Tag Archives: DNA

Electrifying DNA (deoxyribonucleic acid)

All kinds of things have electrical charges including DNA (deoxyribonucleic acid) according to an April 15, 2015 news item on Azonano,

Electrical charges not only move through wires, they also travel along lengths of DNA, the molecule of life. The property is known as charge transport.

In a new study appearing in the journal Nature Chemistry, authors, Limin Xiang, Julio Palma, Christopher Bruot and others at Arizona State University’s Biodesign Institute, explore the ways in which electrical charges move along DNA bases affixed to a pair of electrodes.

Their work reveals a new mechanism of charge transport that differs from the two recognized patterns in which charge either tunnels or hops along bases of the DNA chain.

An April 13, 2015 Arizona State University (ASU) news release (also on EurekAlert and dated April 14, 2015), which originated the news item, explains why this ‘blue sky’ research may prove important in the future,

Researchers predict that foundational work of this kind will have important implications in the design of a new generation of functional DNA-based electronic devices as well as providing new insights into health risks associated with transport-related damage to DNA.

Oxidative damage is believed to play a role in the initiation and progression of cancer. It is also implicated in neurodegenerative disorders like Alzheimer’s, Huntington’s disease and Parkinson’s disease and a range of other human afflictions.

An electron’s movements plays an important role in your body’s chemical reactions (from the news release),

The transfer of electrons is often regarded as the simplest form of chemical reaction, but nevertheless plays a critical role in a broad range of life-sustaining processes, including respiration and photosynthesis.

Charge transport can also produce negative effects on living systems, particularly through the process of oxidative stress, which causes damage to DNA and has been invoked in a broad range of diseases.

“When DNA is exposed to UV light, there’s a chance one of the bases– such as guanine–gets oxidized, meaning that it loses an electron,” Tao says. (Guanine is easier to oxidize than the other three bases, cytosine, thymine, and adenine, making it the most important base for charge transport.)

In some cases, the DNA damage is repaired when an electron migrates from another portion of the DNA strand to replace the missing one. DNA repair is a ceaseless, ongoing process, though a gradual loss of repair efficiency over time is one factor in the aging process. Oxidation randomly damages both RNA and DNA, which can interfere with normal cellular metabolism.

Radiation damage is also an issue for semiconductor devices, Tao notes–a factor that must be accounted for when electronics are exposed to high-energy particles like X rays, as in applications designed for outer space.

Researchers like Xiang and Tao hope to better understand charge transport through DNA, and the molecule provides a unique testing ground for observation. The length of a DNA molecule and its sequence of 4 nucleotides A, T, C and G can be readily modified and studies have shown that both alterations have an effect on how electrical charge moves through the molecule.

When the loss of an electron or oxidation occurs in DNA bases, a hole is left in place of the electron. This hole carries a positive charge, which can move along the DNA length under the influence of an electrical or magnetic field, just as an electron would. The movement of these positively charged holes along a stretch of DNA is the focus of the current study.

The news release goes on to describe charge transport,

Two primary mechanisms of charge transport have been examined in detail in previous research. Over short distances, an electron displays the properties of a wave, permitting it to pass straight through a DNA molecule. This process is a quantum mechanical effect known as tunneling.

Charge transport in DNA (and other molecules) over longer distances involves the process of hopping. When a charge hops from point to point along the DNA segment, it behaves classically and loses its wavelike properties. The electrical resistance is seen to increases exponentially during tunneling behavior and linearly, during hopping.

By attaching electrodes to the two ends of a DNA molecule, the researchers were able to monitor the passage of charge through the molecule, observing something new: “What we found in this particular paper is that there is an intermediate behavior,” Tao says. “It’s not exactly hopping because the electron still displays some of the wave properties.”

Instead, the holes observed in certain sequences of DNA are delocalized, spread over several base pairs. The effect is neither a linear nor exponential increase in electrical resistance but a periodic oscillation. The phenomenon was shown to be highly sequence dependent, with stacked base pairs of guanine-cytosine causing the observed oscillation.

Control experiments where G bases alternated, rather than occurring in a sequential stack, showed a linear increase in resistance with molecular length, in agreement with conventional hopping behavior.

