Tag Archives: DNA nanotechnology

Customizing DNA nanotubes quickly and cheaply

Building on some work published earlier this year, scientists from McGill University (Montréal, Québec) created a new technique for building DNA nanotubes block by block (my March 2, 2015 posting) and, now, the newest research from the McGill team features a way of making long DNA strands with that technique, as mentioned in a May 7, 2015 news item on Azonano,

Imagine taking strands of DNA – the material in our cells that determines how we look and function – and using it to build tiny structures that can deliver drugs to targets within the body or take electronic miniaturization to a whole new level.

While it may still sound like science fiction to most of us, researchers have been piecing together and experimenting with DNA structures for decades. And, in recent years, work by scientists such as McGill University chemistry professor Hanadi Sleiman has moved the use of man-made DNA structures closer to a variety of real-world applications.

But as these applications continue to develop, they require increasingly large and complex strands of DNA. That has posed a problem, because the automated systems used for making synthetic DNA can’t produce strands containing more than about 100 bases (the chemicals that link up to form the strands). It can take hundreds of these short strands to assemble nanotubes for applications such as smart drug-delivery systems.

Here’s a video featuring one of the researchers taking about this latest work from McGill University,

A May 6, 2015 McGill University news release, which originated the news item, describes the long DNA nanotubes in more detail,

In new research published May 5 in Nature Communications, however, Sleiman’’s team at McGill reports that it has devised a technique to create much longer strands of DNA, including custom-designed sequence patterns. What’s more, this approach also produces large amounts of these longer strands in just a few hours, making the process potentially more economical and commercially viable than existing techniques.

The new method involves piecing together small strands one after the other, so that they attach into a longer DNA strand with the help of an enzyme known as ligase.  A second enzyme, polymerase, is then used to generate many copies of the long DNA strand, yielding larger volumes of the material. The polymerase process has the added advantage of correcting any errors that may have been introduced into the sequence, amplifying only the correctly sequenced, full-length product.

Designer DNA materials

The team used these strands as a scaffold to make DNA nanotubes, demonstrating that the technique allows the length and functions of the tubes to be precisely programmed. “In the end, what we get is a long, synthetic DNA strand with exactly the sequence of bases that we want, and with exactly as many repeat units as we want,” explains Sleiman, who co-authored the study with Graham Hamblin, who recently completed his doctorate, and PhD student Janane Rahbani.

“This work opens the door toward a new design strategy in DNA nanotechnology,” Sleiman says. “This could provide access to designer DNA materials that are economical and can compete with cheaper, but less versatile technologies. In the future, uses could range from customized gene and protein synthesis, to applications in nanoelectronics, nano-optics, and medicine, including diagnosis and therapy.”

Here’s a link to and a citation for the paper,

Sequential growth of long DNA strands with user-defined patterns for nanostructures and scaffolds by Graham D. Hamblin, Janane F. Rahbani, & Hanadi F. Sleiman. Nature Communications 6, Article number: 7065 doi:10.1038/ncomms8065 Published 05 May 2015

This article is behind a paywall.

A twist in my DNA

Professor Hao Yan’s team at Arizona State University (ASU) has created some new 2D and 3D DNA objects according to a Mar. 21, 2013 news release on EurekAlert,

In their latest twist to the technology, Yan’s team made new 2-D and 3-D objects that look like wire-frame art of spheres as well as molecular tweezers, scissors, a screw, hand fan, and even a spider web.

The Yan lab, which includes ASU Biodesign Institute colleagues Dongran Han, Suchetan Pal, Shuoxing Jiang, Jeanette Nangreave and assistant professor Yan Liu, published their results in the March 22 issue of Science.

Here’s where the twist comes in,

The twist in their ‘bottom up,’ molecular Lego design strategy focuses on a DNA structure called a Holliday junction. In nature, this cross-shaped, double-stacked DNA structure is like the 4-way traffic stop of genetics — where 2 separate DNA helices temporality meet to exchange genetic information. The Holliday junction is the crossroads responsible for the diversity of life on Earth, and ensures that children are given a unique shuffling of traits from a mother and father’s DNA.

In nature, the Holliday junction twists the double-stacked strands of DNA at an angle of about 60-degrees, which is perfect for swapping genes but sometimes frustrating for DNA nanotechnology scientists, because it limits the design rules of their structures.

“In principal, you can use the scaffold to connect multiple layers horizontally,” [which many research teams have utilized since the development of DNA origami by Cal Tech’s Paul Rothemund in 2006]. However, when you go in the vertical direction, the polarity of DNA prevents you from making multiple layers,” said Yan. “What we needed to do is rotate the angle and force it to connect.”

Making the new structures that Yan envisioned required re-engineering the Holliday junction by flipping and rotating around the junction point about half a clock face, or 150 degrees. Such a feat has not been considered in existing designs.

“The initial idea was the hardest part,” said Yan. “Your mind doesn’t always see the possibilities so you forget about it. We had to break the conceptual barrier that this could happen.”

In the new study, by varying the length of the DNA between each Holliday junction, they could force the geometry at the Holliday junctions into an unconventional rearrangement, making the junctions more flexible to build for the first time in the vertical dimension. Yan calls the backyard barbeque grill-shaped structure a DNA Gridiron.

“We were amazed that it worked!” said Yan. “Once we saw that it actually worked, it was relatively easy to implement new designs. Now it seems easy in hindsight. If your mindset is limited by the conventional rules, it’s really hard to take the next step. Once you take that step, it becomes so obvious.”

The DNA Gridiron designs are programmed into a viral DNA, where a spaghetti-shaped single strand of DNA is spit out and folded together with the help of small ‘staple’ strands of DNA that help mold the final DNA structure. In a test tube, the mixture is heated, then rapidly cooled, and everything self-assembles and molds into the final shape once cooled. Next, using sophisticated AFM and TEM imaging technology, they are able to examine the shapes and sizes of the final products and determine that they had formed correctly.

This approach has allowed them to build multilayered, 3-D structures and curved objects for new applications.

In addition to the EurekAlert version, you can find the full text, images, and video about the team’s paper in the Mar. 21, 2013 news item on ScienceDaily (a citation and link to the team’s paper is also included) or you can read the original Mar. 21, 2013 ASU news release. (Hao Yan’s work was last mentioned here in an Aug. 7, 2012 post.)

All of this talk of twists reminded me of a song by Tanita Tikaram, Twist in My Sobriety. I found this video of an acoustic performance (two guitars and a bass [the musical instrument not the fish]) which is even more sultry than original hit version,

Happy weekend!

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