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Functional Form: The Art of Folding DNA

Joe's Robots

Image by bjornmeansbear via Flickr

You softly crinkle and crunch of a piece of paper in your hands. A form begins to take shape. By twisting and manipulating the folds, a flat plane turns into a 3-D shape, such as a robot. This is the process of origami, the ancient art of paper folding. Creative scientists and mathematicians have recently taken an interest in the engineering applications that origami has to offer.

With origami principles in mind, engineers are studying ways of fitting large objects into small spaces. Think of airbags folded neatly into steering wheels. Origami can simulate the condensing down of an object while providing information about its eventual re-expansion. Origami also has applications that only science fiction authors could have predicted. (Saslow 2010)

The blueprints for a revolutionary new dimension of science are quickly taking shape- on the nano-scale. DNA origami is a process that molds DNA into pre-determined shapes. The process is relatively quick, inexpensive, and the resource- genetic code- is endless.

The technique, now known as DNA origami, was invented by Paul Rothemund. He was looking for a way to compete for the world record of longest sequence of DNA sculpted into something recognizable, set by Ned Seemen. Seemen’s process was complicated; it involved many short sequences of DNA meticulously glued together. Rothemund wanted something simpler. (Shasha & Lazere 2010)

Pure Imagination

Imagine that DNA is a ladder, and each rung is made of a base pairing. Adenine only attaches to Thymine, Cytosine to Guanine. The ladder will twist in different ways depending on the sequence of the rungs. DNA can easily be unzipped down the middle, separating the two bases.

So Rothemund decided to use the origami principle of folding to create his work of art. He imagined taking viral DNA- single strands that are notorious for their long length- and re-zipping then with smaller segments of other single strands. Only the small pieces would have to be synthesized. He created a computer program that would simulate the actual process.

Rothemund programmed the software to know how the single strand, one he already had in his lab, would need to be bonded in order to fold the way he wanted. The molecules would twist and turn as the short single strands “stapled” together parts of the long DNA strand. The program output exactly what sequences were needed.

Rothemund sent the necessary sequences to a lab and they delivered the synthetic molecules to his lab. After procuring the “staples” by mail he mixed the two in a buffer that stabilized the DNA. He heated the solution, cooled it, and then voila- happy faces appeared, his first design. (Sanderson 2010) The strands, mapped out by the computer program, were automatically folded together in an origami like method.

There is a wonderful visualization about 6 minutes into this video of Rothemund’s 2008 presentation at the annual TED conference.

 

Life Imitates Art

Paul Rothemund and Ned Seemen are friendly foes. Seemen, also known as the father of DNA nanotechnology, has worked with Rothemund on the applications on DNA manipulation on many occasions since the early 90’s.

Thanks to Wikipedia

In 1980 Seemen was inspired to synthetically create DNA, and shaping it according to base-pairings. While running DNA crystallography test on specific strands, he realized that a certain shape was formed every time there was a pattern of base pairings. He was looking at M.C. Escher’s “Depth” when it dawned on him- he could arrange certain DNA molecules just like an artist could arrange a drawing. (Shasha & Lazere 2010)

Shaping DNA is not just aesthetically creative; it is potentially useful to society in many ways. Many researchers are now testing the waters for the very real applications of this new art form. In the coming years their findings will achieve utility outside of the lab and in everyday procedures.

The New Frontier

Computer chip circuitry may one day be designed with tiny DNA scaffolds holding parts in place. These parts would replace costly metals, and allow chips to be smaller and faster. Rothemund, being particularly interested in the computing power of molecules, is studying the possibilities with IBM’s Almadem Research Center. (Shasha & Lazere 2010)

Since DNA is a fraction of the size of existing structures, circuitry components could be placed closer than ever before. This equals faster speeds, smaller surface area on circuit boards, and also fewer metals used in the manufacturing process. Imagine the rare metal components on chips being replaced with DNA structures. (DNA ‘Organises’ itself on Silicon)

Looking Ahead

Though folding is becoming both increasingly less expensive and less time consuming, many scientists are still skeptical of the practicality of current theories. (Drexler 2010) The applications of it span many disciplines and are far reaching. As Rothemund explains, “DNA origami was a leap of faith… it was something that I thought was such a high value target, that if it worked out it would be great.” (Shasha & Lazere 2010) DNA has uses in transport systems- both in computer chips- and in the human body.

Researchers are looking towards the medical uses of this new find. Scientists in Denmark have created a hollow box which has a lockable hinged lid, made entirely of DNA. (Rice 2009) These so called “lockboxes” could eventually transport drugs or proteins into the bloodstream and across cell membranes.

Critics include skeptics of genetic engineering and gene therapy. As with any forms of biotechnology, some see the developments as a dangerous meddling with nature’s affairs, especially when applied to the human body.

Viruses are often used to transport the necessary chemicals to manipulate genes. Contemporary medical procedure dictates that viruses be used to transport these materials. This causes unnecessary stress to the body. (Dunlap, Maggi, Soria & Monaco 1997) DNA boxes could be used in a significantly improve this type of delivery.

Though actual folded DNA delivery systems could be five to ten years away, advances are being made every day. For example, in 2010 a “robot” made of DNA was engineered to follow along a DNA track.

Engineers are developing these molecular robots in the hopes that they will be able to assist in diagnosing and treating diseases in the human body. The robots will be deployed to detect diseases, make decisions based on that information, and then deliver a treatment.

Think an autonomous factory robot crossed with a brilliant doctor, working to cure people of life threatening ailments such as cancer. (Rice 2009)

DNA origami is at the crossroads of medicine, biology, engineering, and art.

Previously relegated to the realm of science fiction, these awe-inspiring discoveries in biotechnology and nanotechnology are now unfolding right in front of our eyes. It has become clear that art has a place in science, and science a place in art.

-Allison Schulz

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