IntroductionDNA repair refers to a collection of processes by which acell identifies and corrects damage to the DNAmolecules that encode its genome.Sources of damage:1-loss of a bases resulting in apurinic/apyrimidinic (AP)sites (abasic sites).2-base modifications, such as alkylations ordeamidations which converts cytosine, adenine andguanine to uracil.
3-Replication errors and base conversions can generatemismatch nucleotide pairs4-Failures in normal DNA metabolism bytopoisomerases and nuclease or ionizing radiation cangenerate single-strand and double-strand breaks .5-Photodamage by uv light can generate pyrimidinedimers, such cyclobutane pyrimidine dimers (CPDs)Chemical agents and reactive oxygen species (ROS) canmodify bases .
N.Bs:Majority of DNA damage affect the 1ry structure ofdouble helix .DNA repair is dependent on many factors : -cell type - age of the cell -extracellular environmentA cell that has accumulated a large amount of DNAdamage can enter one of three possible states:1-an irreversible state of dormancy, known as senescence2-cell suicide, also known as apoptosis3-unregulated cell division, which can lead to cancer
DNA Damage & Mutation DAMAGE MUTATION1-Damages are physical 1-A mutation is a change in theabnormalities in the DNA base sequence of the DNA.2-DNA damages can be 2-A mutation cannot berecognized by recognized by enzymes onceenzymes, and, thus, they can the base change is present inbe correctly repaired. both DNA3-If a cell retains DNA strands, and, thus, a mutationdamage, transcription of a cannot be repaired.gene can be 3-Mutations can causeprevented, and, thus, translat alterations in proteinion into a protein will also be function and regulation.blocked Mutations are replicated when the cell replicates
REPAIR MECHANISMS In addition to DNA polymerase 3’à5’ exonuclease(theDNA Pol III has proofreading capabilities thatcorrect replication mistakes by means ofexonuclease activity working 3->5) ..Mammaliancells utilize TWO major DNA repair pathways: - single strand damage -db strand breaks Reverse Excision Non Homo Homo BER NER MMR
A-SS damage : 1- reversal ( direct reversal ) : These mechanisms do not require a template, since thetypes of damage they counteract can occur in only oneof the four bases.(this type repaired without removingabase or nucleotide)E.X:1-The formation of pyrimidine dimers upon irradiationwith UV light results in an abnormal covalent bondbetween adjacent pyrimidine bases. Thephotoreactivation process directly reverses thisdamage by the action of the enzyme photolyase.2- Another type of damage, methylation of guaninebases, is directly reversed by the protein methylguanine methyl transferase (MGMT).
2-Excision : In which the damaged base or bases areremoved and then replaced with the correct ones . a-Base excision repair :DNAs bases may be modified by deamination oralkylation. the DNA glycosylase can recognize thedamaged site and remove its base forming AP site (Apurinic/ Apyrimidinic). Then, the AP endonucleaseremoves the AP site and neighboring nucleotides. Thegap is filled by DNA polymerase I and DNA ligase.N.B: -Each DNA glycosylase is generally specific for onetype of lesion ._ Humans have at least four types glycosylase withdifferent specifictices .
B- Nucleotide excision repair :NER differs from BER in several ways:-It uses different enzymes.-Even though there may be only a single "bad" base tocorrect, its nucleotide is removed along with manyother adjacent nucleotides; that is, NER removes alarge "patch" around the damage .- In NER a multisubunit enzyme hydrolyzes twophosphodiester bonds one on either side of thedistorsion caused by lesion ( in human it hydrolyzesthe 6th bond on 3 side & the 22 bond on the 5 endproducing a fragment of 27-29 nucleotides ) resultingin gap filled by DNA polymerase1 & finally DNA ligaseseals the nick .
C- Mismatch repair : To repair mismatched bases, the system has to knowwhich base is the correct one. In E. coli, this isachieved by a special methylase called the "Dammethylase", which can methylate all adenines thatoccur within (5)GATC sequences. Immediately afterDNA replication, the template strand has beenmethylated, but the newly synthesized strand is notmethylated yet. Thus, the template strand and thenew strand can be distinguished.
