Nuclear nucleotides
The story of nucleotides doesn’t end with the discovery of adenine, cytosine, thymine and guanine.
Although C, T, A and G make up the genetic code of DNA, there’s another base – Uracil, or U – that replaces thymine in RNA, a kind of molecular photocopy that’s made when genes are read. And we also now know that these bases can be chemically altered to extend the genetic code in some very interesting ways.
My personal favourite is methylcytosine. That’s regular cytosine in DNA with a little chemical flag attached to it known as a methyl group – one carbon atom and three hydrogens.
Methylcytosine plays an important role in that mysterious and much-misunderstood phenomenon of epigenetics: the ways in which cells mark out sections of DNA to help them remember which genes are meant to be switched on or off.
For a long time that was thought to be it. Then came along more modifications: formylcytosine, carboxylcytosine and methadenine.
They’re all quite rare in the genomes of complex organisms, and very poorly studied, but it’s looking like these unusual DNA modifications may play particularly important roles in embryonic development, helping to switch genes on at the right time and in the right place, to protect the genome from damage and disruption, or even to pass information on down to the next generation.
But while there is just a small handful of modified DNA bases that we know about, there are more than a hundred times more base modifications that affect the fate and biochemical function of RNA. These RNA modifications have recently been termed the ‘epitranscriptome’ – marking out a whole new field of genetics.
However, our adventure into the epitranscriptome start a bit further back in time – all the way back to the 1940s, when a young biochemist called Waldo Cohn, started work at the Oak Ridge National Laboratory in Tennessee.
Oak Ridge might sound like a nice, gentle place, but the researchers there were up to some pretty savage stuff – namely the Manhattan Project, the secret US government research programme that produced the first nuclear weapons, including the atomic bomb dropped on Hiroshima in 1945.
Cohn’s task in the project was to investigate the biological effects of the kinds of radioactive products that might be produced by atom bombs, known as fission products. So the first thing he needed to do was get hold of some different types of fission products to test.
But, as he soon discovered, the chemists working on the bomb were more focused on isolating weapons-grade plutonium than providing Cohn with specific purified radioactive molecules for his experiments.
There was only one thing for an enterprising, and possibly foolhardy, biochemist to do: he would have to make them himself.
Cohn spent years working on techniques to separate individual radioactive isotopes, eventually transferring into the Chemistry department at Oak Ridge when it became clear he was far more interested in purifying the chemicals than investigating their effects.
After the Second World War, and the ravages wrought by the bombs dropped at Hiroshima and Nagasaki, the focus at Oak Ridge changed to using their nuclear reactor for more benign purposes: making and distributing isotopes for scientific research.
Cohn was asked if he wanted to head up the production facility, but he chose to return to his biochemical research instead, moving to the newly formed biology division in 1947. He decided to investigate the turnover of nucleic acids within living organisms, finding out how long it took them to be created and destroyed – their half-lives, to take a metaphor from radioactivity.
To do this, he planned to inject an animal with radioactive phosphorous, isolate its nucleic acids, break them down into individual nucleotides and then see how radioactive each type of nucleotide had become. But, yet again, Cohn couldn’t keep his mind on the project at hand.
Describing this idea in an interview with the US Department of Energy in 1995, Cohn said:
“It's rather an elementary, stupid experiment, but it was one way of getting started. I never got around to doing those experiments, because I got more interested in the chemistry of separating the four nucleotides, which never [had] been done before in any reasonable way.”
The easily-distracted Cohn started using a technique called ion-exchange chromatography to separate out the four nucleotides in his samples. But then he noticed something strange: there were more than four!
Almost by accident, Cohn had discovered that there were other nucleotides in cells that nobody had even been aware of.
The first new nucleotide he found in 1951 was pseudouridine, a variation on uracil, which turns out to be the most abundant RNA modification in this epitranscriptome. In fact, it was so abundant that at one time it was considered to be the ‘fifth nucleotide.’
Since Cohn identified pseudouridine, the list of known modification has just kept on growing, with more than 150 documented so far.
Perhaps unsurprisingly, scientists have stopped giving them such memorable names, and they’re commonly referred to by a combination of numbers and letters indicating which nucleotide they’re derived from and which modifications they have. For example, a recent discovery was dubbed ms2ct6A. BORING.
Bring back the bird poo!
References and further reading:
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