Self-assembled Nano-circuit boards with DNA Origami and Carbon Nanotubes

Just when Moore’s Law seemed to be hitting a sponge wall of 45nm, IBM inconjunction with Paul Rothemund have paved the way right down to a possible 2nm or 2 billionths of a meter. Now if that wasn’t enough to have even the mildest of technophile’s wonder at the possible increase in processing speed and power that could ensue. There’s something for the SF enthusiast too, because this avenue of research could lead to the first commercial organically self-assembled nano circuit boards.

In 2006 Paul Rothemund published a significant advance in DNA nanotechnology in the science journal Nature. DNA nanotechnology explores DNA’s molecular recognition abilities and uses them to create pre-defined or programmed nanostructures. It perhaps stems from a natural proposition that if DNA is so good at working at the nano level then look to controlling that what already does the job, rather than trying to figure out how to get started from scratch. What Rothemund achieved was a breakthrough in his field, a new method which he dubbed scaffolded DNA Origami.

“An obvious application of patterned DNA origami would be the creation of a nanobreadboard, to which diverse components could be added…molecular electronic or plasmonic circuits might be created by attaching nanowires, carbon nanotubes or gold nanoparticles. These ideas suggest that scaffolded DNA origami could find use in fields as diverse as molecular biology and device physics.”-Paul W.K. Rothemund (Nature Vol 440|16 March 2006|doi:10.1038/nature04586)

Inspired by Richard Feynman’s 1959 challenge to write the Encyclopaedia Britannica on the head of a pin, a task which Feynman calculated would require the use of dots 8 nm size. Rothemund had come closer than any before him and he displayed the process by creating several pictures, amongst them a smiley face, a map of the America’s, and a star. Except these pictures were somewhat special being that they were created by specific DNA manipulation and were only about 2nm (nanometres) by 100nm² large. To get an idea of the scale involved a human hair is 1000 times as wide. Or, it takes five atoms of carbon occupy a space about 1nm wide. It would take 5,000,000 carbon atoms, to make a dot as big as the 1mm diameter of the full stop at the end of this sentence.

Now each picture Rothemund created from 14,000 DNA bases, half of them were part of one single long DNA strand. And the other half composed of 250 short strands each about 30 bases long. Now the long single DNA strand can be thought of as the paint and the short strands as a 250 pixel scaffold canvas. The artist draws by pre-programming each pixel or short DNA to accept bonding to the single long strand or repulse it. Thus when the long strand paints the canvas the short strands guide the long strand into filling the pre-programmed picture. (Aka DNA Staples that form a scaffold which guides and intricately folds the long strand like origami, hence the dub scaffold DNA Origami) Now take Rothemund’s discovery add nearly two years and the power of IBM research and development.

"Right now, the industry road map is, we'll get down to 22 nm-size features on a chip. We're looking at ways to go down beyond that. It's very clear it will be difficult to go smaller than that using the optical lithography we know today. Using DNA will help us do that."-Joe Gordon snr mngr IBM

IBM for the last year and a half has been busy developing DNA Origami along with DNA carbon nanotube quality inspectors and peptides amongst other technologies. With the intent of creating smaller, faster, and cheaper processing chips and data storage solutions. Now as great as DNA Origami is, underpinning this push forward are the rather amazing properties of a carbon nanotube.

Mankind’s first though perhaps unwitting encounter and use of carbon nanotubes is believed to be from around 900 - 1750 CE when the legend of Damascus Steel arose from Damascus in Syria. It has been proposed that a combination of ores specific to the surrounding area and/or imported ore’s and a very complex and secret method of sword making, led to the birth of this legend. One that can be attested by many a crusader witness that saw their own swords sliced in half by the foreign made steel.

A modern examination has revealed the extensive presence of carbon nanotubes and wires in the remaining examples and they are attributed to the uncommon attributes of the ancient Damascus steel.

But by 1750 CE real Damascus steel was no longer crafted at all. Historians have sited possible causes as the depletion of the required ores or/and trade routes and the subsequent atrophy of the associated oral teaching traditions. Damascus steel became a mystery, a legend, which would flummox generations of sword smiths, alchemists, and eventually scientists for 202 years until 1952.

This is not to say carbon nanotubes were never created in this period between but if they were, well we couldn’t see them. It was only with the advent of the transmission electron microscope (TEM) in1938, and 14 subsequent years of its use that Radushkevich and Lukyanovich, two Russian scientists, published the first ever precise images of 50nm carbon nanotubes. Unfortunately the discovery was somewhat suppressed by the Cold War era and non-communist carbon nanotubes were to remain unobserved for another 24 years.

