Tag Archives: DNA

Physics, nanopores, viruses, and DNA

A June 17, 2014 news item on Azonano describes a project which could help scientists decode strands of DNA at top speeds,

Nanopores may one day lead a revolution in DNA sequencing. By sliding DNA molecules one at a time through tiny holes in a thin membrane, it may be possible to decode long stretches of DNA at lightning speeds. Scientists, however, haven’t quite figured out the physics of how polymer strands like DNA interact with nanopores. Now, with the help of a particular type of virus, researchers from Brown University have shed new light on this nanoscale physics.

“What got us interested in this was that everybody in the field studied DNA and developed models for how they interact with nanopores,” said Derek Stein, associate professor of physics and engineering at Brown [Brown University, US] who directed the research. “But even the most basic things you would hope models would predict starting from the basic properties of DNA — you couldn’t do it. The only way to break out of that rut was to study something different.”

A June 16, 2014 Brown University news release (also on EurekAlert), which originated the news item, describes the problems with nanopores,

The concept behind nanopore sequencing is fairly simple. A hole just a few billionths of a meter wide is poked in a membrane separating two pools of salty water. An electric current is applied to the system, which occasionally snares a charged DNA strand and whips it through the pore — a phenomenon called translocation. When a molecule translocates, it causes detectable variations in the electric current across the pore. By looking carefully at those variations in current, scientists may be able to distinguish individual nucleotides — the A’s, C’s, G’s and T’s coded in DNA molecules.

The first commercially available nanopore sequencers may only be a few years away, but despite advances in the field, surprisingly little is known about the basic physics involved when polymers interact with nanopores. That’s partly because of the complexities involved in studying DNA. In solution, DNA molecules form balls of random squiggles, which make understanding their physical behavior extremely difficult.

For example, the factors governing the speed of DNA translocation aren’t well understood. Sometimes molecules zip through a pore quickly; other times they slither more slowly, and nobody completely understands why.

One possible explanation is that the squiggly configuration of DNA causes each molecule to experience differences in drag as they’re pulled through the water toward the pore. “If a molecule is crumpled up next to the pore, it has a shorter distance to travel and experiences less drag,” said Angus McMullen, a physics graduate student at Brown and the study’s lead author. “But if it’s stretched out then it would feel drag along the whole length and that would cause it to go slower.”

The news release then goes on to detail a possible solution to the problem of why DNA translocation varies in speed. Answering this question about DNA translocation could lead to faster and more accurate nanopore sequencing,

The drag effect is impossible to isolate experimentally using DNA, but the virus McMullen and his colleagues studied offered a solution.

The researchers looked at fd, a harmless virus that infects e. coli bacteria. Two things make the virus an ideal candidate for study with nanpores. First, fd viruses are all identical clones of each other. Second, unlike squiggly DNA, fd virus is a stiff, rod-like molecule. Because the virus doesn’t curl up like DNA does, the effect of drag on each one should be essentially the same every time.

With drag eliminated as a source of variation in translocation speed, the researchers expected that the only source of variation would be the effect of thermal motion. The tiny virus molecules constantly bump up against the water molecules in which they are immersed. A few random thermal kicks from the rear would speed the virus up as it goes through the pore. A few kicks from the front would slow it down.

The experiments showed that while thermal motion explained much of the variation in translocation speed, it didn’t explain it all. Much to the researchers’ surprise, they found another source of variation that increased when the voltage across the pore was increased.

“We thought that the physics would be crystal clear,” said Jay Tang, associate professor of physics and engineering at Brown and one of the study’s co-authors. “You have this stiff [virus] with well-defined diameter and size and you would expect a very clear-cut signal. As it turns out, we found some puzzling physics we can only partially explain ourselves.”

The researchers can’t say for sure what’s causing the variation they observed, but they have a few ideas.

“It’s been predicted that depending on where [an object] is inside the pore, it might be pulled harder or weaker,” McMullen said. “If it’s in the center of the pore, it pulls a little bit weaker than if it’s right on the edge. That’s been predicted, but never experimentally verified. This could be evidence of that happening, but we’re still doing follow up work.

