Getting your DNA in a twist

I have a good friend who has just emerged triumphant from a run-in with bowel cancer – she’s in complete remission! Almost as wonderful is the fact that colliding with cancer has converted her from a genuine non-scientist to one who devours biology like fish and chip suppers. Spotting a recent volley of media items about four-stranded ‘quadruple helix’ DNA in human cells, she was on Twitter in a flash: “Does this mean that people with cancer have lots more quadruplex DNA than normal?” As she knows I can’t stand the Tweet cult she was probably amazed to get a reply: short answer: “No.”

But as ever in science, there’s a long(er) response. So, if you’re interested in the gyrations and gymnastics of which your genetic code is capable, read on …

The DNA double helix

The DNA double helix

Beautiful DNA

As you know, DNA comes as a double helix – a 2-chain spiral of small units (called nucleotides) that stick together (the units contain bases, so they’re ‘base-paired’). The oft-reproduced double helix image is beautiful because it’s a repetitive structure and you can easily see how it can be ‘unzipped’ so that each half can be used as a template to make a copy and regions can be ‘read’ to make RNA and proteins – though it was really designed to enable biologists to make endless unzipping jokes about genes and jeans.

The two DNA molecules of the helix stick together because of a balance between three forces: (1) weak electronic attraction between some atoms in the bases (called hydrogen bonds), (2) a sort of glueyness between the bases because their chemical structure means they don’t like water much and they’d rather snuggle up together, and (3) a repulsion between the chains because of the repeated phosphate groups all the way along the backbone (these carry an electric charge and likes repel, as we know).

Ugly DNA

But with all these attractions and repulsions you might think there would be lots of ways nucleic acids could get tangled up with each other – and there is. So the common form of double helix (the beautiful shape) is B-DNA but there’s also A-DNA, C-DNA and Z-DNA. If you just change the conditions a bit (pinch of salt or whatever) you can tweak the interactions so bits of the bases that don’t interact in B-DNA will do so to give a slightly different shape (usually a bit distorted – ugly). As you can see from the structure, Z-DNA is more Homer Simpson than Watson and Crick.

B- and Z-DNA

B- and Z-DNA

B-DNA and Z-DNA

We can’t reproduce the environment of DNA in the nucleus so we don’t really have a clue but the betting is that short bits of DNA jink in and out of these odd structural formations – just as part of the continuous flexing of the molecules. There’s also a couple of other things that can happen that have been known for a long time – again just dependent on the precise conditions in which a piece of DNA finds itself.

Sexy modelling

The first is a variant on the hydrogen bonds that form between bases. One way to think of this is to imagine two circles of five people, each ring holding hands and facing outwards. Each person is an atom in the bases of DNA. Let’s think of base pairing as the two nearest in the circles getting close enough to kiss. That’s one hydrogen bond. But, of course, the two other pairs on either side will now be quite close: if one of them also manages to kiss (tongues may be used) now we have two hydrogen bonds – which is what holds the bases A and T together. But suppose that the pair on the other side (who must also be quite close with all this adjacent necking going on) decide they really fancy joining in and are so excited that they twist the circle out of shape to do so. That this can happen has been known for years (it’s called Hoogsteen base pairing after the voyeur what spotted it) and when it does it can distort the helix enough for a third DNA strand to wrap round the original two – so you get triple-stranded DNA.

A sexual need

Similarly, if you tweak the conditions you can get four strands of DNA to come together and indeed we’ve known for yonks that happens naturally during recombination (that’s when genetic material gets swapped between Mum and Dad chromosomes – the reason for sex). When that happens you can think of four DNA strands forming a cross, each quadrant contains DNA from one strand of a chromosome, base-paired to that in the next quadrant – which is how bits get swapped around.

Non-sexual hugging?

So there’s nothing new about odd DNA shapes but what has made the news is that for the first time, rather than looking at what can be made to happen in a test tube, Shankar Balasubramanian and his pals have looked in whole cells. To do this they made an antibody that sticks only to ‘quadruple helix’ DNA structures – G-quadruplexes. The upshot is that they detected quadruplexes scattered throughout chromosomes and they see more in cells that are rapidly dividing than in ones that are just sitting there (they looked in some cancer cells in culture that do divide quite rapidly – but bear in mind that in tumours cells aren’t diving all that fast). So the inference is that they might form as part of DNA replication and, if you can target them by their antibody, maybe you could do something similar with a drug that would stop cells dividing. And if you could target that to cancer cells you could stop them in their tracks.

And the catch …

Simple. But there are some problems. It’s possible the antibody helps the quadruplexes to form – so it could even be a cunning artifact. But if we assume it isn’t – then we come face to face with a really big problem. There are zillions of ways you can kill cancer cells. The difficulty is that there isn’t one that selects cancer cells from normals. It may be possible (though it’s not evident how) to target quadruplexes and block cell division – but there are lots of cells that we need to divide rapidly just to keep us going – and, if quadruplexes are real, presumably they have ’em. So non-specific killing is probably not a good idea. Twas ever thus.

References

Biffi, G., Tannahill, D., McCafferty, J. and Balasubramanian, S. (2013). Quantitative visualization of DNA G-quadruplex structures in human cells. Nature Chemistry published online: 20 January 2013 | doi: 10.1038/nchem.1548

http://www.cam.ac.uk/research/news/four-stranded-quadruple-helix-dna-structure-proven-to-exist-in-human-cells/

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The Creation of Cancer

Where do cancers come from?’ One of those dreaded childish questions – so best to get your thinking in first, rather than trying to answer on the hoof in the face of that unblinking stare of expectation. In the beginning, as you might say, we need a hand-wavy word on how DNA ‘makes proteins’, why they’re important (‘Proteins R Us’, in short) and what can go wrong with them.

