DNA nanotechnology builds large structures from information-rich seeds

The winners of the 2006 Foresight Institute Feynman Prize in both the theory and experimental work categories, Drs. Erik Winfree and Paul W.K. Rothemund, have extended the scaffolded DNA origami technique invented by Rothemund to use the DNA origami structures as seeds to program the construction of nanotech structures up to 100 times larger. From “DNA origami comes to life“, in New Scientist, written by Colin Barras:

Now the researchers have shown that such [DNA origami] canvases can behave like programmable “seeds” — smaller DNA tiles attach to the seed and the structure snowballs in size to make a structure up to 100 times bigger than the original segment.

To make that happen, the team created two kinds of artificial DNA molecule — a long sequence that folds into the flat “seed” and a number of short sequences that each fold into smaller tiles.

When the two unwound types of DNA undergo cycles of temperature variation between 40 and 90 °C, they fold into seeds and tiles, and then begin to accrete together into the much larger structure. The “growth” process is directed by the sequence of information written into the seed’s DNA.

That seed information coordinates which tiles attach on the first layer of tiles, explains Winfree. The sequences that make up that first layer then carry the information that directs the formation of the next layer of tiles, and so on.

The research was published in the Proceedings of the National Academy of Sciences (abstract). The full text (1.6 MB PDF) is free via Open Access. The authors use the algorithmic self-assembly of DNA tiles to study growth from seeds at a complexity intermediate between the simple growth of chemical or mineral crystals on the one hand, and the complex development of multicellular organisms from the genetic information in the zygote, on the other. They used DNA origami rectangles (75 x 95 nm) as “genomic” information bearing seeds to program the algorithmic self-assembly of DNA tile crystals. 32 adapter strands form 16 tile adapters that bind to specific sites on the right side of the rectangle and to specific types of DNA tiles. When all of the components are mixed, heated, and cooled slowly, the different types of tiles attach to the seed as specified by the right side of the seed, and then additional tiles attach to the first row of tiles in a zig-zag pattern, and grow to form a ribbon crystal. In three different experiments, three different seeds specified growth of ribbons 8, 10, or 12 tiles wide. Given the size of the rectangle seed, the seeds could have been programmed to give ribbons of 7 widths from 4 to 16 tiles. The authors acknowledge a need to improve the error rate and discuss possible improvements. However they conclude that:

Combined with the wealth of available chemistries for attaching biomolecules and nanoparticles to DNA, an improved system for seeded growth of algorithmic crystals could be a powerful platform for programming the growth of molecularly defined structures and information-based materials.

Barras reports further speculation by the researchers:

Winfree and Rothemund speculate that the technique could provide a way to assemble molecular components into useful structures such as tiny electric circuits. It is also possible to use the self-assembling DNA structures to perform computational tasks, adds Winfree.

“It is very powerful for information processing,” he says. “It’s what’s known as a Universal Turing Machine, which means it can carry out any information processing task.”

(Credit: KurzweilAI.net)

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