The new approach using a virus answered questions while leading to new insights and possibilities (from the news release),

A better understanding of translocation speed could improve the accuracy of nanopore sequencing, McMullen says. It would also be helpful in the crucial task of measuring the length of DNA strands. “If you can predict the translocation speed,” McMullen said, “then you can easily get the length of the DNA from how long its translocation was.”

The research also helped to reveal other aspects of the translocation process that could be useful in designing future devices. The study showed that the electrical current tends to align the viruses head first to the pore, but on occasions when they’re not lined up, they tend to bounce around on the edge of the pore until thermal motion aligns them to go through. However, when the voltage was turned too high, the thermal effects were suppressed and the virus became stuck to the membrane. That suggests a sweet spot in voltage where headfirst translocation is most likely.

None of this is observable directly — the system is simply too small to be seen in action. But the researchers could infer what was happening by looking at slight changes in the current across the pore.

“When the viruses miss, they rattle around and we see these little bumps in the current,” Stein said. “So with these little bumps, we’re starting to get an idea of what the molecule is doing before it slides through. Normally these sensors are blind to anything that’s going on until the molecule slides through.”

That would have been impossible to observe using DNA. The floppiness of the DNA molecule allows it to go through a pore in a folded configuration even if it’s not aligned head-on. But because the virus is stiff, it can’t fold to go through. That enabled the researchers to isolate and observe those contact dynamics.

“These viruses are unique,” Stein said. “They’re like perfect little yardsticks.”

In addition to shedding light on basic physics, the work might also have another application. While the fd virus itself is harmless, the bacteria it infects — e. coli — is not. Based on this work, it might be possible to build a nanopore device for detecting the presence of fd, and by proxy, e. coli. Other dangerous viruses — Ebola and Marburg among them — share the same rod-like structure as fd.

“This might be an easy way to detect these viruses,” Tang said. “So that’s another potential application for this.”

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

Stiff filamentous virus translocations through solid-state nanopores by Angus McMullen, Hendrick W. de Haan, Jay X. Tang, & Derek Stein. Nature Communications 5, Article number: 4171 doi:10.1038/ncomms5171 Published 16 June 2014

This paper is behind a paywall.

Chad Mirkin’s periodic table of modified nucleic acid nanoparticles

Chad Mirkin has been pushing his idea for a new periodic table of ‘nanoparticles’ since at least Feb. 2013 (I wrote about this and some of Mirkin’s other work in my Feb. 19, 2013 posting) when he presented it at the 2013 American Association for the Advancement of Science (AAAS) annual meeting in Boston, Massachusetts. From a Feb. 17, 2013 news item on ScienceDaily,

Northwestern University’s Chad A. Mirkin, a leader in nanotechnology research and its application, has developed a completely new set of building blocks that is based on nanoparticles and DNA. Using these tools, scientists will be able to build — from the bottom up, just as nature does — new and useful structures.

Mirkin will discuss his research in a session titled “Nucleic Acid-Modified Nanostructures as Programmable Atom Equivalents: Forging a New Periodic Table” at the American Association for the Advancement of Science (AAAS) annual meeting in Boston.

“We have a new set of building blocks,” Mirkin said. “Instead of taking what nature gives you, we can control every property of the new material we make. [emphasis mine] We’ve always had this vision of building matter and controlling architecture from the bottom up, and now we’ve shown it can be done.”

Mirkin seems a trifle grandiose; I’m hoping he doesn’t have any grand creation projects that require seven days.

Getting back to the new periodic table, the Feb. 13, 2013 Northwestern University news release by Megan Fellman, which originated the news item,  provides a few more details,

Using nanoparticles and DNA, Mirkin has built more than 200 different crystal structures with 17 different particle arrangements. Some of the lattice types can be found in nature, but he also has built new structures that have no naturally occurring mineral counterpart.
….
Mirkin can make new materials and arrangements of particles by controlling the size, shape, type and location of nanoparticles within a given particle lattice. He has developed a set of design rules that allow him to control almost every property of a material.

New materials developed using his method could help improve the efficiency of optics, electronics and energy storage technologies. “These same nanoparticle building blocks have already found wide-spread commercial utility in biology and medicine as diagnostic probes for markers of disease,” Mirkin added.

With this present advance, Mirkin uses nanoparticles as “atoms” and DNA as “bonds.” He starts with a nanoparticle, which could be gold, silver, platinum or a quantum dot, for example. The core material is selected depending on what physical properties the final structure should have.