DNA double-helix

The double helix of DNA

In 1953 Watson and Crick worked out the structure of DNA. It holds, of course, the secret of life and you might observe that it has the appropriate shape of a spiral staircase to nowhere. The ‘genetic code’ is the order of thousands of small bits that are linked together to make the very long molecules of DNA. These bits contain smaller bits called bases – four of them (A, C, G and T) – and they’re firmly stuck together so that each DNA molecule is pretty stable. In addition, bases in one DNA can stick to those in a second strand – hence the double-helix.

Protein

DNA encodes proteins

The essence of life is the transformation of the genetic code into the corresponding sequence of the building blocks that make proteins. The blocks are amino acids, stitched together to make proteins in much the same way as DNA is built from its base-containing units. There are 20 different types that can be glued together in any order, a typical protein containing a thousand amino acids. They tell the protein how to fold up into its final shape – a 3D structure unique for each protein. Many proteins are blobs (like balls of string) but, as you’d guess given that they do everything, they come in all shapes and sizes—cables, sheets, coils, bridges, etc. The idea then is fairly simple: flexible protein chains fold themselves into their working shape – and individual shapes enable proteins to do specific jobs. A simple sum can show that a limitless variety of proteins can be made: they are the machines of life that make all living things work and they have created all the species of life on earth.

Mutations

Proteins make life possible because the exquisite choreography that generates their shape creates localised regions (sticky bits, clefts, cavities, etc.) for interactions with other molecules. These confer amazing versatility: proteins can ‘talk’ to each other and form relay teams that transmit information from one part of a cell to another, they can generate movement (as in muscles), and bring molecules together (e.g., when they act as enzymes driving chemical reactions that otherwise would not occur). But, as we all know, mistakes can happen even in the best-run enterprises. Mistakes in proteins arise from mutations – changes in the DNA code. Many diseases result from single base alterations: if that changes an amino acid the result can be a protein with dramatically altered function. A well-known example is cystic fibrosis: a protein made in the lung has one abnormal amino acid: the effect on its activity causes a build-up of mucus that makes breathing difficult and is a target for fatal infections.

Mutations and cancer

Cancers are also caused by mutations but they’re a bit more complicated, being driven by groups of mutations, rather than by one event. For most cancers these are picked up as we go through life – so the creation of a cancer is a slow process. Most don’t appear until we are over 60 years of age – collecting a suitable hand of mutations takes time. Because several critical mutations are required you’d guess that what tumour cells are up to is evolving a number of tactics for outsmarting their normal counterparts on the survival front. Indeed they are. They multiply in an unregulated way (because they ignore signals that control normal cells), side-step protective mechanisms that usually kill abnormal cells, divert nutrients from normal tissue to themselves, and make new blood vessels for the delivery of food and oxygen. Perhaps most amazingly of all, they seduce and subvert cells of the immune system: these begin by trying to eliminate the tumour but end up playing a key role in its growth – a sort of co-operative corruption.

All this is why cancer needs several mutations, and these are part of a wider genetic mayhem that will kill most cells – because essential survival genes are damaged. The cells that emerge as tumour precursors are molecular freaks in that they’ve both survived and picked up a bag of dirty tricks with which to out-compete their normal brethren. So, molecularly speaking, cancers are rare events. What’s more, there’s no forethought, no premeditation at work here. If the expression ‘unintelligent design’ conveys random chance in a game of genetic roulette then it’s an excellent descriptor of cancer evolution.

Stop me if you’ve heard it

If all this is beginning to sound familiar, so it should. It’s a completely undirected process that usually fails – but when it succeeds represents an extraordinary triumph of the flexibility of DNA and hence the adaptability of cells. Familiar, of course, because it’s a form of evolution that parallels the emergence of new species.

Tree of life

In the revolution started by unveiling the structure of DNA, the biggest advance has been finding a way to work out the order of bases – the genetic code. The first complete human DNA sequence came in 2003. Since then astonishing technical advances have led to thousands of tumours and hundreds of different species being sequenced. From this you can estimate when new species arose and draw a map of the evolution of all major forms of life on earth from a single, common ancestor. The time scale is incomprehensibly vast, but the picture is stunning in its simplicity, showing how everything is related – bugs, plants, fungi and humans – and how that family has emerged over nearly four billion years. This would have delighted Charles Darwin who, in 1859, was able to define evolution by natural selection only on the basis of what he could see. Molecular biology has now revealed its foundations.

Cancer evolution

In many ways tumours do indeed behave like new species: through the acquisition of mutations they out-compete normal neighbours and establish new niches in which to survive and prosper. But tumours are not new organisms: they’re normal cells that have gone off the rails – been hijacked, if you will, by delinquent genes. The big difference is the brief time scale over which tumours develop compared with the almost infinitely slow, step-wise testing of novel genetic variants in species evolution. So becoming a tumour is a very chancy business – but it’s a lot less fraught than making a new form of life. They take any short-term growth advantage conferred by a mutation without concern for the consequences.

Short trials and lots of errors

When a cell picks up its first growth-promoting mutation it has taken an irreversible step towards a life of crime. It’s become a high roller in the cellular casino, addicted to roulette of the Russian variety, and no amount of genetic counselling will reform it. If only it could think, how our tumour cell would long for a guiding hand – a more knowing form of life that could steer its orgies of DNA destruction toward survival. Alas! Like every other life form, tumours are in thrall to the random creator called chemistry. In a tiny few the dice fall favourably and they grow to rule their kingdom – briefly. Oh for an intelligent brain to design them not to kill their life-support system! Like cellular spaceships seeking immortality in the celestial wastes without the know-how to reach escape velocity, they can only burn brightly before crashing. Tumours are indeed a microcosm of evolution, working on an abbreviated time-scale – they’re dynamic Darwinism.