DNA Repair I

Base Excision Repair (BER)

The basic steps of the BER pathway are:
1. Distortion recognition,
2. Base excision,
3. AP-site incision,
4. DNA repair synthesis,
5. DNA ligation.

DNA bases that have been modified by the addition or loss of a small chemical group as described above are repaired by the BER pathway (see video above). The BER-path begins with the removal of a distorted base by an enzyme called DNA glycosylase.

They remove the damaged nitrogenous base while leaving the sugar-phosphate backbone intact, thus creating an apurinic/apyrimidinic site, commonly referred to as an AP site.

Then, an enzyme specialized in synthesizing DNA, called a DNA polymerase, will first remove the now baseless sugar phosphate and then insert the correct nucleotide (C or G) to the complementary strand-base.

The final step in the BER pathway is to tie the DNA strands on both sides of the nick caused by the repair. The sugars that carry the DNA bases are linked together by phosphate groups. The enzyme DNA ligase is sealing the nick again by creating a phosphodiester bond between them.

A phosphodiester bond is a covalent chemical bond that holds together the polynucleotide chains of RNA and DNA by joining a carbon in the pentose sugar of one nucleotide to a carbon in the pentose sugar of the adjacent nucleotide.

Nucleotide Excision Repair (NER)

DNA damage that significantly distorts the double-stranded structure of DNA, is subject to repair by the nucleotide excision repair (NER) pathway. UV light in sunshine can disturb DNA by forming “photoproducts”.

UV radiation excites many types of molecules, causing them to react with each other and with DNA. UV light can catalyze the formation of chemical bonds between adjacent thymine (T) and cytosine (C) bases. These cross-links distort the DNA’s helix structure, and block DNA replication.

DNA distortion is also caused by organic molecules found in mold-contaminated peanuts, smoke, and soot. Ingestion or inhalation of these and similar compounds activates the body’s detoxification systems, which convert hydrophobic molecules into water-soluble forms for removal.

However, their intermediate forms are very reactive with DNA purines, and form DNA base additions. They can impact guanine and adenine, block DNA replication, cause mutations and deletions of large segments of DNA, and cell death.

The mechanism of NER, involving some 30 proteins, is more complex than that of BER, but the basic principles are similar.

How can a multi-protein complex detect so many different types of DNA distortion?

The answer is that the DNA damage must:

1. distort the normal double-stranded structure of DNA, and/or
2. block transcription by RNA polymerase. Unusual twists in double-stranded DNA are recognized by the NER damage-recognition multi-protein complex. They are also used when RNA polymerase stalls at a distorted DNA base.

The double-stranded DNA adjacent to the distortion is unwound by a DNA unwinding enzyme called Helicase. The distorted strand is then cleaved a few nucleotides after the damage, and about 25 nucleotides before it, by specific endo-nucleases associated with the NER protein complex.

Then, the distorted DNA segment is displaced by DNA polymerase and associated proteins, and a corresponding repair patch is synthesized.

DNA ligase joins the newly synthesized piece of DNA to the pre-existing strand.

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