He then attaches hundreds of strands of DNA (oligonucleotides) to the particle. The oligonucleotide’s DNA sequence and length determine how bonds form between nanoparticles and guide the formation of specific crystal lattices.

“This constitutes a completely new class of building blocks in materials science that gives you a type of programmability that is extraordinarily versatile and powerful,” Mirkin said. “It provides nanotechnologists for the first time the ability to tailor properties of materials in a highly programmable way from the bottom up.”

Mirkin and his colleagues have since published a paper about this new periodic table in Angewandte Chemie (May 2013). And, earlier today (July 5, 2013) Philip Ball writing (A self-assembled periodic table) for the Royal Society of Chemistry provided a critique of the idea while supporting it in principle,

Mirkin and his colleagues perceive the pairing of [DNA] strands as somewhat analogous to the covalent pairing of electrons and call their DNA-tagged nanoparticles programmable atom equivalents (PAEs). These PAEs may bind to one another according to particular combinatorial rules and Mirkin proposes a kind of periodic table of PAEs that systematises their possible interactions and permutations.
Well, it’s not hard to start enumerating ways in which PAEs are unlike atoms. Most fundamentally, perhaps, the bonding propensity of a PAE need bear no real relation to the ‘atom’ (the nanoparticle) with which it is associated: a given nanoparticle might be paired with any other, and there’s nothing periodic about those tendencies.

I recommend reading Ball’s piece for the way he analyzes the weaknesses and for why he thinks the effort to organize PAEs conceptually is worthwhile.

For the curious, here’s a link to and a citation for the researchers’ published paper,

Nucleic Acid-Modified Nanostructures as Programmable Atom Equivalents: Forging a New “Table of Elements by Robert J. Macfarlane, Matthew N. O’Brien, Dr. Sarah Hurst Petrosko, and Prof. Chad A. Mirkin. Angewandte Chemie International Edition Volume 52, Issue 22, pages 5688–5698, May 27, 2013. Article first published online: 2 MAY 2013 DOI: 10.1002/anie.201209336

Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim

This article is behind a paywall.

One final comment, this is not the first ‘nanoparticle table of elements’.  Larry Bell mentioned one in his Dec. 7, 2010 NISENet (Nanoscale Informal Science Education Network) blog posting,

The focus of today’s sessions at NSF’s [US National Science Foundation] meeting of nanoscale science and engineering grantees focuses on putting the science to practical use. First up this morning is nanomanufacturing. Mark Tuonimen from the University of Massachusetts at Amherst gave a talk about the Nanoscale Manufacturing Network and one of his images caught my imagination. This image, which comes from the draft Nano2 vision document on the next decade of nanoscale research, illustrates and idea that is sometimes referred to as a periodic table of nanoparticles.

[downloaded from http://www.nisenet.org/blogs/observations_insights/periodic_table_nanoparticles]

[downloaded from http://www.nisenet.org/blogs/observations_insights/periodic_table_nanoparticles]

Bell goes on to describe one way in which a nanoparticle table of elements would have to differ from the traditional chemistry table.

Public domain biotechnology: biological transistors from Stanford University

Andrew Myers’ Mar. 28, 2013 article for the Stanford School of Medicine’s magazine (Inside Stanford Medicine) profiles some research which stands as a bridge between electronics and biology and could lead to biological computing,

… now a team of Stanford University bioengineers has taken computing beyond mechanics and electronics into the living realm of biology. In a paper published March 28 in Science, the team details a biological transistor made from genetic material — DNA and RNA — in place of gears or electrons. The team calls its biological transistor the “transcriptor.”

“Transcriptors are the key component behind amplifying genetic logic — akin to the transistor and electronics,” said Jerome Bonnet, PhD, a postdoctoral scholar in bioengineering and the paper’s lead author.

Here’s a description of the transcriptor (biological transistor) and biological computers (from the article),

In electronics, a transistor controls the flow of electrons along a circuit. Similarly, in biologics, a transcriptor controls the flow of a specific protein, RNA polymerase, as it travels along a strand of DNA.

“We have repurposed a group of natural proteins, called integrases, to realize digital control over the flow of RNA polymerase along DNA, which in turn allowed us to engineer amplifying genetic logic,” said Endy [Drew Endy, PhD, assistant professor of bioengineering and the paper’s senior author].