A further property of DNA is also of importance in considering charge transport. The molecule at room temperature is not like a wire in a conventional electronic device, but rather is a highly dynamic structure, that writhes and fluctuates.

The last bit about writhing and fluctuating makes this work sound fascinating and very challenging.

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

Intermediate tunnelling–hopping regime in DNA charge transport by Limin Xiang, Julio L. Palma, Christopher Bruot, Vladimiro Mujica, Mark A. Ratner, & Nongjian Tao. Nature Chemistry 7, 221–226 (2015) doi:10.1038/nchem.2183 Published online 20 February 2015

This paper is behind a paywall.

Nature’s patterns reflected in gold nanoparticles

A 133 atom gold nanoparticle bears a resemblance to the Milky Way and to DNA’s (deoxyribonucleic acid) double helix according to an April 9, 2015 news item on ScienceDaily,

Our world is full of patterns, from the twist of a DNA molecule to the spiral of the Milky Way. New research from Carnegie Mellon chemists has revealed that tiny, synthetic gold nanoparticles exhibit some of nature’s most intricate patterns.

Unveiling the kaleidoscope of these patterns was a Herculean task, and it marks the first time that a nanoparticle of this size has been crystallized and its structure mapped out atom by atom. The researchers report their work in the March 20  [2015] issue of Science Advances.

“As you broadly think about different research areas or even our everyday lives, these kinds of patterns, these hierarchical patterns, are universal,” said Rongchao Jin, associate professor of chemistry. “Our universe is really beautiful and when you see this kind of information in something as small as a 133-atom nanoparticle and as big as the Milky Way, it’s really amazing.”

An April 8, 2015 Carnegie Mellon University news release (also on EurekAlert but dated April 9) by Jocelyn Duffy, which originated the news release, offers a description of gold nanoparticles along with details about the research,

Gold nanoparticles, which can vary in size from 1 to 100 nanometers, are a promising technology that has applications in a wide range of fields including catalysis, electronics, materials science and health care. But, in order to use gold nanoparticles in practical applications, scientists must first understand the tiny particles’ structure.

“Structure essentially determines the particle’s properties, so without knowing the structure, you wouldn’t be able to understand the properties and you wouldn’t be able to functionalize them for specific applications,” said Jin, an expert in creating atomically precise gold nanoparticles.

With this latest research, Jin and his colleagues, including graduate student Chenjie Zeng, have solved the structure of a nanoparticle, Au133, made up of 133 gold atoms and 52 surface-protecting molecules—the biggest nanoparticle structure ever resolved with X-ray crystallography. While microscopy can reveal the size, shape and the atomic lattice of nanoparticles, it can’t discern the surface structure. X-ray crystallography can, by mapping out the position of every atom on the nanoparticles’ surface and showing how they bond with the gold core. Knowing the surface structure is key to using the nanoparticles for practical applications, such as catalysis, and for uncovering fundamental science, such as the basis of the particle’s stability.

The crystal structure of the Au133 nanoparticle divulged many secrets.

“With X-ray crystallography, we were able to see very beautiful patterns, which was a very exciting discovery. These patterns only show up when the nanoparticle size becomes big enough,” Jin said.

During production, the Au133 particles self-assemble into three layers within each particle: the gold core, the surface molecules that protect it and the interface between the two. In the crystal structure, Zeng discovered that the gold core is in the shape of an icosahedron. At the interface between the core and the surface-protecting molecules is a layer of sulfur atoms that bind with the gold atoms. The sulfur-gold-sulfur combinations stack into ladder-like helical structures. Finally, attached to the sulfur molecules is an outer layer of surface-protecting molecules whose carbon tails self-assemble into fourfold swirls.

“The helical features remind us of a DNA double helix and the rotating arrangement of the carbon tails is reminiscent of the way our galaxy is arranged. It’s really amazing,” Jin said.

These particular patterns are responsible for the high stability of Au133 compared to other sizes of gold nanoparticles. The researchers also tested the optical and electronic properties of Au133 and found that these gold nanoparticles are not metallic. [emphasis mine] Normally, gold is one of the best conductors of electrical current, but the size of Au133 is so small that the particle hasn’t yet become metallic. Jin’s group is currently testing the nanoparticles for use as catalysts, substances that can increase the rate of a chemical reaction.

