Tag Archives: DNA origami

Purifying DNA origami nanostructures with a LEGO robot

Leave a reply

This July 20, 2023 article by Bob Yirka for phys.org highlights some frugal science, Note: A link has been removed,

A team of bioengineers at Arizona State University has found a way to use a LEGO robot as a gradient mixer in one part of a process to create DNA origami nanostructures. In their paper published on the open-access site PLOS [Public Library of Science] ONE, the group describes how they made their mixer and its performance.

To create DNA origami structures, purification of DNA [deoxyribonucleic acid] origami nanostructures is required. This is typically done using rate-zone centrifugation, which involves the use of a relatively expensive piece of a machinery, a gradient mixer. In this new effort, the team at ASU has found that it is possible to build such a mixer using off-the-shelf LEGO kits.

…

I found a video provided by MindSpark Media describing the process on YouTube,

I’d love to know who paid for the video and why. This is pretty slick and it’s not from the Arizona State University’s (ASU) media team.

It gets more interesting on the MindSpark Media About webpage,

MindSpark Media is an independent media unit focusing on all major Media & Marketing services that includes Media Buying and Selling activities, bringing out special features on various supplements/country reports and international features on topics of interest in association with various leading English & Arabic vernaculars in the UAE [United Arab Emirates] and across MENA [Middle East and North Africa].

MindSpark Media is a complete media-selling experience that offers its clientele a wholesome exposure to the best media brands in the country. We also offer an opportunity to meet up and interact with the top brass of the industry & corporates for their advertorial packages including one-to-one interviews with photo-shoot sessions etc.

MindSpark Media delivers client-tailored advertorials that includes their product advertisements, features and interviews published in the form of special reports, supplements & special features, which are released and distributed with top-notch publications in the UAE.

We also focus on advertising activities in the media-buying sector such as Print, Outdoor, TV, Radio and Corporate Video, e-commerce & web-designing for clients in the UAE, MENA and beyond.

…

Perhaps the researchers are hoping to commercialize the work in some fashion? I couldn’t find any mention of a startup or other commercial entity but it’s a common practice these days in the US and, increasingly, many other countries.

Getting back to the research, here’s a link to and a citation for the paper,

Gradient-mixing LEGO robots for purifying DNA origami nanostructures of multiple components by rate-zonal centrifugation by Jason Sentosa, Franky Djutanta, Brian Horne, Dominic Showkeir, Robert Rezvani, Chloe Leff, Swechchha Pradhan, Rizal F. Hariadi. PLOS ONE (2023). DOI: 10.1371/journal.pone.0283134 Published: July 19, 2023

This paper is open access.

Beginner’s guide to folding DNA origami

Leave a reply

I think this Aug. 6, 2010 post, Folding, origami, and shapeshifting and an article with over 50,000 authors is the first time I wrote about DNA (deoxyribonucleic acid) and origami (the Japanese art of paper folding).

Since then, the technique has become even more popular with the result that the US National Institute of Standards and Technology (NIST) has produced a beginner’s guide, according to a Jan. 8, 2021 news item on Nanowerk,

In a technique known as DNA origami, researchers fold long strands of DNA over and over again to construct a variety of tiny 3D structures, including miniature biosensors and drug-delivery containers. Pioneered at the California Institute of Technology in 2006, DNA origami has attracted hundreds of new researchers over the past decade, eager to build receptacles and sensors that could detect and treat disease in the human body, assess the environmental impact of pollutants, and assist in a host of other biological applications.

Although the principles of DNA origami are straightforward, the technique’s tools and methods for designing new structures are not always easy to grasp and have not been well documented. In addition, scientists new to the method have had no single reference they could turn to for the most efficient way of building DNA structures and how to avoid pitfalls that could waste months or even years of research.

That’s why Jacob Majikes and Alex Liddle, researchers at the National Institute of Standards and Technology (NIST) who have studied DNA origami for years, have compiled the first detailed tutorial on the technique. Their comprehensive report provides a step-by-step guide to designing DNA origami nanostructures, using state-of-the-art tools.

