Tag Archives: DNA origami

A DNA origami-based nanoscopic force clamp

Nanoclamp made of DNA strands. Illustration: Christoph Hohmann

Nanoclamp made of DNA strands. Illustration: Christoph Hohmann

An Oct. 21, 2016 news item on ScienceDaily announces a new nanotool,

Physicists at Ludwig-Maximilians-Universitat (LMU) in Munich have developed a novel nanotool that provides a facile means of characterizing the mechanical properties of biomolecules.

An Oct. 21, 2016 Ludwig-Maximilians-Universitat (LMU) press release (also on EurekAlert), which originated the news item, explains the work in more detail (Note: A link has been removed),

Faced with the thousands of proteins and genes found in virtually every cell in the body, biologists want to know how they all work exactly: How do they interact to carry out their specific functions and how do they respond and adapt to perturbations? One of the crucial factors in all of these processes is the question of how biomolecules react to the minuscule forces that operate at the molecular level. LMU physicists led by Professor Tim Liedl, in collaboration with researchers at the Technical University in Braunschweig and at Regensburg University, have come up with a method that allows them to exert a constant force on a single macromolecule with dimensions of a few nanometers, and to observe the molecule’s response. The researchers can this way test whether or not a protein or a gene is capable of functioning normally when its structure is deformed by forces of the magnitude expected in the interior of cells. This new method of force spectroscopy uses self-assembled nanoscopic power gauges, requires no macroscopic tools and can analyze large numbers of molecules in parallel, which speeds up the process of data acquisition enormously.

With their new approach, the researchers have overcome two fundamental limitations of the most commonly used force spectroscopy instruments. In the case of force microscopy and methodologies based on optical or magnetic tweezers, the molecules under investigation are always directly connected to a macroscopic transducer. They require precise control of the position of an object – a sphere or a sharp metal tip on the order of a micrometer in size – that exerts a force on molecules that are anchored to that object. This strategy is technically extremely demanding and the data obtained is often noisy. Furthermore, these procedures can only be used to probe molecules one at a time. The new method dispenses with all these restrictions. “The structures we use operate completely autonomously“, explains Philipp Nickels, a member of Tim Liedl’s research group. “And we can use them to study countless numbers of molecules simultaneously.”

A feather-light touch

The members of the Munich group, which is affiliated with the Cluster of Excellence NIM (Nanosystems Initiative Munich), are acknowledged masters of “DNA origami”. This methodology exploits the base-pairing properties of DNA for the construction of nanostructures from strands that fold up and pair locally in a manner determined by their nucleotide sequences. In the present case, the DNA sequences are programmed to interact with each other in such a way that the final structure is a molecular clamp that can be programmed to exert a defined force on a test molecule. To this end, a single-stranded DNA that contains a specific sequence capable of recruiting the molecule of interest spans from one arm of the clamp to the other. The applied force can then be tuned by changing the length of the single strand base by base. “That is equivalent to stretching a spring ever so-o-o slightly,” says Nickels. Indeed, by this means it is possible to apply extremely tiny forces between 1 and 15 pN (1 pN = one billionth of a Newton) – comparable in magnitude to those that act on proteins and genes in cells. “In principle, we can capture any type of biomolecule with these clamps and investigate its physical properties,” says Tim Liedl.

The effect of the applied force is read out by taking advantage of the phenomenon of Förster Resonant Energy Transfer (FRET). “FRET involves the transfer of energy between two fluorescent dyes and is strongly dependent on the distance between them.” explains Professor Philip Tinnefeld from TU Braunschweig. When the force applied to the test molecule is sufficient to deform it, the distance between the fluorescent markers changes and the magnitude of energy transfer serves as an exquisitely precise measure of the distortion of the test molecule on the nanometer scale.

Together with Dina Grohmann from Universität Regensburg, the team has used the new technique to investigate the properties of the so-called TATA Binding Protein, an important gene regulator which binds to a specific upstream nucleotide sequence in genes and helps to trigger their expression. They found that the TATA protein can no longer perform its normal function if its target sequence is subjected to a force of more than 6 pN. – The new technology has just made its debut. But since the clamps are minuscule and operate autonomously, it may well be possible in the future to use them to study molecular processes in living cells in real time.

Sometimes reading these news releases, my mind is boggled. What an extraordinary time to live.

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

Molecular force spectroscopy with a DNA origami–based nanoscopic force clamp by Philipp C. Nickels, Bettina Wünsch, Phil Holzmeister, Wooli Bae, Luisa M. Kneer, Dina Grohmann, Philip Tinnefeld, Tim Lied. Science  21 Oct 2016: Vol. 354, Issue 6310, pp. 305-307 DOI: 10.1126/science.aah5974

This paper is behind a paywall.