B- Db strand damage : There are two mechanisms bywhich the cell attempts to repair a complete break in aDNA molecule: 1-Direct joining: of the broken ends. This requiresproteins that recognize and bind to the exposed endsand bring them together for ligating. They wouldprefer to see some complementary nucleotides but canproceed without them so this type of joining is alsocalled Nonhomologous End-Joining (NHEJ).Errors in direct joining may be a cause of the varioustranslocations that are associated with cancers.
2-Homologous Recombination:. Here the broken ends are repaired using theinformation on the intact sister chromatid (availablein G2 after chromosome duplication), or on thehomologous chromosome.Two primary models:1-DSBR pathway (sometimes called the double Hollidayjunction model)2- the synthesis-dependent strand annealing (SDSA)pathway.
N.Bs:Whether homologous recombination or NHEJ is used tothe repair double-strand breaks is largely determined byphase of cell cycle.Homologous recombination repairs DNA before the cellenters mitosis (M phase). It occurs during and shortly afterDNA replication, in the S and G2 phases of the cellcycle, when sister chromatids are more easily available.While NHEJ is predominant in the G1 phase of the cellcycle, when the cell is growing but not yet ready to divide .Cyclin-dependent kinases (CDKs), which modify the activityof other proteins by adding phosphate groups to (thatis, phosphorylating) them, are important regulators ofhomologous recombination in eukaryotes.
DNA damage check points The global response to damage is an act directedtoward the cells own preservation and triggersmultiple pathways of macromolecular repair, lesionbypass, tolerance, or apoptosis (&the common featuresof global response are induction of multiple genes, cellcycle arrest, and inhibition of cell division ).-After DNA damage, cell cycle checkpoints are activatedCheckpoint activation pauses the cell cycle and givesthe cell time to repair the damage before continuing todivide .
- DNA damage checkpoints occur at the G1/S and G2/Mboundaries. Checkpoint activation is controlled by twomaster kinases, ATM and ATR. ATM responds to DNAdouble-strand breaks and disruptions in chromatinstructure, whereas ATR primarily responds to stalledreplication forks. These kinases phosphorylatedownstream targets in a signal transduction cascade,eventually leading to cell cycle arrest.P53 is an important downstream target of ATM and -ATR, as it is required for inducing apoptosis followingDNA damage. At the G1/S checkpoint, p53 functionsby deactivating the CDK2/cyclin E complex.Similarly, p21 mediates the G2/M checkpoint bydeactivating the CDK1/cyclin B complex .
-To get an idea of just the first layer of complexity inthese systems, lets assume there is some damage toDNA, such as a single-strand break. Here is the processthat would happen:1-DNA damage is detected by sensor proteins: PARactivation this occurs within seconds of damagedetection. PARP 1 and PARP2 are activated by singlestrand breaks and double strand breaks.2-ATM activation (ATM and ATR kinases as seem tosend out the distress signal to recruit the right DNArepair proteins. They do this by phosphorylatingmediator proteins.) 3-MDCI recruitment (This induces a signaling cascade.)
4-RNF8 recruitment5-RNFi68 recruitment6-BRCA1 and 53BP1 recruitment(Numbers 4-6 are particular proteins that are recruitedin a very specific order to do specific activities to repaira single strand break.)7-Based on certain factors such as timing and order ofrecruitment, any one of these results may happen: thecell cycle could be delayed, DNA could be repaired byreplacing nucleotide bases, differentiation may behalted (senescence), cell death(apoptosis), transcription and splicing controls, ormetabolic regulation.
Hereditary DNA repair disordersDefects in the NER mechanism are responsible forseveral genetic disorders, including:Xeroderma pigmentosum: hypersensitivity tosunlight/UV, resulting in increased skin cancerincidence and premature agingCockayne syndrome: hypersensitivity to UV andchemical agentsTrichothiodystrophy: sensitive skin, brittle hair and nailsMental retardation often accompanies the latter twodisorders, suggesting increased vulnerability ofdevelopmental neurons.
Other DNA repair disorders include:Werners syndrome: premature aging and retardedgrowthBlooms syndrome: sunlight hypersensitivity, highincidence of malignancies (especially leukemias).Ataxia telangiectasia: sensitivity to ionizing radiationand some chemical agents . firstname.lastname@example.org