1) INTRODUCTION TO DNA REPAIR
By the term DNA REPAIR we refer to the process by which a cell identifies and corrects damage to DNA molecule that encodes its genome. In human cells both metabolic factors and environmental factors such as UV light and radiations, can effect DNA molecule and can damage it, and these injuries could be structural or may cause elimination of cell's ability to transcribe the gene. Some injuries may cause harmful mutations in the cell's genome.
So, DNA repair is a process which is constantly active as it responds to the damages in DNA structure, whenever the normal process fails in its functioning.
The rate of DNA repair is dependent on many factors which include cell type, age of the cell, and the extracellular environment. 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:
1) An irreversible state of dormancy, known as senescence.
2) cell suicide, also known as apoptosis or programmed cell death
3) Unregulated cell division, which can lead to the formation of a tumor that is cancerous.
DNA damage due to environmental factors and normal metabolic process inside the cell occurs at the rate of 1000 to1000000 molecular lesions per cell per day. The majority of DNA damage affects the primary structure of double helix i.e. bases themselves are chemically modified. These modifications can disrupt the molecule's regular helical structure by introducing non-native chemical bond that do not fit in the standard double helix. Unlike protein or RNA, DNA usually lacks tertiary structure and therefore damage or disturbance does not occur at that level. However, DNA is super coiled and wound around histone proteins and both superstructures affect the DNA damage.
SOURCE OF DAMAGE:
DNA damage can be subdivided into two main types:
a) Endogenous damage
b) Exogenous damage
These are those damages which attack by reactive oxygen species produced by normal metabolic by-products, especially the process of oxidative de amination.
These damages include replication error.
Exogenous damages are caused due to external agents such as:
1) UV rays from sun.
2) X-RAYS, GAMA RAYS.
3) Hydrolysis or thermal disruption.
4) Human made mutagenic chemicals.
5) Viruses etc.
The replication of damaged DNA before cell division can lead to the incorporation of wrong bases opposite damaged ones. Daughter cell that carry these wrong bases carry mutations from which original DNA is uncover able
MECHANISM OF DNA REPAIR:
There are three mechanisms for DNA REPAIR.
1) BASE EXCISION
2) NUCLEOTIDE EXCISION
3) MISMATCH REPAIR
It is a cellular mechanism through which we can repair damaged DNA throughout a cell cycle. It is basically responsible for removing small, non-helix distorting base lesion from genome. Base excision repair mechanism is important as it removes those damaged base that could cause mutations by mis-pairing and can even lead to break in DNA during the process of replication.
Base excision repair mechanism is short formed as BER.
BER is initiated by DNA glycosylases. Which recognise and remove specific damaged bases, through forming AP sites (abasic site) . AP endonuclease removes the AP sites and its neighbouring nucleotides. The gap is filled by DNA polymerase1 and DNA ligase. The resulting single strand break can then processed by short patch or long patch of BER.
1) NUCLEOTIDE EXCISION
It is one of the methods of DNA repair. DNA molecules require repairs constantly as the damages occur to bases from large verities of sources such as chemicals, UV light from sun etc. It is an important method of repair through which cell can prevent unwanted mutations by removing the vast majority of UV-induced DNA damage which is mostly in the form of thymine dimers and 6-4 photoproducts. The importance of this mechanism is evidenced by severe human disease that result from in born genetic mutation of NER proteins including xeroderma pigmentosum and cockayne's syndrome.
As BER machinery can recognize specific lesion in DNA, NER can correct only damaged bases that can be removed by a specific glycosylase, the NER enzymes recognise bulky distortion in shape of DNA double helix. Recognition of these distortion leads to removal of short single stranded DNA segment that include the lesion, creating a single strand gap in DNA. This is filled in by DNA polymerase, which uses the undamaged strand as a template. NER can be divided into two sub pathways that differ in their recognition of helix distorting DNA damage.
1) GLOBAL GENOMIC NER
2) TRANCRIPTION COUPLED NER