DNA origami as Van Gogh’s Starry Night

This glowing reproduction of "The Starry Night" contains 65,536 pixels and is the width of a dime across. Credit: Ashwin Gopinath/Caltech

This glowing reproduction of “The Starry Night” contains 65,536 pixels and is the width of a dime across.
Credit: Ashwin Gopinath/Caltech

It may take you a few seconds (it did me) but it’s possible to see Van Gogh’s Starry Night in this image. A July 12, 2016 news item on ScienceDaily reveals more,

Using folded DNA [deoxyribonucleic acid] to precisely place glowing molecules within microscopic light resonators, researchers at Caltech have created one of the world’s smallest reproductions of Vincent van Gogh’s The Starry Night.

A July 12, 2016 Caltech news release (also on EurekAlert) by Richard Perkins, which originated the news item, provides more information about the image, DNA origami, and this latest research on coupling light emitters to photonic crystal cavities (Note: Links have been removed),

The monochrome image—just the width of a dime across—was a proof-of-concept project that demonstrated, for the first time, how the precision placement of DNA origami can be used to build chip-based devices like computer circuits at smaller scales than ever before.

DNA origami, developed 10 years ago by Caltech’s Paul Rothemund (BS ’94), is a technique that allows researchers to fold a long strand of DNA into any desired shape. The folded DNA then acts as a scaffold onto which researchers can attach and organize all kinds of nanometer-scale components, from fluorescent molecules to electrically conductive carbon nanotubes to drugs.

“Think of it a bit like the pegboards people use to organize tools in their garages, only in this case, the pegboard assembles itself from DNA strands and the tools likewise find their own positions,” says Rothemund, research professor of bioengineering, computing and mathematical sciences, and computation and neural systems. “It all happens in a test tube without human intervention, which is important because all of the parts are too small to manipulate efficiently, and we want to make billions of devices.”

The process has the potential to influence a variety of applications from drug delivery to the construction of nanoscale computers. But for many applications, organizing nanoscale components to create devices on DNA pegboards is not enough; the devices have to be wired together into larger circuits and need to have a way of communicating with larger-scale devices.

One early approach was to make electrodes first, and then scatter devices randomly on a surface, with the expectation that at least a few would land where desired, a method Rothemund describes as “spray and pray.”

In 2009, Rothemund and colleagues at IBM Research first described a technique through which DNA origami can be positioned at precise locations on surfaces using electron-beam lithography to etch sticky binding sites that have the same shape as the origami. For example, triangular sticky patches bind triangularly folded DNA.

Over the last seven years, Rothemund and Ashwin Gopinath, senior postdoctoral scholar in bioengineering at Caltech, have refined and extended this technique so that DNA shapes can be precisely positioned on almost any surface used in the manufacture of computer chips. In the Nature paper, they report the first application of the technique—using DNA origami to install fluorescent molecules into microscopic light sources.

“It’s like using DNA origami to screw molecular light bulbs into microscopic lamps,” Rothemund says.

In this case, the lamps are microfabricated structures called photonic crystal cavities (PCCs), which are tuned to resonate at a particular wavelength of light, much like a tuning fork vibrates with a particular pitch. Created within a thin glass-like membrane, a PCC takes the form of a bacterium-shaped defect within an otherwise perfect honeycomb of holes.

“Depending on the exact size and spacing of the holes, a particular wavelength of light reflects off the edge of the cavity and gets trapped inside,” says Gopinath, the lead author of the study. He built PCCs that are tuned to resonate at around 660 nanometers, the wavelength corresponding to a deep shade of the color red. Fluorescent molecules tuned to glow at a similar wavelength light up the lamps—provided they stick to exactly the right place within the PCC.

“A fluorescent molecule tuned to the same color as a PCC actually glows more brightly inside the cavity, but the strength of this coupling effect depends strongly on the molecule’s position within the cavity. A few tens of nanometers is the difference between the molecule glowing brightly, or not at all,” Gopinath says.

By moving DNA origami through the PCCs in 20-nanometer steps, the researchers found that they could map out a checkerboard pattern of hot and cold spots, where the molecular light bulbs either glowed weakly or strongly. As a result, they were able to use DNA origami to position fluorescent molecules to make lamps of varying intensity. Similar structures have been proposed to power quantum computers and for use in other optical applications that require many tiny light sources integrated together on a single chip.

“All previous work coupling light emitters to PCCs only successfully created a handful of working lamps, owing to the extraordinary difficulty of reproducibly controlling the number and position of emitters in a cavity,” Gopinath says. To prove their new technology, the researchers decided to scale-up and provide a visually compelling demonstration. By creating PCCs with different numbers of binding sites, Gopinath was able to reliably install any number from zero to seven DNA origami, allowing him to digitally control the brightness of each lamp. He treated each lamp as a pixel with one of eight different intensities, and produced an array of 65,536 of the PCC pixels (a 256 x 256 pixel grid) to create a reproduction of Van Gogh’s “The Starry Night.”

