DNA Damage and Repair

Deoxyribonucleic acid (DNA) is an important biological molecule. It is in all your cells. DNA is like your body’s instruction manual. It tells your cells how to do their everyday processes. 

Sometimes, DNA molecules are damaged by things such as ionizing radiation. Ionizing radiation is all around us and always has been. In fact, life on Earth has evolved in the presence of ionizing radiation. 

Over time, organisms evolved ways to repair damage to their DNA. Lucky for us, the repair process in human cells is very good at repairing DNA damage as it happens. 

How does DNA damage happen?

Most DNA damage from radiation involves chemical modification of the nucleotides. These modifications introduce chemical bonds that shouldn’t be there. Those chemical bonds warp the DNA’s shape. 

Cells have many different ways to repair this damage.The repair mechanism they use depends on how damaged the DNA sequence is.

How is damage to a nucleotide repaired?

Sometimes, radiation damages a single base on one strand of DNA. This can occur chemically when a hydroxyl (OH-) free radical reacts with a hydrogen atom and forms hydrogen peroxide (H₂O₂). It is fairly easy to repair damage like this if the complementary (or opposite) strand is undamaged. This is because the DNA sequence on the complementary strand can serve as a template during DNA replication. 

In this case, the cell uses a mechanism called Base Excision Repair (BER). This is the process of cutting out and replacing a single nucleotide. 

First, an enzyme called DNA glycosylase extracts the damaged part. Then an enzyme called AP endonuclease finds the gap in the sugar-phosphate backbone and removes neighbouring nucleotides. Next, DNA polymerase assembles the missing base. Finally, DNA ligase rejoins the sugar-phosphate backbone.

Sometimes a series of bases is damaged. In this case, the enzymes won’t just remove and replace a single base. Instead, they will cut out the entire damaged segment of the DNA strand and replace it. This process is called Nucleotide Excision Repair (NER). 

How are breaks in the sugar-phosphate backbone repaired?

High-energy ionizing radiation can blast through the sugar-phosphate backbone. This causes either single-strand breaks (SSB) or double-strand breaks (DSB). 

For SSBs, the first step is detection of the break. That’s the job of an enzyme called poly (ADP-ribose) polymerase (PARP). This enzyme signals other repair proteins to come to the break. Polynucleotide kinase (PNK) then cleans up the broken ends of the phosphate backbone, while DNA polymerase fills the gap until only a tiny gap remains. The gap is joined together again by DNA ligase. This process is called Single-Strand Break Repair (SSBR). 

Unlike SSB, DSBs can be extremely harmful to cells. They can interfere with DNA replication and protein synthesis. They can also lead to chromosomal rearrangements. This occurs when a piece of one chromosome becomes attached to another chromosome. Rearrangements like these are associated with some cancers, such as chronic myeloid leukemia. 

DSBs are repaired through one of two mechanisms: non-homologous end-joining (NHEJ) and homologous recombination (HR). 

NHEJ is the main way breaks caused by ionizing radiation are repaired. In NHEJ, a KU heterodimer binds to the broken ends of the DNA and helps the two strands line up properly. Then an endonuclease (Artemis) cleans up the break by removing neighbouring nucleotides. A Non-homologous end-joining factor (XLF)  prepares the link to be ligated (connected together) by an enzyme called DNA ligase IV. The ligase uses pieces of DNA near the break in the phosphate backbone to fill in the gap and rejoin the strands. 

In HR, the homologous (sister) chromosome is used as a template for the repair. A similar or identical portion of the DNA strand is resected (cut out). Then a strand takeover occurs. DSB creates a gap in the broken strand. During the takeover, the healthy part of the strand is replicated and used to fill this gap.

How are breaks in hydrogen bonds repaired?

Sometimes ionizing radiation can break the hydrogen bonds connecting base pairs. Luckily, the hydrogen bonds are not covalent. This means that electrons are not shared by the atoms. Because of this, these bonds can be broken and rejoined relatively easily.

You are exposed to small amounts of ionizing radiation every day. Ionizing radiation can damage DNA. But as you’ve just learned, your body has truly remarkable biochemical mechanisms to repair that damage!