DNA replication, also known as semi-conservative replication, is the process by which DNA is essentially doubled. It is an important process that takes place within the dividing cell.
In this article, we shall look briefly at the structure of DNA, at the precise steps involved in replicating DNA (initiation, elongation and termination), and the clinical consequences that can occur when this goes wrong.
DNA is made up of millions of nucleotides. These are molecules composed of a deoxyribose sugar, with a phosphate and a base (or nucleobase) attached to it. These nucleotides are attached to each other in strands via phosphodiester bonds to form a ‘sugar-phosphate backbone’. The bond formed is between the third carbon atom on the deoxyribose sugar of one nucleotide (henceforth known as the 3’) and the fifth carbon atom of another sugar on the next nucleotide (known as the 5’).
N.B: 3′ is pronounced ‘three prime’ and 5′ is pronounced ‘five prime’.
There are two strands running in opposite or antiparallel directions to each other. These are attached to each other throughout the length of the strand through the bases on each nucleotide. There are 4 different bases associated with DNA; Cytosine, Guanine, Adenine, and Thymine. In normal DNA strands, Cytosine binds to Guanine, and Adenine binds to Thymine. The two strands together form a double helix.
Stages of DNA replication
DNA replication can be thought of in three stages; Initiation, Elongation, Termination
DNA synthesis is initiated at particular points within the DNA strand known as ‘origins’, which are specific coding regions. These origins are targeted by initiator proteins, which go on to recruit more proteins that help aid the replication process, forming a replication complex around the DNA origin. There are multiple origin sites, and when replication of DNA begins, these sites are referred to as replication forks.
Within the replication complex is the enzyme DNA Helicase, which unwinds the double helix and exposes each of the two strands, so that they can be used as a template for replication. It does this by hydrolysing the ATP used to form the bonds between the nucleobases, therefore breaking the bond holding the two strands together.
DNA Primase is another enzyme that is important in DNA replication. It synthesises a small RNA primer, which acts as a ‘kick-starter’ for DNA Polymerase. DNA Polymerase is the enzyme that is ultimately responsible for the creation and expansion of the new strands of DNA.
Once the DNA Polymerase has attached to the original, unzipped two strands of DNA (i.e. the template strands), it is able to start synthesising the new DNA to match the templates. It is essential to note that DNA polymerase is only able to extend the primer by adding free nucleotides to the 3’ end.
One of the templates is read in a 3’ to 5’ direction, which means that the new strand will be formed in a 5’ to 3’ direction. This newly formed strand is referred to as the Leading Strand. Along this strand, DNA Primase only needs to synthesise an RNA primer once, at the beginning, to initiate DNA Polymerase. This is because DNA Polymerase is able to extend the new DNA strand by reading the template 3′ to 5′, synthesising in a 5′ to 3′ direction as noted above.
However, the other template strand (the lagging strand) is antiparallel, and is therefore read in a 5’ to 3’ direction. Continuous DNA synthesis, as in the leading strand, would need to be in the 3′ to 5′ direction, which is impossible as we cannot add bases to the 5′ end. Instead, as the helix unwinds, RNA primers are added to the newly exposed bases on the lagging strand and DNA synthesis occurs in fragments, but still in the 5′ to 3′ direction as before. These fragments are known as Okazaki fragments.
The process of expanding the new DNA strands continues until there is either no more DNA template left to replicate (i.e. at the end of the chromosome), or two replication forks meet and subsequently terminate. The meeting of two replication forks is not regulated and happens randomly along the course of the chromosome.
Once DNA synthesis has finished, it is important that the newly synthesised strands are bound and stabilized. With regards to the lagging strand, two enzymes are needed to achieve this; RNAase H removes the RNA primer that is at the beginning of each Okazaki fragment, and DNA Ligase joins fragments together to create one complete strand.
Clinical Relevance – Sickle Cell Anaemia
Sickle Cell Anaemia is an autosomal recessive condition which is caused by a single base substitution, in which only one base is changed for another. In some cases this can result in a ‘silent mutation’ in which the overall gene is not affected, however in diseases such as Sickle Cell Anaemia it results in the strand coding for a different protein.
In this case an adenine base is swapped for a thymine base in one of the genes coding for haemoglobin; this results in glutamic acid being replaced by valine. When this is being transcribed into a polypeptide chain the properties it possesses are radically changed as glutamic acid is hydrophilic, whereas valine is hydrophobic. This hydrophobic region results in haemoglobin having an abnormal structure that can cause blockages of capillaries leading to ischaemia and potentially necrosis of tissues and organs – this is known as a vaso-occlusive crisis.
These crises are typically managed with a variety of pain medication, including opioids and NSAIDs depending on the severity. Red blood cell transfusions may be required in emergencies, for example if the blockage occurs in the lungs.