Using transcriptors, the team has created what are known in electrical engineering as logic gates that can derive true-false answers to virtually any biochemical question that might be posed within a cell.

They refer to their transcriptor-based logic gates as “Boolean Integrase Logic,” or “BIL gates” for short.

Transcriptor-based gates alone do not constitute a computer, but they are the third and final component of a biological computer that could operate within individual living cells.

The article also offers a description of Boolean logic and the workings of standard computers,

Digital logic is often referred to as “Boolean logic,” after George Boole, the mathematician who proposed the system in 1854. Today, Boolean logic typically takes the form of 1s and 0s within a computer. Answer true, gate open; answer false, gate closed. Open. Closed. On. Off. 1. 0. It’s that basic. But it turns out that with just these simple tools and ways of thinking you can accomplish quite a lot.

“AND” and “OR” are just two of the most basic Boolean logic gates. An “AND” gate, for instance, is “true” when both of its inputs are true — when “a” and “b” are true. An “OR” gate, on the other hand, is true when either or both of its inputs are true.

In a biological setting, the possibilities for logic are as limitless as in electronics, Bonnet explained. “You could test whether a given cell had been exposed to any number of external stimuli — the presence of glucose and caffeine, for instance. BIL gates would allow you to make that determination and to store that information so you could easily identify those which had been exposed and which had not,” he said.

Here’s how they created a transcriptor (from the article),

To create transcriptors and logic gates, the team used carefully calibrated combinations of enzymes — the integrases mentioned earlier — that control the flow of RNA polymerase along strands of DNA. If this were electronics, DNA is the wire and RNA polymerase is the electron.

“The choice of enzymes is important,” Bonnet said. “We have been careful to select enzymes that function in bacteria, fungi, plants and animals, so that bio-computers can be engineered within a variety of organisms.”

On the technical side, the transcriptor achieves a key similarity between the biological transistor and its semiconducting cousin: signal amplification.

Refreshingly the team made this decision (from the article),

To bring the age of the biological computer to a much speedier reality, Endy and his team have contributed all of BIL gates to the public domain so that others can immediately harness and improve upon the tools.

“Most of biotechnology has not yet been imagined, let alone made true. By freely sharing important basic tools everyone can work better together,” Bonnet said.

Here’s a citation and a link to the researchers’ paper in Science,

Amplifying Genetic Logic Gates by Jerome Bonnet, Peter Yin, Monica E. Ortiz, Pakpoom Subsoontorn, and Drew Endy. Science 1232758 Published online 28 March 2013 [DOI:10.1126/science.1232758]

This paper is behind a paywall. As for Myers’ article, it’s well worth reading for its clear explanations and forays into computing history.

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.

DNA-marked valuables in London

It seems like an odd Christmas eve announcement but the Dec. 24, 2012 news item on Azonano highlights a new initiative from the UK Metropolitan Police Service (MPS),

Applied DNA Sciences, Inc., (Twitter: @APDN), a provider of DNA-based anti-counterfeiting technology and product authentication solutions, announced today that the UK Metropolitan Police Service (MPS) will be using its proprietary DNANet™ property marking kits as part of a major initiative to reduce crime in targeted London neighborhoods.

… The unequaled forensic merit of DNANet markers empower municipalities to apprehend and convict criminals. In the long term, crime deterrence rises from enhanced policing and prosecution power. [emphasis mine] Street and home signage announcing the use of DNANet markers will place potential offenders on alert, offering additional deterrence value.

Chief Inspector Robyn Williams, who is responsible for Neighbourhood Policing and Partnership in Lambeth, said: “The response from Lambeth residents to this Burglary crime prevention and reduction scheme has been extremely positive with an almost 100% take up rate of addresses visited to date. Police in Lambeth will continue to adopt and utilise innovative tactics including DNANet property marking that will support us in keeping our residents safe.”

Enhanced policing and prosecution power will deter crime? Intriguingly, the movie version of Les Misérables opened Dec. 25, 2012 and. as I recall the story, the lead’s (Jean Valjean) criminal past is due to extreme poverty. Perhaps the elimination of poverty would help alleviate some crime? In any event, people who steal from your home aren’t usually the biggest criminals and DNA marking will not lead to arrests of corrupt stock traders, bankers, and others of that ilk who not only ‘steal’ but have also, in the not so recent past, helped to bring down econ0mies.

