DNA Motor Transports Cargo Along Carbon Nanotube

Illustration: Tae-Gon Cha/Purdue University

DNA nanotechnology has become one of the great hopes of molecular manufacturing in which large-scale objects could potentially be assembled from the most basic building blocks, atom-by-atom. Research is slowly revealing that many of the assumptions about DNA manufacturing are accurate, such as the ability of meeting design specifications down to atomically precise accuracy.

In the latest development for DNA manufacturing, researchers at Purdue University have developed a DNA motor that can transport nanoparticles up and down a carbon nanotube. While protein-based motors are doing this all the time in biological systems, the DNA the researchers have developed marks the first time that a synthetic molecule has been used to accomplish the same feat.

The DNA-based motor does not travel as fast as a protein-based motor does, but it does have the benefit of being controlled, of operating outside its natural environment and can be switched on or off.

The research, which was published in the journal Nature Nanotechnology (“A synthetic DNA motor that transports nanoparticles along carbon nanotubes”), demonstrated that DNA enzymes could transport cadmium sulfide nanocrystals along the length of a single-walled nanotube, deriving energy to carry its cargo by eating up RNA left along its path.

"Our motors extract chemical energy from RNA molecules decorated on the nanotubes and use that energy to fuel autonomous walking along the carbon nanotube track," said Jong Hyun Choi, a Purdue University assistant professor of mechanical engineering, in a press release.

The DNA enzyme has a core and two arms that come out from the top and bottom of the core. Movement of the DNA occurs as that core of the DNA enzyme cleaves a strand off the RNA. After one strand of RNA has been sliced off, the upper arm of the DNA enzyme grabs onto another strand of RNA and pulls the entire body along.

When the researchers concede that the DNA is slower at moving then their protein-based counterparts, they aren’t kidding. It took 20 hours for the DNA motor to move down the length of the carbon nanotube, which was several microns long.

While the researchers believe that increasing the temperature and acidity of the environment could speed up the process, it’s not clear how much they could speed it up.

It’s also not clear how RNA will always be around to help DNA motors to travel around in different environments. While molecular manufacturing adherents will no doubt be encouraged by this research, we may not need to worry about “grey goo” overrunning our planet as nanobots go about eating everything up to feed themselves.


ORIGINAL: IEEE Spectrum
By Dexter Johnson
Posted 19 Dec 2013 | 21:14 GMT

Nanotechnology milestone: general method for designing stable proteins

ORIGINAL: Foresight Institute

Comparison of computational models with experimentally determined structure: design model (left) and NMR structure (right). Credit: Nobuyasu Koga et al./Nature)

Yet another milestone along the protein design molecular engineering path to advanced nanotechnology has been reached, thanks to the efforts of the laboratory of David Baker, one of the 2004 winners of the Foresight Feynman Prize in Nanotechnology for Theoretical work. From KurzweilAI “How to design proteins from scratch“:

… By following a set of rules, they designed five proteins from scratch that fold reliably into predicted conformations. In a blind test, the team showed that the synthesized proteins closely match the predicted structures.

“What you have now is a flexible set of building blocks for nanoscale assembly,” says Jeremy England, a molecular biophysicist at the Massachusetts Institute of Technology in Cambridge, who was not involved in the work. …

More detail is given in a commentary in Nature, the journal in which the research was published “Proteins made to order: Researchers design proteins from scratch with predictable structures“:.

… Baker’s proteins are in a sense “platonic ideals”, he says: simple backbone constructs with every amino acid optimized to fold into the prescribed, stable structure. In this way they differ from natural proteins, whose folded structures represent a compromise between the competing requirements of optimum folding and biological function, leading to “frustrated” parts of the sequence that may be essential for function but are destabilizing to the fold. As evidence of their stability, the designed proteins melt at about 100 °C, Koga says, compared to 40–50 °C for a natural protein. …

The best summary of the significance of this result is given by the authors in the conclusion of their paper (reference numbers omitted from quotation):

The design principles and methodology we have described should allow the ready design of a wide range of robust and stable protein building blocks for the next generation of engineered functional proteins. Almost all protein design and engineering efforts so far have repurposed naturally occurring proteins that evolved for some other, often unrelated, function. It should now become possible to custom-design protein scaffolds ideal for the desired function, and to build larger assemblies and materials from robust ideal building blocks.

From the standpoint of advanced nanotechnology/molecular manufacturing, the “build larger assemblies” part is especially interesting. The abstract of the research is available on the journal web site, and the authors have made a full text PDF available on the Baker lab web site.

—James Lewis, PhD

This entry was posted on Wednesday, November 21st, 2012 at 1:13 PM and is filed under Atomically Precise Manufacturing (APM), Bionanotechnology, Computational nanotechnology, Molecular Nanotechnology, Molecular manufacturing, Nano, Nanobiotechnology, Nanotech, Nanotechnology, Productive Nanosystems, Research.