Now that the team can reliably combine molecules with PCCs, they are working to improve the light emitters. Currently, the fluorescent molecules last about 45 seconds before reacting with oxygen and “burning out,” and they emit a few shades of red rather than a single pure color. Solving both these problems will help with applications such as quantum computers.

“Aside from applications, there’s a lot of fundamental science to be done,” Gopinath says.

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

Engineering and mapping nanocavity emission via precision placement of DNA origami by Ashwin Gopinath, Evan Miyazono, Andrei Faraon, & Paul W. K. Rothemund. Nature (2016) doi:10.1038/nature18287 Published online 11 July 2016

This paper is behind a paywall.

DNA as a framework for rationally designed nanostructures

After publishing a June 15, 2016 post about taking DNA (deoxyribonucleic acid) beyond genetics, it seemed like a good to publish a companion piece featuring a more technical explanation of at least one way DNA might provide the base for living computers and robots. From a June 13, 2016 BrookHaven National Laboratory news release (also on EurekAlert),

A cube, an octahedron, a prism–these are among the polyhedral structures, or frames, made of DNA that scientists at the U.S. Department of Energy’s (DOE) Brookhaven National Laboratory have designed to connect nanoparticles into a variety of precisely structured three-dimensional (3D) lattices. The scientists also developed a method to integrate nanoparticles and DNA frames into interconnecting modules, expanding the diversity of possible structures.

These achievements, described in papers published in Nature Materials and Nature Chemistry, could enable the rational design of nanomaterials with enhanced or combined optical, electric, and magnetic properties to achieve desired functions.

“We are aiming to create self-assembled nanostructures from blueprints,” said physicist Oleg Gang, who led this research at the Center for Functional Nanomaterials (CFN), a DOE Office of Science User Facility at Brookhaven. “The structure of our nanoparticle assemblies is mostly controlled by the shape and binding properties of precisely designed DNA frames, not by the nanoparticles themselves. By enabling us to engineer different lattices and architectures without having to manipulate the particles, our method opens up great opportunities for designing nanomaterials with properties that can be enhanced by precisely organizing functional components. For example, we could create targeted light-absorbing materials that harness solar energy, or magnetic materials that increase information-storage capacity.”

The news release goes on to describe the frames,

Gang’s team has previously exploited DNA’s complementary base pairing–the highly specific binding of bases known by the letters A, T, G, and C that make up the rungs of the DNA double-helix “ladder”–to bring particles together in a precise way. Particles coated with single strands of DNA link to particles coated with complementary strands (A binds with T and G binds with C) while repelling particles coated with non-complementary strands.

They have also designed 3D DNA frames whose corners have single-stranded DNA tethers to which nanoparticles coated with complementary strands can bind. When the scientists mix these nanoparticles and frames, the components self-assemble into lattices that are mainly defined by the shape of the designed frame. The Nature Materials paper describes the most recent structures achieved using this strategy.

“In our approach, we use DNA frames to promote the directional interactions between nanoparticles such that the particles connect into specific configurations that achieve the desired 3D arrays,” said Ye Tian, lead author on the Nature Materials paper and a member of Gang’s research team. “The geometry of each particle-linking frame is directly related to the lattice type, though the exact nature of this relationship is still being explored.”

So far, the team has designed five polyhedral frame shapes–a cube, an octahedron, an elongated square bipyramid, a prism, and a triangular bypyramid–but a variety of other shapes could be created.

“The idea is to construct different 3D structures (buildings) from the same nanoparticle (brick),” said Gang. “Usually, the particles need to be modified to produce the desired structures. Our approach significantly reduces the structure’s dependence on the nature of the particle, which can be gold, silver, iron, or any other inorganic material.”

Nanoparticles (yellow balls) capped with short single-stranded DNA (blue squiggly lines) are mixed with polyhedral DNA frames (from top to bottom): cube, octahedron, elongated square bipyramid, prism, and triangular bipyramid. The frames' vertices are encoded with complementary DNA strands for nanoparticle binding. When the corresponding frames and particles mix, they form a framework. Courtesy of Brookhaven National Laboratory

Nanoparticles (yellow balls) capped with short single-stranded DNA (blue squiggly lines) are mixed with polyhedral DNA frames (from top to bottom): cube, octahedron, elongated square bipyramid, prism, and triangular bipyramid. The frames’ vertices are encoded with complementary DNA strands for nanoparticle binding. When the corresponding frames and particles mix, they form a framework. Courtesy of Brookhaven National Laboratory

There’s also a discussion about how DNA origami was used to design the frames,

To design the frames, the team used DNA origami, a self-assembly technique in which short synthetic strands of DNA (staple strands) are mixed with a longer single strand of biologically derived DNA (scaffold strand). When the scientists heat and cool this mixture, the staple strands selectively bind with or “staple” the scaffold strand, causing the scaffold strand to repeatedly fold over onto itself. Computer software helps them determine the specific sequences for folding the DNA into desired shapes.

