it to break the covalent bonds linking adjacent pyrimidines .

4. Another example:- removal of the methyl group from the methylated base O 6 -methylguanine. In this case, a methyltransferase removes the methyl group from the guanine residue by transferring it to one of its own cysteine residues. This is costly to the cell because the methyltransferase is not catalytic ; having once accepted a methyl group, it cannot be used again .

5. Excision Repair :- The most prevalent way in which DNA is cleansed of damaged bases is by repair systems that remove and replace the altered bases . The two principal repair systems are base excision repair and nucleotide excision repair . BASE EXCISION REPAIR :- In base excision repair, an enzyme called a glycosylase recognizes and removes the damaged base by hydrolyzing the glycosidic bond.

6. The resulting abasic sugar is removed from the DNA backbone in a further endonucleolytic step . Endonucleolytic cleavage also removes apurinic and apyrimidinic sugars that arise by spontaneous hydrolysis. After the damaged nucleotide has been entirely removed from the backbone, a repair DNA polymerase and DNA ligase restore an intact strand using the undamaged strand as a template.

7. A total of 11 different DNA glycosylases have been identified in human cells . DNA glycosylases are lesion-specific and cells have multiple DNA glycosylases with different specificities . Thus, a specific glycosylase recognizes uracil (generated as a consequence of deamination of cytosine), and another is responsible for removing oxoG (generated as a consequence of oxidation of guanine ).

8. What if a damaged base is not removed by base excision before DNA replication ? Ans – There is always a fail safe system

9. Example:- In the case of oxoG , which has the tendency to mispair with A, a fail-safe system exists. A dedicated glycosylase recognizes oxoG:A base pairs generated by misincorporation of an A opposite an oxoG on the template strand. In this case, however, the glycosylase removes the A. Thus, the repair enzyme recognizes an A opposite an oxoG as a mutation and removes the undamaged but incorrect base.

10. Nucleotide Excision Repair :- Unlike base excision repair , the nucleotide excision repair enzymes do not recognize any particular lesion. Rather, this system works by recognizing distortions to the shape of the double helix. Such distortions trigger a chain of events that lead to the removal of a short single-strand segment (or patch) that includes the lesion . This removal creates a single-strand gap in the DNA, which is filled in by DNA polymerase using the undamaged strand as a template and thereby restoring the original nucleotide sequence.

11. Nucleotide excision repair in E. coli is largely accomplished by four proteins: UvrA , UvrB , UvrC , and UvrD . A complex of two UvrA and two UvrB molecules scans the DNA, with the two UvrA subunits being responsible for detecting distortions to the helix .

12. Upon encountering a distortion, UvrA exits the complex, and the remaining dimer of UvrB melts the DNA to create a single-stranded bubble around the lesion. Next , the UvrB dimer recruits UvrC , and UvrC creates two incisions: one located 4 or 5 nucleotides 3’ to the lesion and the other 8 nucleotides 5’ to the lesion.

13. These cleavages create a 12- to 13-residue-long DNA strand that contains the lesion. The lesion-containing strand is removed from the rest of the DNA by the action of the DNA helicase UvrD , resulting in a 12- to 13-nucleotide-long gap. Finally, DNA Pol I and DNA ligase fill in the gap.

14. Not only is nucleotide excision repair capable of mending damage throughout the genome, but it is also capable of rescuing RNA polymerase, the progression of which has been arrested by the presence of a lesion in the transcribed (template) strand of a gene . This phenomenon, known as transcription-coupled repair . This involves recruitment to the stalled RNA polymerase of nucleotide excision repair proteins. RNA polymerase serves as another damage-sensing protein in the cell . Central to transcription-coupled repair in eukaryotes is the general transcription factor TFIIH .( TFIIH unwindstheDNAtemplate during the initiation of transcription). Subunits of TFIIH include the DNA helix-opening proteins XPA and XPD. Thus, TFIIH is responsible for two separate functions: its strand-separating helicases melt the DNA around a lesion during nucleotide excision repair (including transcription-coupled repair) and 2. Also help to open the DNA template during the process of gene transcription.

15. What happens when this nucleotide excision repair fails to occur ? Ans - cells are limited in their ability to repair UV-induced DNA damage like thymine dimers. this can lead to severe health conditions. Example- X eroderma pigmentosum .( xp ) xeroderma pigmentosum (XP ), an autosomal-recessive disease that renders afflicted individuals highly sensitive to sunlight and results in skin lesions , including skin cancer. Seven genes have been identified in which mutations give rise to XP. These genes specify proteins (such as XPA, XPC, XPD, XPF, and XPG) in the human pathway for nucleotide excision repair (NER ). a variant form of XP called XP-V is caused by a defect in the translesion DNA polymerase, Pol Ƞ

16. What happens at the cellular level in individuals with XP ? Ans - In the presence of defective NER, cells are limited in their ability to repair UV-induced DNA damage like thymine dimers. Following exposure to sunlight, the amount of DNA damage increases in the cells of individuals with XP, causing an increase in mutagenesis and cell death . In case of xp –v Cells possessing a mutant Pol Ƞ are hindered in their ability to bypass thymine dimers during replication and must resort to using another translesion polymerase for bypass to avoid a block in replication. Because Pol Ƞ correctly inserts As across from a thymine dimer, the use of other translesion polymerases may increase the frequency of mutagenesis.