*ETA April 14, 2015 at 9015 PDT: Coincidentally, researchers in Finland have been examining gold nanoparticles and the size at which they are considered metals and at which they are considered molecules (mentioned in my April 14, 2015 posting [Gold atoms: sometimes they’re a metal and sometimes they’re a molecule]).*

Getting back to patterns, the researchers have provided an A-ray image of Au133,

 Caption: The X-ray crystallographic structure of the gold nanoparticle is shown. Gold atoms = magenta; sulfur atoms = yellow; carbon atoms = gray; hydrogen atoms = white. Credit: Carnegie Mellon


Caption: The X-ray crystallographic structure of the gold nanoparticle is shown. Gold atoms = magenta; sulfur atoms = yellow; carbon atoms = gray; hydrogen atoms = white.
Credit: Carnegie Mellon

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

Structural patterns at all scales in a nonmetallic chiral Au133(SR)52 nanoparticle by Chenjie Zeng, Yuxiang Chen, Kristin Kirschbaum, Kannatassen Appavoo, Matthew Y. Sfeir, Rongchao Jin. Science Advances 20 Mar 2015: Vol. 1 no. 2 e1500045 DOI: 10.1126/sciadv.1500045

This paper appears to be open access.

Tel Aviv University and the quest for super-slim, bendable displays

It’s beginning to seem like the quest for the Holy Grail. That is, the search for an object more myth than fact, but researchers at Tel Aviv University (TAU) believe they are on the right track to develop a slim, flexible screen according to a March 30, 2015 news item on Nanowerk (Note: A link has been removed),

From smartphones and tablets to computer monitors and interactive TV screens, electronic displays are everywhere. As the demand for instant, constant communication grows, so too does the urgency for more convenient portable devices — especially devices, like computer displays, that can be easily rolled up and put away, rather than requiring a flat surface for storage and transportation.

A new Tel Aviv University study, published recently in Nature Nanotechnology (“Light-emitting self-assembled peptide nucleic acids exhibit both stacking interactions and Watson–Crick base pairing”), suggests that a novel DNA-peptide structure can be used to produce thin, transparent, and flexible screens. The research, conducted by Prof. Ehud Gazit and doctoral student Or Berger of the Department of Molecular Microbiology and Biotechnology at TAU’s Faculty of Life Sciences, in collaboration with Dr. Yuval Ebenstein and Prof. Fernando Patolsky of the School of Chemistry at TAU’s Faculty of Exact Sciences, harnesses bionanotechnology to emit a full range of colors in one pliable pixel layer — as opposed to the several rigid layers that constitute today’s screens.

A March 30, 2015 American Friends of Tel Aviv University news release, which originated the news item, describes the material’s advantages and how the researchers developed it,

“Our material is light, organic, and environmentally friendly,” said Prof. Gazit. “It is flexible, and a single layer emits the same range of light that requires several layers today. By using only one layer, you can minimize production costs dramatically, which will lead to lower prices for consumers as well.”

For the purpose of the study, a part of Berger’s Ph.D. thesis, the researchers tested different combinations of peptides: short protein fragments, embedded with DNA elements which facilitate the self-assembly of a unique molecular architecture.

Peptides and DNA are two of the most basic building blocks of life. Each cell of every life form is composed of such building blocks. In the field of bionanotechnology, scientists utilize these building blocks to develop novel technologies with properties not available for inorganic materials such as plastic and metal.

“Our lab has been working on peptide nanotechnology for over a decade, but DNA nanotechnology is a distinct and fascinating field as well. When I started my doctoral studies, I wanted to try and converge the two approaches,” said Berger. “In this study, we focused on PNA — peptide nucleic acid, a synthetic hybrid molecule of peptides and DNA. We designed and synthesized different PNA sequences, and tried to build nano-metric architectures with them.”

Using methods such as electron microscopy and X-ray crystallography, the researchers discovered that three of the molecules they synthesized could self-assemble, in a few minutes, into ordered structures. The structures resembled the natural double-helix form of DNA, but also exhibited peptide characteristics. This resulted in a very unique molecular arrangement that reflects the duality of the new material.