The folding of the single-stranded DNA scaffold introduces anchoring points that contain free “sticky” ends–unpaired strings of DNA bases–where nanoparticles coated with complementary single-strand tethers can attach. These sticky ends can be positioned anywhere on the DNA frame, but Gang’s team chose the corners so that multiple frames could be connected.

For each frame shape, the number of DNA strands linking a frame corner to an individual nanoparticle is equivalent to the number of edges converging at that corner. The cube and prism frames have three strands at each corner, for example. By making these corner tethers with varying numbers of bases, the scientists can tune the flexibility and length of the particle-frame linkages.

The interparticle distances are determined by the lengths of the frame edges, which are tens of nanometers in the frames designed to date, but the scientists say it should be possible to tailor the frames to achieve any desired dimensions.

The scientists verified the frame structures and nanoparticle arrangements through cryo-electron microscopy (a type of microscopy conducted at very low temperatures) at the CFN and Brookhaven’s Biology Department, and x-ray scattering at the National Synchrotron Light Source II (NSLS-II), a DOE Office of Science User Facility at Brookhaven.

The team started with a relatively simple form (from the news release),

In the Nature Chemistry paper, Gang’s team described how they used a similar DNA-based approach to create programmable two-dimensional (2D), square-like DNA frames around single nanoparticles.

DNA strands inside the frames provide coupling to complementary DNA on the nanoparticles, essentially holding the particle inside the frame. Each exterior side of the frame can be individually encoded with different DNA sequences. These outer DNA strands guide frame-frame recognition and connection.

Gang likens these DNA-framed nanoparticle modules to Legos whose interactions are programmed: “Each module can hold a different kind of nanoparticle and interlock to other modules in different but specific ways, fully determined by the complementary pairing of the DNA bases on the sides of the frame.”

In other words, the frames not only determine if the nanoparticles will connect but also how they will connect. Programming the frame sides with specific DNA sequences means only frames with complementary sequences can link up.

Mixing different types of modules together can yield a variety of structures, similar to the constructs that can be generated from Lego pieces. By creating a library of the modules, the scientists hope to be able to assemble structures on demand.

Finally, the discussion turns to the assembly of multifuctional nanomaterials (from the news release),

The selectivity of the connections enables different types and sizes of nanoparticles to be combined into single structures.

The geometry of the connections, or how the particles are oriented in space, is very important to designing structures with desired functions. For example, optically active nanoparticles can be arranged in a particular geometry to rotate, filter, absorb, and emit light–capabilities that are relevant for energy-harvesting applications, such as display screens and solar panels.

By using different modules from the “library,” Gang’s team demonstrated the self-assembly of one-dimensional linear arrays, “zigzag” chains, square-shaped and cross-shaped clusters, and 2D square lattices. The scientists even generated a simplistic nanoscale model of Leonardo da Vinci’s Vitruvian Man.

“We wanted to demonstrate that complex nanoparticle architectures can be self-assembled using our approach,” said Gang.

Again, the scientists used sophisticated imaging techniques–electron and atomic force microscopy at the CFN and x-ray scattering at NSLS-II–to verify that their structures were consistent with the prescribed designs and to study the assembly process in detail.

“Although many additional studies are required, our results show that we are making advances toward our goal of creating designed matter via self-assembly, including periodic particle arrays and complex nanoarchitectures with freeform shapes,” said Gang. “Our approach is exciting because it is a new platform for nanoscale manufacturing, one that can lead to a variety of rationally designed functional materials.”

Here’s an image illustrating among other things da Vinci’s Vitruvian Man,

A schematic diagram (left) showing how a nanoparticle (yellow ball) is incorporated within a square-like DNA frame. The DNA strands inside the frame (blue squiggly lines) are complementary to the DNA strands on the nanoparticle; the colored strands on the outer edges of the frame have different DNA sequences that determine how the DNA-framed nanoparticle modules can connect. The architecture shown (middle) is a simplistic nanoscale representation of Leonardo da Vinci's Vitruvian Man, assembled from several module types. The scientists used atomic force microscopy to generate the high-magnification image of this assembly (right). Courtesy Brookhaven National Laboratory

A schematic diagram (left) showing how a nanoparticle (yellow ball) is incorporated within a square-like DNA frame. The DNA strands inside the frame (blue squiggly lines) are complementary to the DNA strands on the nanoparticle; the colored strands on the outer edges of the frame have different DNA sequences that determine how the DNA-framed nanoparticle modules can connect. The architecture shown (middle) is a simplistic nanoscale representation of Leonardo da Vinci’s Vitruvian Man, assembled from several module types. The scientists used atomic force microscopy to generate the high-magnification image of this assembly (right). Courtesy Brookhaven National Laboratory

I enjoy the overviews provided by various writers and thinkers in the field but it’s details such as these that are often most compelling to me.

