IBM experimenting with DNA to build chips

Scientists at IBM are conducting research into arranging carbon nanotubes--strands of carbon atoms that can conduct electricity--into arrays with DNA molecules. Once the nanotube array is meticulously constructed, the laboratory-generated DNA molecules could be removed, leaving an orderly grid of nanotubes. The nanotube grid, conceivably, could function as a data storage device or perform calculations.

"These are DNA nanostructures that are self-assembled into discrete shapes. Our goal is to use these structures as bread boards on which to assemble carbon nanotubes, silicon nanowires, quantum dots," said Greg Wallraff, an IBM scientist and a lithography and materials expert working on the project. "What we are really making are tiny DNA circuit boards that will be used to assemble other components."

The work, which builds on the groundbreaking research on "DNA origami" conducted by California Institute of Technology's Paul Rothemund, is only in the preliminary stages. Nonetheless, a growing number of researchers believe that designer DNA could become the vehicle for turning the long-touted dream of "self-assembly" into reality.

Chips made on these procedures could also be quite small. Potentially, DNA could address, or recognize, features as small as two nanometers. Cutting-edge chips today have features that average 45 nanometers. (A nanometer is a billionth of a meter.)

"There is nothing else out there that we can do that with," said Jennifer Cha, an IBM biochemist working on getting the biological and nonbiological molecules to interact.

Right now, products get manufactured in a top-down approach with machinery and equipment manipulating raw materials. In self-assembly, the intrinsic chemical and physical properties of molecules, along with environmental factors, coax the raw materials into complex structures. It works with snowflakes, after all.

Getting the raw materials to behave in a precise, orderly manner, however, remains a challenge, which is where DNA comes in. DNA consists of specific chemical bases (guanine, cytosine) that bind and react in somewhat predictable ways with each other.

"The sequence (of base pairs in DNA) is well known," said Cha. "Most people are acknowledging that DNA and these biological scaffolds are actually quite useful to at least pattern very small systems."

How it works
In creating chip arrays, DNA assembly might work as follows: scientists would first create scaffolds of designer DNA manipulated into specific shapes. Rothemund has made DNA structures in the shapes of circles, stars, and happy faces.

A pattern would then be etched into a photo-resistant surface with e-beam lithography and the combination of several interacting thin films. A solution of the designer DNA would then be poured on the patterned surface and the DNA would space themselves out according to the patterns on the substrate and the chemical/physical forces between the molecules.

The nanotubes would then be poured in. Interactions between the nanotubes and the DNA would occur until they formed the desired pattern. Single strand DNA, along with origami, could be used in concert.

Another key part in the system revolves around peptides that can bind to the DNA and a nonbiologically inspired molecule like a nanotube.

"Building a DNA scaffold is not trivial because you need the biological system to recognize something that doesn't exist at all in biology," said Cha. "We can also use these biomechanical scaffolds to position inorganic nanomaterials. Potentially, we could also use these biomechanical systems to synthesize inorganic materials."

Although it's early, progress is occurring. Researchers have published papers on how DNA can coil around nanotubes and disperse them in water. Papers detailing how DNA can arrange nanotubes will come soon. Future experiments will need to be conducted into aligning nanotubes into arrays. Other researchers in this field include Nadrian Seeman at New York University and Thom LaBean at Duke University.

IBM will also examine ways of employing DNA to sort nanotubes, said Cha. Not all nanotubes are equal. The arrangement and relative position of carbon atoms in a nanotube, called chirality, can change the properties of a nanotube. Some nanotubes can't conduct electricity, for instance, even though they were made with others that do conduct electrons. Separating good from bad nanotubes currently requires applying an electric field, soaking them in solutions, or selecting by hand.

If DNA manufacturing can become a reality, worries about the pace of progress in the computing world slowing down because of the difficulties involved in following Moore's Law would likely fade, at least for a while. Chipmakers shrink the size of the features of their chips every two years. While this improves the performance, producing smaller circuits has strained the financial and technical resources of the industry. The limits of lithography (used to "draw" circuits) have prompted many, including Intel co-founder Gordon Moore, to predict that the pace of progress would slow down.

With DNA, chipmakers could phase out multibillion fabrication facilities stocked with lithography systems, which cost tens of millions of dollars, and the other "top-down" style equipment.

