Reproducing Works of Art with DNA Origami
Researchers from Caltech have developed an inexpensive, facile technique for creating very large self-assembling DNA origami structures with customisable patterns. The work, published in Nature yesterday, is the first time that DNA origami has been used to build such large structures and provides other researchers with a relatively simple method for creating their own. The team demonstrated the success of their technique by using it to recreate Leonardo da Vinci’s iconic Mona Lisa painting.
DNA origami was a technique that was originally developed in 2006 and involves combining one long strand of DNA with many smaller one, to fold the complex into a predetermined shape. The smaller DNA fragments, known as staples, bind to specific regions of the long strand, as determined by Watson and Crick DNA binding pairs, and pull the long strand into a specific conformation. This single structure is known as a DNA origami ‘tile.’ Each tile is very small, but multiple tiles can be bound together into a larger structure like a mosaic. Molecules can be selectively attached to the tiles to create raised pattern that is visible using atomic force microscopy.
In the past this technique has been used to create small images, such as a smiley face that was 100nm wide. Researchers have also been hoping to be able to use the principle to create tiny molecular devices, which would have a range of real-world applications. Unfortunately, however, to do so would require using much larger structures than had previously been synthesised.
To try to increase the possible size of DNA origami structures, a team of researchers at Caltech tried a new approach. To start with, they developed software that was capable of observing an image of the Mona Lisa and then deriving the DNA sequences necessary for each DNA origami tile. The problem then was that they required so many tiles, they needed to use a vast range of edge combinations for the tiles so that they would assemble in the correct orientation.
“We could make each tile with unique edge staples so that they could only bind to certain other tiles and self-assemble into a unique position in the superstructure,” said Grigory Tikhomirov, PhD, lead author of the study. “But then we would have to have hundreds of unique edges, which would be not only very difficult to design but also extremely expensive to synthesize. We wanted to only use a small number of different edge staples but still get all the tiles in the right places.”
The team’s solution, dubbed Fractal Assembly, was remarkably simple. Instead of synthesising the tiles and then mixing them all together at once, they started building the mosaic in distinct, unconnected pieces and then gradually combining different sections to build a complete image. This approach meant that each tile could use the same four edges without a risk of the tiles combining incorrectly.
“Once we have synthesized each individual tile, we place each one into its own test tube for a total of 64 tubes,” said Philip Petersen, co-first author. “We know exactly which tiles are in which tubes, so we know how to combine them to assemble the final product. First, we combine the contents of four particular tubes together until we get 16 two-by-two squares. Then those are combined in a certain way to get four tubes each with a four-by-four square. And then the final four tubes are combined to create one large, eight-by-eight square composed of 64 tiles. We design the edges of each tile so that we know exactly how they will combine.”
The outcome of this novel approach was a DNA origami structure that was 64 times larger than the very first structure in 2006, but which used the same number of DNA molecules. To demonstrate the effectiveness of their technique, the team used it to build several images and mosaics, one of which is a copy of da Vinci’s Mona Lisa.
As part of their study, the team created computational software that will allow other researchers to use the same technique quickly and effectively. The software is now available online.
“Other researchers have previously worked on attaching diverse molecules such as polymers, proteins, and nanoparticles to much smaller DNA canvases for the purpose of building electronic circuits with tiny features, fabricating advanced materials, or studying the interactions between chemicals or biomolecules,” said Petersen. “Our work gives them an even larger canvas to draw upon.”