Taking DNA beyond genetics with living computers and nanobots

You might want to keep a salt shaker with you while reading a June 7, 2016 essay by Matteo Palma (Queen Mary’s University of London) about nanotechnology and DNA on The Conversation website (h/t June 7, 2016 news item on Nanowerk).

This is not a ‘hype’ piece as Palma backs every claim with links to the research while providing a good overview of some very exciting work but the mood is a bit euphoric so you may want to keep the earlier mentioned salt shaker nearby.

Palma offers a very nice beginner introduction especially helpful for someone who only half-remembers their high school biology (from the June 7, 2016 essay)

DNA is one of the most amazing molecules in nature, providing a way to carry the instructions needed to create almost any lifeform on Earth in a microscopic package. Now scientists are finding ways to push DNA even further, using it not just to store information but to create physical components in a range of biological machines.

Deoxyribonucleic acid or “DNA” carries the genetic information that we, and all living organisms, use to function. It typically comes in the form of the famous double-helix shape, made up of two single-stranded DNA molecules folded into a spiral. Each of these is made up of a series of four different types of molecular component: adenine (A), guanine (G), thymine (T), and cytosine (C).

Genes are made up from different sequences of these building block components, and the order in which they appear in a strand of DNA is what encodes genetic information. But by precisely designing different A,G,T and C sequences, scientists have recently been able to develop new ways of folding DNA into different origami shapes, beyond the conventional double helix.

This approach has opened up new possibilities of using DNA beyond its genetic and biological purpose, turning it into a Lego-like material for building objects that are just a few billionths of a metre in diameter (nanoscale). DNA-based materials are now being used for a variety of applications, ranging from templates for electronic nano-devices, to ways of precisely carrying drugs to diseased cells.

He highlights some Canadian work,

Designing electronic devices that are just nanometres in size opens up all sorts of possible applications but makes it harder to spot defects. As a way of dealing with this, researchers at the University of Montreal have used DNA to create ultrasensitive nanoscale thermometers that could help find minuscule hotspots in nanodevices (which would indicate a defect). They could also be used to monitor the temperature inside living cells.

The nanothermometers are made using loops of DNA that act as switches, folding or unfolding in response to temperature changes. This movement can be detected by attaching optical probes to the DNA. The researchers now want to build these nanothermometers into larger DNA devices that can work inside the human body.

He also mentions the nanobots that will heal your body (according to many works of fiction),

Researchers at Harvard Medical School have used DNA to design and build a nanosized robot that acts as a drug delivery vehicle to target specific cells. The nanorobot comes in the form of an open barrel made of DNA, whose two halves are connected by a hinge held shut by special DNA handles. These handles can recognise combinations of specific proteins present on the surface of cells, including ones associated with diseases.

When the robot comes into contact with the right cells, it opens the container and delivers its cargo. When applied to a mixture of healthy and cancerous human blood cells, these robots showed the ability to target and kill half of the cancer cells, while the healthy cells were left unharmed.

Palma is describing a very exciting development and there are many teams worldwide working on ways to make drugs more effective and less side effect-ridden. However there does seem to be a bit of a problem with targeted drug delivery as noted in my April 27, 2016 posting,

According to an April 27, 2016 news item on Nanowerk researchers at the University of Toronto (Canada) along with their collaborators in the US (Harvard Medical School) and Japan (University of Tokyo) have determined that less than 1% of nanoparticle-based drugs reach their intended destination …

Less than 1%? Admittedly, nanoparticles are not the same as nanobots but the problem is in the delivery, from my April 27, 2016 posting,

… the authors argue that, in order to increase nanoparticle delivery efficiency, a systematic and coordinated long-term strategy is necessary. To build a strong foundation for the field of cancer nanomedicine, researchers will need to understand a lot more about the interactions between nanoparticles and the body’s various organs than they do today. …

I imagine nanobots will suffer a similar fate since the actual delivery mechanism to a targeted cell is still a mystery.

I quite enjoyed Palma’s essay and appreciated the links he provided. My only proviso, keep a salt shaker nearby. That rosy future is going take a while to get here.

