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Posts Tagged ‘nanotechnology’

Functional Form: The Art of Folding DNA

April 11, 2011 3 comments
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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Benford’s Flies

February 23, 2011 4 comments

A few weeks ago I met science fiction author Gregory Benford. My friends Jason Sussberg and David Alvarado were shooting for their documentary about radical life extension, so I tagged along and went with them to Irvine for the interview with Benford regarding the work of his company Genescient. My copy of In the Ocean of Night tucked into my jacket pocket, I relished the opportunity to chew the fat with a major juggernaut of the sci-fi world.

Benford’s biotechnology company, Genescient, researches and develops a new field of science known as Genomics 2.0. More specifically they’ve been testing proprietary gene sequencing on a strain of Drosophila fruit flies, known as the “Methuselah flies.” Three decades of selective breeding has created reproductive longevity and optimal health in these buggers. Benford sees a way to parlay the knowledge gleaned from the fly experiments to fashion lines of pharmacogenomics that may greatly increase the human lifespan. Ultimately Benford envisions a future of advanced gene therapy that allows humans to regularly live to over 150 years-old.

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He’s hardly the only one who believes in life extension. A vast panoply of futurists now maintain it is more than possible that 21st century humans will use the overlapping bridges of biotechnology, nanotechnology, and mind uploading to not only reverse the effects of aging but to evolve to new, machine-based, substrates of consciousness entirely. Once buoyed by artificial intelligence, these efforts will reach the point at which technology is progressing so exponentially the future will be unpredictable and incomprehensible. This is known as the Singularity.

My friends’ documentary, The Methuselah Generation, will delve headlong into these theories, primarily investigating biotechnological methods to life extension. Other futurists, like economist Robin Hanson and the world renown Aubrey de Grey of the SENS Foundation, will present rousing thought experiments pertaining to the future of human life. The documentary, which the filmmakers are shooting in both 3D and 2D codecs, will also explore the social, economic, judicial, and emotional impacts of extended lifespans. For example, does a person convicted of a life sentence get to live forever in prison, eternally sapping taxpayer dollars? Will poor people be able to come along for the ride, or will the future be a rich-and-privileged only society? Say your friends and family can’t afford the life extension therapies. How appealing is a future in which everyone you know is dead?

Gregory Benford’s interview took place at his home in Irvine. Though I made a conscious effort not to be nosey I couldn’t help but notice that beside his 1975 Nebula Award (one of the two he claimed) lay a Big Bang Theory DVD nestled in it’s Netflix sleeve. I was currently writing a spec script for the show and thought about querying Benford about what he thought about the pop nerd sci sitcom. Instead I asked him about the original Chesley Bonestell paintings bedecking his office.


They sell well now, he said. “Death is good for art sales.”

“I guess life extension is bad for art,” Jason quipped.

During his interview, Benford touched upon the Methuselah flies, biotechnology, intersections between science and science fiction, the death of his first wife, which motivated him to create Genescient in the first place, and the Singularity. With the “Rapture of the nerds” becoming so conversationally popular these days–what with Ray Kurzweil’s Transcendent Man release, Patton Oswalt’s #Etewaf meme in Wired, and Time Magazine’s recent state-of-the-singularity piece–it was simply too tempting not to ask the man who first created the computer virus what he thought the Singularity would be like. The answer, which I’ll remember until the day I die (or, in the event I don’t die, for several hundred years), was rather simple:

Benford reading during the Singularity
A day after the Singularity you won’t be able to read the newspaper.

If that’s the case, the human economy itself will be up for grabs. Who knows how capital will be generated in an age of immortality and abundance? But Genescient will always have its flies. And if the whole biotechnology thing doesn’t work out they can always sell a new line of the fake ice cubes with dead flies in their centers.

After all, we’ll still need practical jokes after the Singularity.

Jake Anderson

Nano Origami

February 21, 2011 1 comment

And so we watched “Between the Folds”, a documentary about artists and scientists who are pushing the envelope of modern origami. In the last decade, this ancient art form has acquired revolutionary scientific applications in the fields of medicine, biology, natural science, space, and nanotechnology.

And so our minds were blown. And so we consulted Google.

In addition to origami’s progression through the entire human gamut of styles and aesthetics, origami-based mathematical models now provide algorithms for airbag collapse research, foldable satellite lenses that can unfurl in orbit, and synthetic proteins which could help fight major diseases.

Origami is also finding a home in nanotechnology, or the study of manipulating matter on an atomic and molecular level. Scientists are increasingly seeing the usefulness of DNA as a polymer to act as a scaffold for the assembly of nanomachinery. Computational bioengineer Paul Rothemund figured out how to fold a genome into a pre-determined two-dimensional shape, a technique he calls DNA origami. It offers precision molecular engineering for nanoengineers and bioengineers alike. Rothemund says DNA origami could help improve optical structures and plasmonic devices, which may boost the speed of information transfer to something close to light speed.

nanotechnology

molecular drug delivery boxes

Hao Yan, a biochemist at Arizona State University in Tempe has been looking to use DNA origami as the basis for an artificial leaf that makes hydrogen fuel from water. Yan is trying to harness the power of electron flow. “If we can really control all the electron-transfer sites then we can improve the efficiency.”

DNA nanotechnologist William Shih wants to expedite the creation of DNA lock-boxes, which he says could be tapped for internal microscopic drug delivery. However, he must figure out a way to have the box move through a cell membrane. The lock boxes might one day carry drugs to specific destinations in the body or serve as logic gates in a DNA-based computer.

Ultimately, researchers imagine DNA origami supporting artificial organs, and neuronal networks connected to electrical circuitry.

-Jake Anderson and Allie Schulz

Sources used:

Sanderson, K. (2010, March 10). “Bioengineering: What to Make with DNA Origami”.

Rice, J. (2009, May 7). “A Lockbox Built from DNA”. Technology Review.

Saslow, R. (2010, May 11). “When Origami Meets Rocket Science”.

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