Tag Archives: Cryo-EM structure of a 3D DNA-origami object

Breakthroughs with self-assembling DNA-based nanoscaled structures

With all the talk about self-assembling DNA nanotechnology, it’s possible to misunderstand the stage of development this endeavour occupies as the title, Reality check for DNA Nanotechnology, for a Dec. 13, 2012 news release on EurekAlert suggests,

… This emerging technology employs DNA as a programmable building material for self-assembled, nanometer-scale structures. Many practical applications have been envisioned, and researchers recently demonstrated a synthetic membrane channel made from DNA. Until now, however, design processes were hobbled by a lack of structural feedback. Assembly was slow and often of poor quality.

In fact, the news release is touting two breakthroughs,

Now researchers led by Prof. Hendrik Dietz of the Technische Universitaet Muenchen (TUM) have removed these obstacles.

One barrier holding the field back was an unproven assumption. Researchers were able to design a wide variety of discrete objects and specify exactly how DNA strands should zip together and fold into the desired shapes. They could show that the resulting nanostructures closely matched the designs. Still lacking, though, was the validation of the assumed subnanometer-scale precise positional control. This has been confirmed for the first time through analysis of a test object designed specifically for the purpose. A technical breakthrough based on advances in fundamental understanding, this demonstration has provided a crucial reality check for DNA nanotechnology.

In a separate set of experiments, the researchers discovered that the time it takes to make a batch of complex DNA-based objects can be cut from a week to a matter of minutes, and that the yield can be nearly 100%. They showed for the first time that at a constant temperature, hundreds of DNA strands can fold cooperatively to form an object — correctly, as designed — within minutes. Surprisingly, they say, the process is similar to protein folding, despite significant chemical and structural differences. “Seeing this combination of rapid folding and high yield,” Dietz says, “we have a stronger sense than ever that DNA nanotechnology could lead to a new kind of manufacturing, with a commercial, even industrial future.” And there are immediate benefits, he adds: “Now we don’t have to wait a week for feedback on an experimental design, and multi-step assembly processes have suddenly become so much more practical.”

Dexter Johnson comments in his Dec. 18, 2012 posting (which includes an embedded video) on the Nanoclast blog (located on the Institute of Electrical and Electronics Engineers [IEEE] website),

The field of atomically precise manufacturing—or molecular manufacturing—has taken a big step towards realizing its promise with this latest research.  We may still be a long way from realizing the “nanotech rapture”  but certainly knowing that the objects built meet their design specifications and can be produced in minutes rather than weeks has to be recognized as a significant development.

Three papers have been published on these breakthroughs, here are the citations,

Xiao-chen Bai, Thomas G. Martin, Sjors H. W. Scheres, Hendrik Dietz. Cryo-EM structure of a 3D DNA-origami object. Proceedings of the National Academy of Sciences of the USA, Dec. 4, 2012, 109 (49) 20012-20017; on-line in PNAS Early Edition, Nov. 19, 2012. DOI: 10.1073/pnas.1215713109

Jean-Philippe J. Sobczak, Thomas G. Martin, Thomas Gerling, Hendrik Dietz. Rapid folding of DNA into nanoscale shapes at constant temperature. Science, vol. 338, issue 6113, pp. 1458-1461. DOI: 10.1126/science.1229919

See also: Martin Langecker, Vera Arnaut, Thomas G. Martin, Jonathan List, Stephan Renner, Michael Mayer, Hendrik Dietz, and Friedrich C. Simmel. Synthetic lipid membrane channels formed by designed DNA nanostructures. Science, vol. 338, issue 6109, pp. 932-936. DOI: 10.1126/science.1225624