DNA damage

[SUMAN-SAJAN]

DNA damage
There are many agents, both natural and artificial, that cause DNA damage, resulting in many types of DNA damage that affect cells in different ways





Agents that Damage DNA
• Certain wavelengths of radiation
• ionizing radiation such as gamma rays and x-rays
• ultraviolet rays, especially the UV-C rays (~260 nm) that are absorbed strongly by DNA but also the longer-wavelength UV-B that penetrates the ozone shield.
• Highly-reactive oxygen radicals produced during normal cellular respiration as well as by other biochemical pathways.
• Chemicals in the environment
• many hydrocarbons, including some found in cigarette smoke.





Types of DNA Damage

1. All four of the bases in DNA (A, T, C, G) can be covalently modified at various positions.
One of the most frequent is the loss of an amino groupin a C being converted to a U.
2.Mismatches of the normal bases because of a failure of proofreading during DNA replication.
Common example: incorporation of the pyrimidine U (normally found only in RNA) instead of T.
3. Breaks in the backbone.
Can be limited to one of the two strands (a single-stranded break, SSB) or
on both strands (a double-stranded break (DSB).
Ionizing radiation is a frequent cause, but some chemicals produce breaks as well.
4.Crosslinks Covalent linkages can be formed between bases
• on the same DNA strand ("intrastrand") or
• on the opposite strand ("interstrand").





DNA Repair
Any damage of DNA has to be repaired so that the integrity of genetic material be maintained.
The basic mechanism of DNA repair can be summarized as following.
• The damage portion of the genome is recognized, then removed by DNA repair enzymes(nucleases),resulting formation of gap in the DNA chain.
• DNA polymerase fill this gap.
• Finally, the ligase seals the nick and completes the repair.





Types of DNA repair
A. Direct Reversal of Base Damage
B. Excision Repair
• Base Excision Repair (BER)
• Nucleotide Excision Repair (NER)
• Mismatch Repair (MMR)





Direct Reversal of Base Damage
The most frequent cause of point mutations in humans is the spontaneous addition of a methyl group (CH3-) (an example of alkylation) to Cs followed by deamination to a T. Fortunately, most of these changes are repaired by enzymes, called glycosylases, that remove the mismatched T restoring the correct C. This is done without the need to break the DNA backbone.





Base Excision Repair (BER)
DNA's bases may be modified by deamination or alkylation. The position of the modified (damaged) base is called the "abasic site" or "AP site". In E.coli, the DNA glycosylase can recognize the AP site and remove its base. Then, the AP endonuclease removes the AP site and neighboring nucleotides. The gap is filled by DNA polymerase I and DNA ligase.





Nucleotide Excision Repair (NER)
NER differs from BER in several ways.
• It uses different enzymes.
• Even though there may be only a single "bad" base to correct, its nucleotide is removed along with many other adjacent nucleotides; that is, NER removes a large "patch" around the damage.

proteins UvrA, UvrB, and UvrC are involved in removing the damaged nucleotides (e.g., the dimer induced by UV light). The gap is then filled by DNA polymerase I and DNA ligase. In yeast, the proteins similar to Uvr's are named RADxx ("RAD" stands for "radiation"), such as RAD3, RAD10. etc





Photoreactivation
Light repair
phr gene - codes for deoxyribodipyrimidine photolyase that, with cofactor folic acid, binds in dark to T dimer. When light shines on cell, folic acid absorbs the light and uses the energy to break bond of T dimer; photolyase then falls off DNA.





Mismatch Repair (MMR)
Mismatch repair deals with correcting mismatches of the normal bases; that is, failures to maintain normal Watson-Crick base pairing(A•T, C•G)
It can enlist the aid of enzymes involved in both base-excision repair (BER) and nucleotide-excision repair (NER) as well as using enzymes specialized for this function





To repair mismatched bases, the system has to know which base is the correct one. In E. coli, this is achieved by a special methylase called the "Dam methylase", which can methylate all adenines that occur within (5')GATC sequences. Immediately after DNA replication, the template strand has been methylated, but the newly synthesized strand is not methylated yet. Thus, the template strand and the new strand can be distinguished