DNA: You’re Doing It Right

Or: wrapping up salmon semen

When I started out, I justified this blog’s creation by imagining that I would try to make the process of science a bit clearer. This would involve describing what actually happens in that murky void between some clever sod having an idea and the media wildly exaggerating them. In my head, this was inevitably accompanied by self-aggrandising metaphors: imagine beacons lighting the way for lost souls desperate for enlightenment and you’re in the right ball park. All I appear to have produced, however, are a few introspective musings, perhaps better described as sputtering gas flames when it comes to how illuminating and insightful they are. To remedy this, I thought it would be useful to explain what I am doing in Grenoble, as this might just constitute something worth reading.

Ludicrous dreams and badly-thought-out metaphors

My position at the Institute Laue-Langevin (ILL) is a stagiaire – which I am reliably informed is equivalent to an intern, except for the fact that in France they must legally draw a salary. Thus France gains a green tick in my Big Book of Everything and, as my supervisor quipped, “score one for socialism.”

I have a long-suffering  post-graduate on an Erasmus Mundus masters course looking after me and for the past three weeks, her glorious role has consisted of patiently answering my simple questions and coping with my constant lack of understanding. Eventually though, the mists parted and the gist of the experiment slowly permeated into my consciousness.

The institute has a nuclear reactor which produces neutrons, particles that, along with protons, lie at the heart of atoms. These can be focused into beams that are used to investigate certain properties of materials. The principle of this is relatively straightforward: by looking (closely, with a really big lens, if you’d like a nice idea of what isn’t happening) at how the neutrons bounce off the  nuclei of a material, you can infer a lot about its structure and how it behaves. The actual process involves complex quantum-mechanical treatments of the neutron  and target but, thankfully, that’s a story for another day.

A different sort of Neutron

My supervisor, the masters student and myself are looking into DNA (hence the excitement about it in my last post) and its different forms. Although still essentially the same ol’ double helix, it can exist as  A, B, and Z-DNA. The first two are identical aside from the former being slightly more compact, whereas the Z form’s “ladder” twists in a different direction. The plan is to put some samples in front of a beam of neutrons and see whether we can force the molecules to change between the forms by exerting different pressures.

My first reaction was slightly-less-than-perceptive: “This is pretty fucking cool.” We’re investigating the behaviour of the molecule that codes for every single bit of our bodies. This collection of nucleotides is the reason that life is still hanging on here about four billion years after it started out and what allows you to spend about half of your time awake looking at what other people are doing on the internet; it’s pretty fundamental stuff.

Salmon sperm is a very plentiful source of DNA, so large quantities of this are necessary for the experiment (hence the admittedly attention-seeking subtitle) and it all must be aligned in the same way in order for the neutron scattering to reveal anything useful. It is then necessary to catch these DNA threads on a rotating cylinder in order to fix a large amount of it. While being an interesting mechanical process in itself, it literally takes hours to complete and must be meticulously observed in order for the samples to produce results that we can analyse. When sharing my woes with a friend at the ILL, he nodded sagely,  remarking that about 70% of his time was spent cleaning his apparatus. I clearly have a long way to go with understanding the life of a chemist.

Thanks guys!

After a few weeks of this, my enthusiasm has faltered slightly, especially due to my incompetence when it comes to any manual tasks. The noticeable absence of equations from the work also makes me slightly uneasy, as I’ve developed a habit of fleeing to numbers and data whenever I’m uncertain about something. This is tricky when your day’s work involves trying to catch minuscule white threads with a glass rod while swearing as loudly as possible.

However, we have been granted some elusive beam time, which means an end to the production of DNA samples and experimenting with neutron diffraction for up to 48 hours. Expect posts in the coming weeks to contain a hint feverish excitement with tinges of narcolepsy-induced bitterness.

More information on neutron scattering (courtesy of the Institute of Physics) at http://www.iop.org/publications/iop/2011/file_47455.pdf


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