December 6, 2021

I, Science

The science magazine of Imperial College

Our DNA endures a constant bombardment of damaging agents, so how does it cope? ...


DNA and the concept of genes fascinated me from the word go. To me, studying life from the perspective of DNA is like standing at the centre of the universe and looking out across the complexity that has been generated by the forces of nature. DNA is the code, the computer, the brain. Kids learn in school that DNA is made of a sugar-phosphate backbone, with the 4 bases A, T, C and G at the center of the helix. They learn that humans have 46 chromosomes, and that DNA contains genes.

But DNA is so much more than the static helical molecule you have been imagining. DNA isn’t just a chemical, it’s alive. It’s dynamic and changing; it responds to the environment and meets challenges in the face of danger.

The field of epigenetics has exploded in the last 15 years. Epigenetics is the study of the way in which DNA develops and responds to the environment. The way in which DNA folds itself in the nucleus (is it compact like a sausage or sparse like a hair ball?), the chemical groups that are stuck on the DNA (for example, methyl and acetyl chemical groups on the DNA affect gene expression) and the way DNA is replicated for growth or separated during cell division – these are epigenetic processes.

But more than simply existing and functioning, DNA must respond to the absolute bombardment from damaging agents that it endures on a daily basis. Whether these agents be UV light from sunshine, toxic substances from smoking, or just the intrinsic chemical environment of a cell, the nucleus must manage its damaged DNA and ensure that it is repaired. Every day, the cells in your body are working hard to stifle and repair DNA damage.

If DNA damage is not repaired, the genome can fragment and fray, genes can be lost or gained or swapped. Whole chromosomes can become jumbled. A cell must make sure this does not occur. Unrepaired DNA damage can lead to genetic instability, tumorigenesis and cancer.

It’s amazing the way a cell can recognize a single miniscule DNA damage event, and cause the entire cell to stop what it is doing and focus on the repair of that break. For my PhD, I am focusing primarily on the repair of DNA double stranded breaks. I have chosen to study this in budding yeast. Yeast might sound mundane; but I promise you, they’re great.

For starters, they’re genetically extremely similar to humans. Secondly, because of a quirk of their biology, I am able to insert a single double stranded break into the DNA of yeast cells myself by simply changing the sugar solution they’re growing in. Then, I can study how the DNA responds to the double stranded break that I have inserted.

By creating a double stranded break and then taking samples of cells, say, every two hours, I can analyze the DNA repair as it occurs. I do this by extracting the DNA from my samples, amplifying the DNA across the break site (by PCR, or Polymerase Chain Reaction) and then putting the DNA into wells in a specialized gel. I apply an electric field to the gel, and because the DNA is negatively charged I can drag the DNA through the gel thus separating DNA fragments according to size (a process called gel electrophoresis). When I look at the bands of DNA that are present at my different time points, I can see which different repair intermediates are present. I can see how long the DNA took to repair.

If I repeat this experiment but after mutating specific genes in the yeast before causing the double strand break, I can start to uncover key genes that are required for the DNA repair. For example, if I mutated a gene and found that repair intermediates no longer appeared when I ran my gel, I would know that the gene I had mutated may well be involved in the repair pathway.

A particular set of genes I am interested in are those that code for the SMC proteins; the Structural Maintenance of Chromsomes proteins. These proteins are beautiful triangle-shaped molecular machines. Their triangle shape is thought to embrace the DNA in specific ways; looping it and stapling it in place. Perhaps the SMC proteins can even slide along the DNA, travelling from one place to another. One SMC protein complex in particular, the Smc5-Smc6 complex (a boring name for a super cool protein complex), is thought to play a key role in repair of DNA.

Science allows the curious, the passionate and (quite frankly) the obsessed, to explore an unimaginable world of complexity inside the nucleus of each of our cells. If we are ever to understand life on Earth and the progression of diseases such as cancer, we must keep asking questions, experimenting, discussing and pushing boundaries, and who knows, maybe one day we’ll have a breakthrough.