Nature celebrates some nanotechnology anniversaries

An April 5, 2016 editorial in Nature magazine celebrates some nanotechnology milestones (Note: Links have been removed),

In March 1986, the atomic force microscope (AFM) was introduced by Gerd Binnig, Calvin Quate and Christoph Gerber with a paper in the journal Physical Review Letters titled simply ‘Atomic force microscope’1. This was 5 years (to the month) after the precursor to the AFM, the scanning tunnelling microscope (STM), had first been successfully tested at IBM’s Zurich Research Laboratory by Binnig and the late Heinrich Rohrer, and 7 months before Binnig and Rohrer were awarded a share of the Nobel Prize in Physics for the design of the STM (the prize was shared with Ernst Ruska, the inventor of the electron microscope). Achieving atomic resolution with the AFM proved more difficult than with the STM. It was, for example, only two years after its invention that the STM provided atomic-resolution images of an icon of surface science, the 7 × 7 surface reconstruction of Si(111) (ref. 2), whereas it took 8 years to achieve a similar feat with the AFM3, 4.

The editorial also provides an explanation of how the AFM works,

The AFM works by scanning a sharp tip attached to a flexible cantilever across a sample while measuring the interaction between the tip and the sample surface. The technique can operate in a range of environments, including in liquid and in air, and unlike the STM, it can be used with insulating materials; in their original paper, Binnig and colleagues used the instrument to analyse an aluminium oxide sample.

Then, the editorial touches on DNA (deoxyribonucleic acid) nanotechnology (Note: Links have been removed),

The history of structural DNA nanotechnology can, like the AFM, be traced back to the early 1980s, when Nadrian Seeman suggested that the exquisite base-pairing rules of DNA could be exploited to build artificial self-assembled structures11. But the founding experiment of the field came later. In April 1991, Seeman and Junghuei Chen reported building a cube-like molecular complex from DNA using a combination of branched junctions and single-stranded ‘sticky’ ends12. A range of significant advances soon followed, from 2D DNA arrays to DNA-based nanomechanical devices.

Then, in March 2006, the field of structural DNA nanotechnology experienced another decisive moment: Paul Rothemund reported the development of DNA origami13. This technique involves folding a long single strand of DNA into a predetermined shape with the help of short ‘staple’ strands. Used at first to create 2D structures, which were incidentally characterized using the AFM, the approach was quickly expanded to the building of intricate 3D structures and the organization of other species such as nanoparticles and proteins. …

Happy reading!

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!

Nano-encrypted morse code in DNA (deoxyribonucleic acid)

This is not the first time something has written something into DNA. (J. Craig Venter included a quote from a James Joyce work into the DNA (mostly for fun) of one of his synthetic biology projects as per my Mar. 16, 2011 posting about Venter and the James Joyce estate’s copyright claim.) However, Professor Yi Lu and his team at the University of Illinois at Urbana-Champaign had a somewhat different purpose in mind when they encrypted morse code into DNA. From the Mar. 12, 2013 news item on Nanowerk,

Hidden in a tiny tile of interwoven DNA is a message. The message is simple, but decoding it unlocks the secret of dynamic nanoscale assembly.

Researchers at the University of Illinois at Urbana-Champaign have devised a dynamic and reversible way to assemble nanoscale structures and used it to encrypt a Morse code message. Led by Yi Lu, the Schenck Professor of Chemistry, the team published its development in the Journal of the American Chemical Society (“Nano-Encrypted Morse Code: A Versatile Approach to Programmable and Reversible Nanoscale Assembly and Disassembly”).

The Mar. 11, 2013 University of Illinois news release, which originated the news item and was written by Liz Ahlberg, explains how this ‘morse code’ encryption will lead to programmable assembly and disassembly,

“I think a critical challenge facing nanoscale science and engineering is reversible assembly,” Lu said. “Researchers are now pretty good at putting components in places they desire, but not very good at putting something on and taking it off again. Many applications need dynamic assembly. You don’t just want to assemble it once, you want to do it repeatedly, and not only using the same component, but also new components.”

The group took advantage of a chemical system common in biology. The protein streptavidin binds very strongly to the small organic molecule biotin – it grabs on and doesn’t let go. A small chemical tweak to biotin yields a molecule that also binds to streptavidin, but holds it loosely.

The researchers started with a template of DNA origami – multiple strands of DNA woven into a tile. They “wrote” their message in the DNA template by attaching biotin-bound DNA strands to specific locations on the tiles that would light up as dots or dashes. Meanwhile, DNA bound to the biotin derivative filled the other positions on the DNA template.

Then they bathed the tiles in a streptavidin solution. The streptavidin bonded to both the biotin and its derivative, making all the spots “light up” under an atomic force microscope and camouflaging the message. To reveal the hidden message, the researchers then put the tiles in a solution of free biotin. Since it binds to streptavidin so much more strongly, the biotin effectively removed the protein from the biotin derivative, so that only the DNA strands attached to the unaltered biotin kept hold of their streptavidin. The Morse code message, “NANO,” was clearly readable under the microscope.