“Once we discovered the DNA-like organization, we tested the ability of the structures to bind to DNA-specific fluorescent dyes,” said Berger. “To our surprise, the control sample, with no added dye, emitted the same fluorescence as the variable. This proved that the organic structure is itself naturally fluorescent.”

The structures were found to emit light in every color, as opposed to other fluorescent materials that shine only in one specific color. Moreover, light emission was observed also in response to electric voltage — which make it a perfect candidate for opto-electronic devices like display screens.

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

Light-emitting self-assembled peptide nucleic acids exhibit both stacking interactions and Watson–Crick base pairing by Or Berger, Lihi Adler-Abramovich, Michal Levy-Sakin, Assaf Grunwald, Yael Liebes-Peer, Mor Bachar, Ludmila Buzhansky, Estelle Mossou, V. Trevor Forsyth, Tal Schwartz, Yuval Ebenstein, Felix Frolow, Linda J. W. Shimon, Fernando Patolsky, & Ehud Gazit. Nature Nanotechnology (2015) doi:10.1038/nnano.2015.27 Published online 16 March 2015

This paper is behind a paywall but a free preview is available via ReadCube Access.

CRISPR gene editing technique and patents

I have two items about the CRISPR gene editing technique. The first concerns a new use for the CRISPR technique developed by researchers at Johns Hopkins University School of Medicine described in a Jan. 5, 2015 Johns Hopkins University news release on EurekAlert,

A powerful “genome editing” technology known as CRISPR has been used by researchers since 2012 to trim, disrupt, replace or add to sequences of an organism’s DNA. Now, scientists at Johns Hopkins Medicine have shown that the system also precisely and efficiently alters human stem cells.

“Stem cell technology is quickly advancing, and we think that the days when we can use iPSCs [human-induced pluripotent stem cells] for human therapy aren’t that far away,” says Zhaohui Ye, Ph.D., an instructor of medicine at the Johns Hopkins University School of Medicine. “This is one of the first studies to detail the use of CRISPR in human iPSCs, showcasing its potential in these cells.”

CRISPR originated from a microbial immune system that contains DNA segments known as clustered regularly interspaced short palindromic repeats. The engineered editing system makes use of an enzyme that nicks together DNA with a piece of small RNA that guides the tool to where researchers want to introduce cuts or other changes in the genome.

Previous research has shown that CRISPR can generate genomic changes or mutations through these interventions far more efficiently than other gene editing techniques, such as TALEN, short for transcription activator-like effector nuclease.

Despite CRISPR’s advantages, a recent study suggested that it might also produce a large number of “off-target” effects in human cancer cell lines, specifically modification of genes that researchers didn’t mean to change.

To see if this unwanted effect occurred in other human cell types, Ye; Linzhao Cheng, Ph.D., a professor of medicine and oncology in the Johns Hopkins University School of Medicine; and their colleagues pitted CRISPR against TALEN in human iPSCs, adult cells reprogrammed to act like embryonic stem cells. Human iPSCs have already shown enormous promise for treating and studying disease.

The researchers compared the ability of both genome editing systems to either cut out pieces of known genes in iPSCs or cut out a piece of these genes and replace it with another. As model genes, the researchers used JAK2, a gene that when mutated causes a bone marrow disorder known as polycythemia vera; SERPINA1, a gene that when mutated causes alpha1-antitrypsin deficiency, an inherited disorder that may cause lung and liver disease; and AAVS1, a gene that’s been recently discovered to be a “safe harbor” in the human genome for inserting foreign genes.

Their comparison found that when simply cutting out portions of genes, the CRISPR system was significantly more efficient than TALEN in all three gene systems, inducing up to 100 times more cuts. However, when using these genome editing tools for replacing portions of the genes, such as the disease-causing mutations in JAK2 and SERPINA1 genes, CRISPR and TALEN showed about the same efficiency in patient-derived iPSCs, the researchers report.

Contrary to results of the human cancer cell line study, both CRISPR and TALEN had the same targeting specificity in human iPSCs, hitting only the genes they were designed to affect, the team says. The researchers also found that the CRISPR system has an advantage over TALEN: It can be designed to target only the mutation-containing gene without affecting the healthy gene in patients, where only one copy of a gene is affected.