Potentially, DNA techniques could allow manufacturers to produce features that are smaller than patterns that could be achieved even with the most advanced lithography systems, predicted Wallraff. E-beam lithography, which is extremely difficult to use in mass manufacturing, goes down to 10 nanometers.

"Of course, the devil is in the details," said Wallraff. "These are self-assembly procedures and error rates--missing features could be the downfall."

Link to original article on the Reaearch (a PDF Document ) :

techniques of DNA nanotechnology

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Folding DNA to create nanoscale shapes and patterns

Paul W. K. Rothemund1

‘Bottom-up fabrication’, which exploits the intrinsic properties of atoms and molecules to direct their self-organization, is widely used to make relatively simple nanostructures. A key goal for this approach is to create nanostructures of high complexity, matching that routinely achieved by ‘top-down’ methods. The self-assembly of DNA molecules provides an attractive route towards this goal. Here I describe a simple method for folding long, single-stranded DNA molecules into arbitrary two-dimensional shapes. The design for a desired shape is made by raster-filling the shape with a 7-kilobase single-stranded scaffold and by choosing over 200 short oligonucleotide ‘staple strands’ to hold the scaffold in place. Once synthesized and mixed, the staple and scaffold strands self-assemble in a single step. The resulting DNA structures are roughly 100 nm in diameter and approximate desired shapes such as squares, disks and five-pointed stars with a spatial resolution of 6 nm. Because each oligonucleotide can serve as a 6-nm pixel, the structures can be programmed to bear complex patterns such as words and images on their surfaces. Finally, individual DNA structures can be programmed to form larger assemblies, including extended periodic lattices and a hexamer of triangles (which constitutes a 30-megadalton molecular complex).

In 1959, Richard Feynman put forward the challenge of writing the Encyclopaedia Britannica on the head of a pin1, a task which he calculated would require the use of dots 8 nm in size. Scanning probe techniques have essentially answered this challenge: atomic force microscopy2 (AFM) and scanning tunnelling microscopy3,4 (STM) allow us to manipulate individual atoms. But these techniques create patterns serially (one line or one pixel at a time) and tend to require ultrahigh vacuum or cryogenic temperatures. As a result, methods based on self-assembly are considered as promising alternatives that offer inexpensive, parallel synthesis of nanostructures under mild conditions5. Indeed, the power of these methods has been demon- strated in systems based on components ranging from porphyrins6 to whole viral particles7. However, the ability of such systems to yield structures of high complexity remains to be demonstrated. In particular, the difficulty of engineering diverse yet specific binding interactions means that most self-assembled structures contain just a few unique positions that may be addressed as ‘pixels’.

Nucleic acids can help overcome this problem: the exquisite specificity of Watson–Crick base pairing allows a combinatorially large set of nucleotide sequences to be used when designing binding interactions. The field of ‘DNA nanotechnology’8,9 has exploited this property to create a number of more complex nanostructures, including two-dimensional arrays with 8–16 unique positions and less than 20 nm spacing10,11, as well as three-dimensional shapes such as a cube12 and truncated octahedron13. However, because the synthesis of such nanostructures involves interactions between a large number of short oligonucleotides, the yield of complete structures is highly sensitive to stoichiometry (the relative ratios of strands). The synthesis of relatively complex structures was thus thought to require multiple reaction steps and purifications, with the ultimate complexity of DNA nanostructures limited by necessarily low yields. Recently, the controlled folding of a long single DNA strand into an octahedron was reported14, an approach that may be thought of as ‘single-stranded DNA origami’. The success of this work suggested that the folding of long strands could, in principle, proceed without many misfoldings and avoid the problems of stoichiometry and purification associated with methods that use many short DNA strands.

I now present a versatile and simple ‘one-pot’ method for using numerous short single strands of DNA to direct the folding of a long, single strand of DNA into desired shapes that are roughly 100 nm in diameter and have a spatial resolution of about 6 nm. I demonstrate the generality of this method, which I term ‘scaffolded DNA origami’, by assembling six different shapes, such as squares, triangles and five- pointed stars. I show that the method not only provides access to structures that approximate the outline of any desired shape, but also enables the creation of structures with arbitrarily shaped holes or surface patterns composed of more than 200 individual pixels. The patterns on the 100-nm-sized DNA shapes thus have a complexity that is tenfold higher than that of any previously self-assembled arbitrary pattern and comparable to that achieved using AFM and STM surface manipulation4.

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Folding DNA to create nanoscale shapes and patterns