The researchers also demonstrated non-Morse characters, creating tiles that could switch back and forth between a capital “I” and a lowercase “i” as streptavidin and biotin were alternately added. (See an animation of the process.)

All the work leading is to this (from the news release),

“This is an important step forward for nanoscale assembly,” Lu said. “Now we can encode messages in much smaller scale, which is interesting. There’s more information per square inch. But the more important advance is that now that we can carry out reversible assembly, we can explore much more versatile, much more dynamic applications.”

Next, the researchers plan to use their technique to create other functional systems. Lu envisions assembling systems to perform a task in chemistry, biology, sensing, photonics or other area, then replacing a component to give the system an additional function. Since the key to reversibility is in the different binding strengths, the technique is not limited to the biotin-streptavidin system and could work for a variety of molecules and materials.

“As long as the molecules used in the assembly have two different affinities, we can apply this particular concept into other templates or processes,” Lu said.

Interested parties can find the paper here,

Nano-Encrypted Morse Code: A Versatile Approach to Programmable and Reversible Nanoscale Assembly and Disassembly by Ngo Yin Wong, Hang Xing, Li Huey Tan, and Yi Lu. J. Am. Chem. Soc., 2013, 135 (8), pp 2931–2934 DOI: 10.1021/ja3122284 Publication Date (Web): February 2, 2013 Copyright © 2013 American Chemical Society

The article is behind a paywall.

Rail system and choreography metaphors in a couple of science articles

If you are going to use a metaphor/analogy when you’re writing about a science topic  because you want to reach beyond an audience that’s expert on the topic you’re covering or you want to grab attention from an audience that’s inundated with material, or you want to play (for writers, this can be a form of play [for this writer, anyway]), I think you need to remain true to your metaphor. I realize that’s a lot tougher than it sounds.

I’ve got examples of the use of metaphors/analogies in two recent pieces of science writing.

First, here’s the title for a Jan. 23, 2012 article by Samantha Chan for The Asian Scientist,

Scientists Build DNA Rail System For Nanomotors, Complete With Tracks & Switches

Then, there’s the text where the analogy/metaphor of a railway system with tracks and switchers is developed further and abandoned for origami tiles,

Expanding on previous work with engines traveling on straight tracks, a team of researchers at Kyoto University and the University of Oxford have used DNA building blocks to construct a motor capable of navigating a programmable network of tracks with multiple switches.

In this latest effort, the scientists built a network of tracks and switches atop DNA origami tiles, which made it possible for motor molecules to travel along these rail systems.

Sometimes, the material at hand is the issue. ‘DNA origami tiles’ is a term in this field so Chan can’t change it to ‘DNA origami ties’ which would fit with the railway analogy. By the way, the analogy itself comes from (or was influenced by) the title the scientists chose for their published paper in Nature Nanotechnology (it’s behind a paywall),

A DNA-based molecular motor that can navigate a network of tracks

All in all, this was a skillful attempt to get the most out of a metaphor/analogy.

For my second example, I’m using a Jan. 12, 2012 news release by John Sullivan for Princeton University which was published in Jan. 12, 2012 news item on Nanowerk. Here’s the headline from Princeton,

Ten-second dance of electrons is step toward exotic new computers

This sets up the text for the first few paragraphs (found in both the Princeton news release and the Nanowerk news item),

In the basement of Hoyt Laboratory at Princeton University, Alexei Tyryshkin clicked a computer mouse and sent a burst of microwaves washing across a silicon crystal suspended in a frozen cylinder of stainless steel.

The waves pulsed like distant music across the crystal and deep within its heart, billions of electrons started spinning to their beat.

Reaching into the silicon crystal and choreographing the dance of 100 billion infinitesimal particles is an impressive achievement on its own, but it is also a stride toward developing the technology for powerful machines known as quantum computers.

Sullivan has written some very appealing text for an audience who may or may not know about quantum computers.

Somebody on Nanowerk changed the headline to this,

Choreographing dance of electrons offers promise in pursuit of quantum computers

Here, the title has been skilfully reworded for an audience that knows more quantum computers while retaining the metaphor. Nicely done.

Sullivan’s text goes on to provide a fine explanation of an issue in quantum computing, maintaining coherence, for an audience not expert in quantum computing. The one niggle I do have is a shift in the metaphor,

To understand why it is so hard, imagine circus performers spinning plates on the top of sticks. Now imagine a strong wind blasting across the performance space, upending the plates and sending them crashing to the ground. In the subatomic realm, that wind is magnetism, and much of the effort in the experiment goes to minimizing its effect. By using a magnetically calm material like silicon-28, the researchers are able to keep the electrons spinning together for much longer.