…

Here’s an image illustrating some of the techniques for DNA origami,

Caption: Collage shows some of the techniques and designs employed in DNA origami. Credit: K. Dill/NIST

A Jan. 8, 2021 US NIST news release (also on EurekAlert), which originated the news item, provide more detail as to the authors’ motivations, objectives, and future plans for their beginner’s guide,

“We wanted to take all the tools that people have developed and put them all in one place, and to explain things that you can’t say in a traditional journal article,” said Majikes. “Review papers might tell you everything that everyone’s done, but they don’t tell you how the people did it. “

DNA origami relies on the ability of complementary base pairs of the DNA molecule to bind to each other. Among DNA’s four bases — adenine (A), cytosine (C), guanine (G) and thymine (T) — A binds with T and G with C. This means that a specific sequence of As, Ts, Cs and Gs will find and bind to its complement.

The binding enables short strands of DNA to act as “staples,” keeping sections of long strands folded or joining separate strands. A typical origami design may require 250 staples. In this way, the DNA can self-assemble into a variety of shapes, forming a nanoscale framework to which an assortment of nanoparticles — many useful in medical treatment, biological research and environmental monitoring — can attach.

The challenges in using DNA origami are twofold, said Majikes. First, researchers are fabricating 3D structures using a foreign language — the base pairs A, G, T and C. In addition, they’re using those base-pair staples to twist and untwist the familiar double helix of DNA molecules so that the strands bend into specific shapes. That can be difficult to design and visualize. Majikes and Liddle urge researchers to strengthen their design intuition by building 3D mock-ups, such as sculptures made with bar magnets, before they start fabrication. These models, which can reveal which aspects of the folding process are critical and which ones are less important, should then be “flattened” into 2D to be compatible with computer-aided design tools for DNA origami, which typically use two-dimensional representations.

DNA folding can be accomplished in a variety of ways, some less efficient than others, noted Majikes. Some strategies, in fact, may be doomed to failure.

“Pointing out things like ‘You could do this, but it’s not a good idea’ — that type of perspective isn’t in a traditional journal article, but because NIST is focused on driving the state of technology in the nation, we’re able to publish this work in the NIST journal,” Majikes said. “I don’t think there’s anywhere else that would have given us the leeway and the time and the person hours to put all this together.”

Liddle and Majikes plan to follow up their work with several additional manuscripts detailing how to successfully fabricate nanoscale devices with DNA.

Here’s a link to and a citation for the beginner’s guide,

DNA Origami Design: A How-To Tutorial by Majikes, Jacob M. and Liddle, J. Alexander. Journal of Research of the National Institute of Standards and Technology Volume 126, Article No. 126001 (2021) Published online Jan. 8, 2021. DOI: 10.6028/jres.126.001

This is open access and it include such gems as this,

1.2 Education or Skill Level

Readers of this tutorial should be familiar with the physical properties of B-DNA, single-stranded DNA (ssDNA), and crossover junctions. In addition, once ready to create a structure for a specific application, the designer should determine the full list of functional requirements. This list includes answers to the following questions: What should the structure do? What specific properties are critical to the system’s performance?

1.3 Prerequisites

The designer should have either sufficient paper for manual design (not recommended) or a design program such as cadnano [1] (all versions sufficient), nanoengineer®, ParaboninSēquio®, or equivalent.1 A registered account with three-dimensional (3D) structure prediction servers such as CanDo [2, 3] is also recommended.

1.4Tools or Equipment

Equipment includes desktop or laptop computer equipment, craft supplies for macroscale models, and DNA nanotechnology computer-aided design (CAD) software.

Feel free to go forth and fold!

A DNA origami-based nanoscopic force clamp

Leave a reply

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

Leave a reply

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

Leave a reply

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

Leave a reply

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

Leave a reply

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

Leave a reply

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)

Leave a reply

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.