In 1976 a three man team Endo, Koyama and Oberlin at the Shinshu University in Nagano City, Japan published a paper that visibly described the process and accompanying TEM images that created single walled nanotubes composed of graphene (graphite). But it was not until 1991 that interest and serious development of carbon nanotubes was kick started by Sumio Iijima at NEC. Whilst studying the insoluble remains of a graphite rod burnt by an arc or electrical discharge through the rod. Iijima using a TEM discovered carbon nanotubes present in the remains and then further developed and refined the process by adding metal catalysts to the carbon within the arc discharge. Which is all very fascinating but what is it about single walled carbon nanotubes that make them so special?

Single Walled Carbon Nanotubes are like garden chain link fences composed of joined carbon hexagons that curve into a seamless single tube, which can be of a varying diameter from under 1nm to over 50nm but can exceed over 1,000,000 times that in their length. Now at these nano scales the tube is considered to essentially be one dimensional and therefore electrons travel through them at ballistic conduction speeds though quantum effects that occur at this scale. Which is to say the electric charge can travel virtually unimpeded or with little or no resistance when compared to the resistance of copper or sliver, and that means they move much faster and don’t loose any power on the way. These properties also make them exceptional thermal conductors possibly the best in the world so far. At an estimated 6000 watts/(metre/kelvin) they beat Copper sitting at 385 W/(m·K) by a massive 5615 watts. But of course this is all dependant on minimal or zero defects in their construction process, the more defects the less they act in the above manner.

It is no wonder Damascus steel gained such a fearsome reputation because carbon nanotubes are not only six times lighter than modern steel but more that 500 times stronger. With a theoretical tensile strength of 100 gigapascals (GPa) which is ten times that required to form diamonds, or just 280 GPa’s less then the pressure at the core of the Earth. Fearsome indeed especially if you add the flexibility of each tube to undergo a 120º degree bend and still jump back to its original form with no deformations. This is due to the natural tight bonding of carbon atoms to each other and their once joined affinity for very stable hexagonal rings. Which effectively means carbon atoms self assemble into carbon nanotubes in the presence of the right catalysts and this has been the method of their production. This also causes the tubes to effectively heal themselves if they are damaged by bringing in free carbon atoms to regain the tubes original structure.

Add these properties all together and you can well see why carbon nanotubes are of such a great interest to IBM and many other industries. An interest that has seen the price of single walled carbon nanotubes go from US$ 1,500/gram in 2000 to US$ 50 in 2007. But getting back to the IBM nanotech project, now with the understanding of what these two nanotechnologies, DNA Origami and single walled Carbon Nanotubes can do. What happens when we marry them together along with additional DNA manipulation and the use of peptides to create self-assembled nano-circuit boards?

"The specific structure of DNA has unique features. It's basically programmable. You can design DNA into unique shapes, with specific attachment sites. Then we pour this DNA solution onto a silicon substrate, and the DNA assembles itself exactly where we want it to on the chip, and then we assemble the components on top of that." -Greg Wallraff scientist IBM

Well this is exactly what IBM is trying to achieve and they have made significant progress in doing so, but are quick to say the end game is still a long way off. Ten to twenty years by Wallraff’s estimation. When they do get it right the process should go something like this.

First highly intricate DNA scaffolds will be created using an extension of Rothemund’s original scaffold DNA Origami staples. They will essentially become the small scale nanometre templates/scaffolds within the larger microprocessor template. A larger template will then be etched onto a silicon substrate or bread board creating a larger pattern to hold the DNA templates. The DNA solution is then pored onto the board and self-assembles its own template scaffolds within the larger etched pattern. Peptides are then added and brought into place by an attraction to pre-determined DNA strand scaffold points. Peptides have the unique ability in being able to adhere to organic and non-organic structures and can be created to act as a bridge of connection and attraction to certain DNA strands and carbon nanotubes. They can act as lynch pins to bolster the properties of the DNA scaffold. Next a final solution of DNA long strands and carbon nanotubes are pored into the mix. Through the pre-determined interaction of the DNA scaffold, peptides and DNA long strands, the carbon nanotubes are sorted (quality controlled) and assembled into place to form the precise and complex structures of a full micro-processor(s). And Walla! One self-assembled, self healing, super processor with carbon nanotube wiring at 1-2nm wide. Drain and serve with a large helping of future shock, and that’s just the beginning.

For while carbon nanotubes have some excellent properties and are just so damn small, in the above processes they are basically just replacing current micro-processor wiring. There is another possibility within the properties of carbon nanotubes to act as the first intermolecular logic gate. Meaning they can be turned into transistors with an on/off status capability and thereby form not only the wiring but the transistors themselves. This could result in another whole new breed of ultra small, ultra fast carbon nanotube micro-processors. Through further developments of DNA and they could self-replicate/repair and all at the nanometre scale.

The possibilities are truly staggering Rothemund and IBM have turned a new corner in nanotechnology that should see the next decade prove to be most interesting. And of course Mr Moore can be assured that his famous law still seems to apply and will continue to do so for some time to come.

Self-assembled Nano-circuit boards with DNA Origami and Carbon Nanotubes was written By Ivor W. Hartmann.