Mar 15, 2006
DNA origami creates complex nanostructures
A researcher from the California Institute of Technology, US, has used strands of DNA to create complex 2D nanostructures. The "scaffolded DNA origami" technique could have applications in fields from molecular biology to semiconductor devices.
"The construction of custom DNA origami is so simple that the method should make it much easier for scientists from diverse fields to create and study the complex nanostructures they might want," said Paul Rothemund of Caltech. "A physicist, for example, might attach nano-sized semiconductor 'quantum dots' in a pattern that creates a quantum computer. A biologist might use DNA origami to take proteins which normally occur separately in nature and organize them into a multi-enzyme factory that hands a chemical product from one enzyme machine to the next in the manner of an assembly line."
Rothemund made DNA strands into structures such as squares, smiley faces, stars, rectangles and hollow triangles, each about 100 nm across. He based each shape on a single strand of DNA roughly 7000 nucleotides long taken from a virus. (A nucleotide is the structural unit that makes up DNA and some other biological molecules.) The so-called "scaffold strand" was folded into the desired shape and held together by short "staple strands" of DNA.
"In my work, billions of DNA nanostructures are made in parallel, quickly under very mild conditions," said Rothemund. "The component DNA strands are just mixed together in a little bit of saltwater, heated to near boiling and allowed to cool over about an hour and a half."
Attaching additional DNA helices enabled the creation of pixel patterns on top of the nanostructures, with a pixel diameter of 6 nm. In this way, Rothemund created a map of the Western Hemisphere and wrote the word DNA in 30 nm high letters. He also linked the origami nanostructures together, for example making hexagons by joining origami triangles.
According to Rothemund, the real key to the approach is that by design none of the short sequences ever bind to each other. "Each short DNA strand is designed to only bind to the long scaffold," he said. "Because of this, the long scaffold becomes the magic ingredient – as long as it is pure and unfragmented, the structures can form and the relative ratios of the rest of the DNA strands don't matter."
As a result, researchers can simply throw all the ingredients together, without having to perform each construction step individually, as other DNA nanotech techniques do. There's also no need to measure the proportions of the different types of DNA too precisely – as long as there are plenty of staple strands present the process should work.
"Another virtue of my experiments is that I use the same long single strand over and over again (the natural virus sequence) and I just change the ∼200 short staple strands," said Rothemund. "This means I don't have to do a custom long synthesis every time I want to make a new structure."
The structures are currently limited to around 100 nm by the size of pristine long single strand DNA that's available. "Synthesizing and purifying longer single strands is certainly possible: right now people routinely handle double-stranded DNA millions of bases long," said Rothemund. "If we could use million-base long single strands then we could create a DNA origami [structure] 1 μm on a side with about 20,000 pixels. This seems possible and may be done in the next few years."
What's more, the origami method could be extended straightforwardly to create 3D structures.
"This work makes one kind of DNA nanotechnology cheap and easy for everyone - it moves DNA nanotechnology a step away from research and towards practical engineering," said Rothemund.
The work was reported in Nature.
About the author
Liz Kalaugher is editor of nanotechweb.org.