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Mar 19, 2006

Genetic Engineering's Next Challenge: The Smiley Face

Genetic engineering holds a great deal of promise, from potentially curing a variety of human ailments to addressing nutritional deficiencies through transgenic crops. One project even aims to engineer into bacteria the ability to generate a variety of alternative fuels. When it comes to genetic engineering and its emerging potential, it seems that the only real limit to the field is that it can only be used to design or improve something that is actually alive.

Despite this “limitation,” some scientists have found that the raw material used in genetic engineering, DNA, could be an attractive building material for inanimate objects, on the nanoscale at least. When one takes into account DNA’s well-defined structure and fundamental symmetry, coupled with the infinite variability available through different lengths of chains of various permutations of its four constituent bases—adenine, guanine, cytosine, and thymine—this interest isn’t very surprising. These aspects of DNA stem from the specific pairing of its bases: adenine always binds to thymine, guanine to cytosine. This fundamental property allows a living cell to replicate its DNA and read the embedded code that details the sequences of all of the cell’s RNA and proteins. This property also makes DNA potentially useful for a variety of technical applications.

This week, a research article and accompanying news piece in Nature (subscription required) detail a compelling, and arguably very cool, breakthrough in the field of DNA nanotechnology. The report, by Paul Rothemund of Caltech, details a simple but apparently effective technique of designing and building virtually any two-dimensional shape using one long strand and several short pieces of DNA.

The method is fairly straightforward, and after a few planning steps nature takes care of the rest. After the desired shape has been chosen, the shape is conceptually filled in with rows of parallel DNA double helixes. The next step involves mapping one long single strand of DNA onto this template so that it zigzags over the entire surface, providing the shape with a great deal of stability. This piece of DNA is only single-stranded, though, so short pieces of DNA are then designed to be complementary to specific pieces of this long strand completing the double helixes. These pieces provide additional cross-links as well. After the DNA has been designed and manufactured, the individual pieces just have to be mixed together, and they’ll self-assemble into the desired shape, whatever that may be.

This is all well and good in theory, but, as they say, the proof of the pudding is in the eating:


In this figure, the top two rows are diagrams of the planned shape, and the bottom two rows are actual images taken with atomic force microscopy. The images in the third row from the top are 165nm wide each (roughly 1/150,000 of an inch). My personal favorite here is the “disk with three holes,” which most people would probably call a smiley face (you’ve got to love the unnecessarily dry language in these reports).

Even cooler than these images, in my opinion, are the next set, where some of the short cross-linking pieces of DNA were changed to create pixels:


The bright spots are areas more dense in DNA, formed when the cross-links fold upon themselves to form a double helix that sticks out of the image.

This is pretty neat, but can this technology be used for anything useful, instead of just making small low-resolution microscopic images? The author concludes the paper with his vision for the technology:
An obvious application of patterned DNA origami would be the creation of a 'nanobreadboard', to which diverse components could be added. The attachment of proteins, for example, might allow novel biological experiments aimed at modelling complex protein assemblies and examining the effects of spatial organization, whereas 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.

Rothemund’s use of the term “DNA origami” reminded me of a story I wrote for The Battalion last year entitled “Biochemical Origami”. There, I explored the search to understand how proteins fold into their three-dimensional shapes, which turns out to be a much more complicated area:
Our bodies are made up of different types of cells, which are themselves made up of different types of molecules. Some of the molecules, called proteins, are linear chains of different chemical blocks called amino acids and the true workhorses of the biochemical world.

A snake-like chain of amino acids without a distinct shape is virtually useless. Therefore, a protein must fold into a varying three-dimensional shape to function properly. This holds true in all life forms, from complex humans to bacteria made of only one tiny cell.

Nick Pace, professor of biochemistry at A&M, studies protein folding. He is one of many scientists trying to solve the "protein folding problem.”

"Protein folding means being able to predict the three-dimensional structure of a protein," Pace said.

Correct folding is important, Pace said, because "many diseases are protein folding diseases," including Alzheimer's disease, Huntington's disease and cystic fibrosis. In these diseases, incorrect folding of important proteins causes the disease's symptoms.

Think of protein folding as biochemical origami - a bland chemical chain masterfully folded into an elegant and efficient protein machine.

Theoretically, the specific order of amino acids should determine the three-dimensional shape of the protein, just like a sheet of paper able to fold itself into an elegant origami swan….

…In theory, protein folding is simple. Proteins are subject to the same physical laws as anything else. If one could understand the forces involved in protein folding, predicting the structure of new proteins should be fairly simple.

"It just turns out," Pace said, "that the physics involved in protein folding is a lot more complicated than we thought it would be."

Predicting the shapes of proteins—which are made up of combinations twenty different amino acids and do not following any simple geometric rules (i.e. no base pairing)—has proven extremely elusive. The basic shape of DNA, on the other hand, has been known since James Watson and Francis Crick first solved it in 1953. This discrepancy fits well with the differing roles DNA and proteins perform in the cell, with DNA functioning as a relatively stable linear code but proteins performing most of the varied and complex tasks that keep living things alive. It should not be surprising, then, that scientists have found these properties in DNA compatible with self-assembling nanoparticles, capitalizing on billions of years of evolution to take nanotechnology another impressive step forward.

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