DNA Origami Comes of Age

by Steven D. Buckingham Labtimes 03/2016

It’s been just ten years since Paul Rothemund found a simple way to generate nanoscale DNA structures similar to paper origamis. Today, DNA origamis may help to construct nanomachines or deliver DNA into cells.

Someone I know uses a laptop as a book end. “That’s not what it is for,” I explained. “It is meant to be a sophisticated information storage and processing device, and you are using it as a piece of construction.” That is what has been happening lately with DNA. As far as most of us are concerned, DNA uses base-pairing for the purpose of replication and the fact that it also holds the two strands together is almost a side-effect.

DNA robot designed with the DNA origami programme CanDo.

Rightly so, perhaps. But some labs have taken their lead from my friend and have decided to misuse this elegant information storage device and hijack it for quite different purposes. Instead of using base-pairing to copy information, they have used it to tangle DNA up into sheets and tiles, to make tiny structures and even machines. It is called DNA origami. And it all began with the Holliday knot. Back in the deep mists of time (the 1960s) a British geneticist called Robin Holliday worked out a crazy variation of homologous recombination. We are all familiar with the way two strands can recombine using AT/CG pairing but Holliday suggested that something odd might happen, when you force not two but four strands to pair up. He proposed that if you do that, you could end up with a four-arm structure.

Jumping game

How can that happen? Well, first imagine you are zipping up strands – sticking strand A, say, onto strand B. Now imagine we add a third strand, C, complementary to A. As A gets stuck onto B, it “jumps” onto strand C at some point. At that very point, the jilted strand B pairs up with a fourth strand D, complementary to B. Result: a cross-shaped, four-armed structure – the Holliday junction.

Our genetically-minded, cell-cycle aware readers will point out that this is nothing special and, indeed, the Holliday junction is a precursor to many types of genetic recombination. But where DNA origami comes in, is where you realise that you can play the jumping game in different ways. Jump once and you get a Holliday junction. Keep on jumping in a regular pattern and you get a woven sheet, or tile, of DNA. It is a bit like weaving with DNA, using base-pair complementarity to stick the fibres together.

DNA origami is usually done by taking a single-stranded genome of the M13 bacteriophage. This is a big loop that you are going to fold up into the shape you want. You then add strands of DNA called “staples” because they staple the loop into shape. Thanks to complementarity, the DNA staples automatically tangle up in a predictable way, to give you the shape you want.

And there is no limit to that shape – you can have tubes, poles, plates, whatever. Most often, you will build up your final structure by making standard shapes (such as tiles) and stacking them together into something more complicated (like cubes). Paul Rothemund, the inventor of DNA origami, made circles, triangles and even smiley faces at the 100 nm scale (Nature 440: 297–302), while Castro et al. (Nat Methods 8: 221–9) even made model robots, just 75 nm tall.

But how is it done in practice? It is surprisingly easy, once you know how. Or rather, once you have loaded the software. Programmes like CanDo (http://cando-dna-origami.org) allow you to specify the shape you want and it will tell you the sequences of DNA staples you need to mix up with scaffold, to get your nanostructure. You then synthesise your staples, add them to your M13 genome and start the annealing reaction. Simple! At least, with a bit of tweaking the conditions. Okay, a lot of tweaking.

What is it good for?

But other than making tiny models of R2D2, what is the point? Actually, DNA origami could turn out to be useful in a whole host of ways. For one, they are a good way of getting DNA into cells without electroporation, because, when the assemblies stick to the surface of cells, they provide a really high local concentration of DNA. Even better, you can make nanomachines that will physically deliver the DNA into the cell, like a tiny drill.

And once you realise you can make just about any shape you want, the imagination starts to run wild. This March, Yonggang Ke et al. (Nature Comms. 7: 10935) described how they had made a DNA actuator out of four rigid arms of DNA joined into a rhombus. Two arms are joined by an adjustable strut made of a mixture of scaffold and staples, whereas the other two are loaded with the cargo molecule, in this case two fragments of green fluorescent protein. By adding just the right staples, they could open or close the rhombus and control the distance between the two cargo molecules (as measured by fluorescence intensity).

DNA origami, once the fine-tuning has been done, offers a phenomenally quick way of making nanoscale machines. If anyone finds a way of adding controlled movement, the future of this technique will look very exciting indeed.

Last Changed: 21.06.2016