From a technical perspective, the Applied DNA Sciences website (the company is based in the US) doesn’t offer a great deal of detail about their DNA marking products although there is a description of covert marking (from the Law Enforcement product page),

An item is marked with a stealth DNA marker – not detectable by offenders. Upon item recovery, a surface swab sample is taken and evaluated in the Applied DNA Sciences technology center. Additionally, surface swabs of offender hands and clothing are analyzed. Presence of the marker provides forensic evidence/offender linkage to crimes. Perfect for ransom recovery and narcotics operations.

An overt marking description follows on that page.

From Cornell University, a liquid that remembers its shape

Sometimes one experiences a frisson (shiver) when reading about a piece of research. Let’s see how you do with this Dec. 4, 2012 news item on Nanowerk,

A bit reminiscent of the Terminator T-1000, a new material created by Cornell researchers is so soft that it can flow like a liquid and then, strangely, return to its original shape.

Rather than liquid metal, it is a hydrogel, a mesh of organic molecules with many small empty spaces that can absorb water like a sponge. It qualifies as a “metamaterial” with properties not found in nature and may be the first organic metamaterial with mechanical meta-properties.

The Dec. 3, 2012 Cornell University news article by Bill Steele, which originated the news item,goes on to explain the interest in hydrogels and what makes this particular formulation so special,

Hydrogels have already been considered for use in drug delivery — the spaces can be filled with drugs that release slowly as the gel biodegrades — and as frameworks for tissue rebuilding. The ability to form a gel into a desired shape further expands the possibilities. For example, a drug-infused gel could be formed to exactly fit the space inside a wound.

The new hydrogel is made of synthetic DNA. In addition to being the stuff genes are made of, DNA can serve as a building block for self-assembling materials. Single strands of DNA will lock onto other single stands that have complementary coding, like tiny organic Legos. By synthesizing DNA with carefully arranged complementary sections Luo’s [Dan Luo, professor of biological and environmental engineering] research team previously created short stands that link into shapes such as crosses or Y’s, which in turn join at the ends to form meshlike structures to form the first successful all-DNA hydrogel. Trying a new approach, they mixed synthetic DNA with enzymes that cause DNA to self-replicate and to extend itself into long chains, to make a hydrogel without DNA linkages.

“During this process they entangle, and the entanglement produces a 3-D network,” Luo explained. But the result was not what they expected: The hydrogel they made flows like a liquid, but when placed in water returns to the shape of the container in which it was formed.

“This was not by design,” Luo said.

See the material for yourself,

Hydrogels made in the form of the letters D, N and A collapse into a liquid-like state on their own but return to the original shape when surrounded by water Provided/Luo Lab

Nature Nanotechnology published the team’s research online Dec. 2, 2012 and, unusually, the article is open access (at least for now),

A mechanical metamaterial made from a DNA hydrogel by Jong Bum Lee, Songming Peng, Dayong Yang,  Young Hoon Roh, Hisakage Funabashi, Nokyoung Park, Edward J. Rice, Liwei Chen, Rong Long, Mingming Wu & Dan Luo in Nature Nanotechnology  (2012) doi:10.1038/nnano.2012.211 published online Dec. 2, 2012

Depending on your reading interests and time available, Bill Steele’s Cornell University article has more detail than I’ve provided here or you can check out the well illustrated article in Nature Nanotechnology. As these things go, it’s quite readable as you can see with the abstract (Note: I have removed footnotes),

Metamaterials are artificial substances that are structurally engineered to have properties not typically found in nature. To date, almost all metamaterials have been made from inorganic materials such as silicon and copper, which have unusual electromagnetic or acoustic properties that allow them to be used, for example, as invisible cloaks superlenses or super absorbers for sound. Here, we show that metamaterials with unusual mechanical properties can be prepared using DNA as a building block. We used a polymerase enzyme to elongate DNA chains and weave them non-covalently into a hydrogel. The resulting material, which we term a meta-hydrogel, has liquid-like properties when taken out of water and solid-like properties when in water. Moreover, upon the addition of water, and after complete deformation, the hydrogel can be made to return to its original shape. The meta-hydrogel has a hierarchical internal structure and, as an example of its potential applications, we use it to create an electric circuit that uses water as a switch.