Wasn’t there a way to stay with dance? You could have had dancers spinning props or perhaps the dancers themselves being blown off course and avoided the circus performers. Yes, the circus is more colourful and appealing but, in this instance, I would have worked to maintain the metaphor first introduced, assuming I’d noticed that I’d switched metaphors.

So, I think I can safely say that using metaphors is tougher than it looks.

Coatings that shake off bacteria and biological photocopying

The American Vacuum Society (AVS) is holding its 58th International Symposium and Exhibition from Oct. 30 – Nov. 4, 2011 in Nashville, Tennessee. Presentations are not focused on vacuuming (hoovering) floors but rather on something called vacuum science and they span from a presentation on bacteria and coatings to another on photocopying DNA to more.

From the Oct. 31, 2011 news item on Nanowerk,

“Sea water is a very aggressive biological system,” says Gabriel Lopez, whose lab at Duke University studies the interface of marine bacterial films with submerged surfaces. While the teeming abundance of ocean life makes coral reefs and tide pools attractive tourist destinations, for ships whose hulls become covered with slime, all this life can, quite literally, be a big drag. On just one class of U.S. Navy destroyer, biological build-up is estimated to cost more than $50 million a year, mostly in extra fuel, according to a 2010 study performed by researchers from the U.S. Naval Academy and Naval Surface Warfare Center in Maryland. Marine biofouling can also disrupt the operation of ocean sensors, heat-exchangers that suck in water to cool mechanical systems, and other underwater equipment.

I think rather than describing sea water as ‘aggressive’  which suggests intent, I’d use ‘active’ as Lopez does later in another context (excerpted from the news item),

Lopez and his group focus on a class of materials called stimuli-responsive surfaces. As the name implies, the materials will alter their physical or chemical properties in response to a stimulus, such as a temperature change. The coatings being tested in Lopez’s lab wrinkle on the micro- or nano-scale, shaking off slimy colonies of marine bacteria in a manner similar to how a horse might twitch its skin to shoo away flies. The researchers also consider how a stimulus might alter the chemical properties of a surface in a way that could decrease a marine organism’s ability to stick.

At the AVS Symposium, held Oct. 30 – Nov. 4 in Nashville, Tenn., Lopez will present results from experiments on two different types of stimuli-responsive surfaces: one that changes its texture in response to temperature and the other in response to an applied voltage. The voltage-responsive surfaces are being developed in collaboration with the laboratory of Xuanhe Zhao, also a Duke researcher, who found that insulating cables can fail if they deform under voltages. “Surprisingly, the same failure mechanism can be made useful in deforming surfaces of coatings and detaching biofouling,” Zhao said.

“The idea of an active surface is inspired by nature,” adds Lopez, who remembers being intrigued by the question of how a sea anemone’s waving tentacles are able to clean themselves. [emphasis mine] Other biological surfaces, such as shark skin, have already been copied by engineers seeking to learn from nature’s own successful anti-fouling systems.

(I did profile some biomimicry work being done with shark skin in my comments on part 4 of the Making Stuff programmes broadcast as part of the Nova series on PBS (US Public Broadcasting Stations) in my Feb. 10, 2011 posting.)

This next presentation is in the area of synthetic biology. From the Oct. 31, 2011 news item (DNA origami from inkjet synthesis produced strands) on Nanowerk,

In the emerging field of synthetic biology, engineers use biological building blocks, such as snippets of DNA, to construct novel technologies. One of the key challenges in the field is finding a way to quickly and economically synthesize the desired DNA strands. Now scientists from Duke University have fabricated a reusable DNA chip that may help address this problem by acting as a template from which multiple batches of DNA building blocks can be photocopied. The researchers have used the device to create strands of DNA which they then folded into unique nanoscale structures.

“We found that we had an “immortal” DNA chip in our hands,” says Ishtiaq Saaem, a biomedical engineering researcher at Duke and member of the team. [emphasis mine] “Essentially, we were able to do the biological copying process to release material off the chip tens of times. [emphasis mine] The process seems to work even using a chip that we made, used, stored in -20C for a while, and brought out and used again.”

After releasing the DNA from the chip, the team “cooked” it together with a piece of long viral DNA. “In the cooking process, the viral DNA is stapled into a desired shape by the smaller chip-derived DNA,” explains Saaem. One of the team’s first examples of DNA origami was a rectangle shape with a triangle attached on one side, which the researchers dubbed a “nano-house.” The structure could be used to spatially orient organic and inorganic materials, serve as a scaffold for drug delivery, or act as a nanoscale ruler, Saaem says.

I’m not very comfortable with the notion of an “immortal DNA chip” but then I have many reservations about synthetic biology. Still, I think it’s important to pay attention and consider the possibility that my fears about synthetic biology might make as much sense as the fears many had about electricity in the 19th century.