For anyone not familiar with the Terminator movies, here’s an essay in Wikipedia about the ‘franchise’. Pay special note to the second movie in the series, Terminator 2: Judgment Day which introduced a robot (played by Robert Patrick) that could morph from a liquidlike state into various lethal entities.

What is Dr. Who’s sonic screwdriver?

Dr. Who, a British Broadcasting Corporation science fiction television programme, has an enormous following worldwide. I am not one of those followers as you might have guessed from the headline, which means I didn’t understand this pop culture reference, from the April 23, 2012 news item on Nanowerk,

For fans of the hit series Doctor Who, the Sonic Screwdriver will be a familiar device. But now an international team of EU-funded researchers has taken equipment designed for magnetic resonance imaging (MRI)-guided focused ultrasound surgery and demonstrated a real Sonic Screwdriver, lifting and spinning a free-floating 10 cm-diameter rubber disk with an ultrasound beam.

I’m going to concentrate on the project first since this EU (European Union) funded project has a somewhat confusing configuration, which I’ll try to tease apart later in this posting. From the news item,

Dr Mike MacDonald, of the Institute for Medical Science and Technology (IMSAT) in the [University of Dundee, Scotland] United Kingdom, comments: ‘This experiment not only confirms a fundamental physics theory but also demonstrates a new level of control over ultrasound beams which can also be applied to non-invasive ultrasound surgery, targeted drug delivery and ultrasonic manipulation of cells.’

The theory the team were testing had not previously been proved in a single experiment; it is valid for both sound and light, and is used in fields like quantum communications and biophotonics. The theory states that the ratio of angular momentum to energy in a vortex beam is equal to the ratio of the number of intertwined helices to the frequency of the beam.

Dr Christine Demore from IMSAT comments: ‘For the first time, our experimental results confirm directly the validity of this fundamental theory. Previously this ratio could only be assumed from theory as the angular momentum and power in a beam had only ever been measured independently.’

The ultrasound beam generated by the researchers resembles the ‘double-helix’ structure of DNA but with many more twisted strands, or helices. This vortex beam generates a rotating, angular component of momentum that can exert torque on an object. In the recent publication, they showed how they could generate vortex beams with many intertwined helices, using a 1 000-element ultrasound transducer array as an acoustic hologram. These beams are so powerful they can levitate and spin the 90 g-disk made of ultrasonic absorber in water.

Here’s a 30 secs. video of the ‘sonic screwdriver’,

Ray Walters in his April 20, 2012 article  for Geek.com offers a description using measurements that are more commonly used in Canada and the US for what we’re seeing in the video [I have removed a link from the following passage],

Depicted in the video above, the “Sonotweezers” [aka, sonic screwdriver] project as it’s officially known, uses an ultrasound beam that is structured like a strand of DNA. The difference being that there are many more twisted strands that can be used to bring torque to bear on objects for movement. The team has used its device to levitate and spin a 3.17 ounce, 10cm diameter rubber disk that was suspended in water.

To make this happen, the research team used a 1000-element ultrasound transducer array to create what’s called an acoustic hologram.

The project known as ‘Sonotweezers’ at the University of Dundee,  is part of a larger European Union project, Nanoporation, which is investigating drug delivery to cancer cell using MRI (magnetic resonance imaging) and guided focused ultrasound. The larger project includes a couple of Israeli teams, neither of which seem to be involved with the Sonotweezers/sonic screwdriver project. I gather some of the funding for the Sonotweezers project comes from the UK’s Engineering and Physical Sciences Ressearch Council (EPSRC). You can find out more about the Scottish team at the University of Dundee, Sonotweezers, and EPSRC in the April 19, 2012 press release on the University of Dundee website.

Simon Fraser University uses gold nanoparticles for anti-folding

It always amazes me when something pops in my email and turns out to be related to one of my latest postings. Today, Simon Fraser University sent me a news release about Paul Li and his lab-on-a-chip work where he’s trying to keep DNA strands separate. From the news release,

A Simon Fraser University chemist who pioneered lab-on-a-biochip technology six years ago has struck gold in the research world again, this time literally.

Paul Li has combined nanoscale-sized-particles of gold with two powerful tools in molecular biology to make DNA analysis more than 10 times faster at room temperature, rather than previously required higher temperatures.

Li has sped up gene identification by fusing the slide-like microarray’s ability to identify known DNA gene sequences with the multi-channel microfluidic device’s ability to quickly analyse small amounts of liquid.

The palm-sized hybrid biochip is roughly the same thickness as the Canadian Loonie.

But what really makes the invention a biomedical gold mine is the addition of gold nanoparticles to the liquid being analysed on it. Mixed with DNA, tiny spheres of gold act as mini magnets that adhere to each of the DNA’s twin strands.

When the DNA is heated, the two strands separate. The gold nanoparticles keep them apart, which enables scientists to probe each strand with other pieces of DNA that are engineered to recognize known gene sequences.

“The key benefit of the gold is that it allows us to do our analysis at room temperature (25 degrees C),” explains Li. “That is half the conventional temperature needed, which requires the use of an apparatus that tolerates high temperatures.

“More importantly, DNA sequences with slight differences are now differentiated by the nanoparticle, but not by the high temperature.”

This invention will revolutionize researchers’ ability to probe biological samples and detect genes for forensic analysis, disease detection and drug development.

I may have stretched this just a bit by calling anti-folding but this process which uses the gold nanoparticles to keep the DNA strands from adhering to each other contrasts with the work mentioned in today’s earlier post, Folding, origami, and shapeshifting and an article with over 50,000 authors, where DNA was used to keep ensure that carbon nanotubes don’t adhere to each other.

Two subcultures: science knitters and graffiti knitters, could they come together?

I had no idea that there’s a whole subculture of scientists devoted to knitting. Not just any knitting, science knitting. Thanks to Andrew Maynard at 2020 Science blog (July 25, 2010 posting), I have discovered Woolly Thoughts a website devoted to knitting, crocheting, and mathematics.

In fact, there’s a plethora of websites, blogs, and a subset on Ravelry (social networking for knitters) devoted to science/math knitters, much of which you can find in Andrew’s posting.

One item that particularly my fancy was a piece of ‘illusion knitting’ designed by Alice Bell, a science communication lecturer at the Imperial College of London. Illusion knitting is where the same piece of knitting reveals of one of two different images depending on the angle of sight. Bell’s creation, the Rosalind scarf, can look like stripes from one angle and like a piece of DNA from another angle.

For anyone not familiar with Franklin (from the San Diego Super Computer Center at the University of Southern California web page),

There is probably no other woman scientist with as much controversy surrounding her life and work as Rosalind Franklin. Franklin was responsible for much of the research and discovery work that led to the understanding of the structure of deoxyribonucleic acid, DNA. The story of DNA is a tale of competition and intrigue, told one way in James Watson’s book The Double Helix, and quite another in Anne Sayre’s study, Rosalind Franklin and DNA. James Watson, Francis Crick, and Maurice Wilkins received a Nobel Prize for the double-helix model of DNA in 1962, four years after Franklin’s death at age 37 from ovarian cancer.

Here’s Bell in her Rosalind scarf,

Alice Bell in her Rosalind scarf

This is the angle for the stripes, to see the DNA go to the Feb. 7, 2010 posting on her Slipped Stitch blog or to Andrew’s posting where you can find more goodies like this,

Knitting and crocheting as a means of creating complex geometrical forms has a long and illustrious history. Alan Turing was often seen knitting Möbius strips and other shapes in his lunchtime apparently, according to this 2008 MSNBC [article]. The work of Taimina and others on exploring hyperbolic planes – and their relevance to biology – has been groundbreaking (I know it’s crochet, but Margaret Wertheim’s TED talk on crochet coral and complex math is excellent, [go here]).

Vancouver (Canada) is home to at least two members of another knitting subculture as I found out earlier this year with the publication of a book by two locals, Mandy Moore and Leanne Prain, Yarn Bombing; The Art of Crochet and Knit Graffiti. Their Yarn Bombing blog features projects from around the world. I took a particular liking to Bee Bombs,

Annie's bee bombs in Amsterdam

I wonder if we could get some science yarn bombs going for the 2012 annual meeting of the American Association for the Advancement of Science meeting to take place here in Vancouver?