The findings, together with a related study that was published earlier in a leading journal of stem cell research (Cell Stem Cell), offer reassurance that CRISPR will be a useful tool for editing the genes of human iPSCs with little risk of off-target effects, say Ye and Cheng.

“CRISPR-mediated genome editing opens the door to many genetic applications in biologically relevant cells that can lead to better understanding of and potential cures for human diseases,” says Cheng.

Here’s a link to and citation for the paper by the Johns Hopkins researchers,

Efficient and Allele-Specific Genome Editing of Disease Loci in Human iPSCs by Cory Smith, Leire Abalde-Atristain, Chaoxia He, Brett R Brodsky, Evan M Braunstein, Pooja Chaudhari, Yoon-Young Jang, Linzhao Cheng and Zhaohui Ye. Molecular Therapy (24 November 2014) | doi:10.1038/mt.2014.226

This paper is behind a paywall.

Not mentioned in the Johns Hopkins Medicine news release is a brewing patent battle over the CRISPR technique. A Dec. 31, 2014 post by Glyn Moody for Techdirt lays out the situation (Note: Links have been removed),

Although not many outside the world of the biological sciences have heard of it yet, the CRISPR gene editing technique may turn out to be one of the most important discoveries of recent years — if patent battles don’t ruin it. Technology Review describes it as:

    an invention that may be the most important new genetic engineering technique since the beginning of the biotechnology age in the 1970s. The CRISPR system, dubbed a “search and replace function” for DNA, lets scientists easily disable genes or change their function by replacing DNA letters. During the last few months, scientists have shown that it’s possible to use CRISPR to rid mice of muscular dystrophy, cure them of a rare liver disease, make human cells immune to HIV, and genetically modify monkeys.

Unfortunately, rivalry between scientists claiming the credit for key parts of CRISPR threatens to spill over into patent litigation …

Moody describes three scientists vying for control via their patents,

[A researcher at the MIT-Harvard Broad Institute, Feng] Zhang cofounded Editas Medicine, and this week the startup announced that it had licensed his patent from the Broad Institute. But Editas doesn’t have CRISPR sewn up.

That’s because [Jennifer] Doudna, a structural biologist at the University of California, Berkeley, was a cofounder of Editas, too. And since Zhang’s patent came out, she’s broken off with the company, and her intellectual property — in the form of her own pending patent — has been licensed to Intellia, a competing startup unveiled only last month.

Making matters still more complicated, [another CRISPR researcher, Emmanuelle] Charpentier sold her own rights in the same patent application to CRISPR Therapeutics.

Moody notes,

Whether obvious or not, it looks like the patent granted may complicate turning the undoubtedly important CRISPR technique into products. That, in its turn, will mean delays for life-changing and even life-saving therapies: for example, CRISPR could potentially allow the defective gene that causes serious problems for those with cystic fibrosis to be edited to produce normal proteins, thus eliminating those problems.

It’s dispiriting to think that potentially valuable therapies could be lost to litigation battles particularly since the researchers are academics and their work was funded by taxpayers. In any event, I hope sanity reigns and they are able to avoid actions which will grind research down to a standstill.

The Analysis of Beauty; an email from William Hogarth

Given that William Hogarth has been dead for 250 years (1697 – 1764), it was bit startling to receive an email from him. For the record, he was announcing a sound installation that’s part of the ‘gap in the air; a festival of sonic art’ being held in Edinburgh (Nov. 15, 2014 – Feb. 14, 2015).

Hogarth’s (or the artists’ group known as ‘Disinformation’) installation is presenting (from the Feb. 6, 2014 email announcement),

“The Analysis of Beauty” by Disinformation
 

Talbot Rice Gallery
The University of Edinburgh
Old College
South Bridge
Edinburgh EH8 9YL
[email protected]
0131 650 2210

Reception + preview 12.30 (lunch-time) 15 Nov 2014
Sound installation 15 to 29 Nov 2014

http://rorschachaudio.com/2014/11/04/talbot-rice-edinburgh-disinformation/

http://www.facebook.com/events/1548961118673406/

#theanalysisofbeauty @talbotrice75

“The eye hath this sort of enjoyment in winding walks, and serpentine rivers, and all sorts of objects, whose forms, as we shall see hereafter, are composed principally of what I call the waving and serpentine lines. Intricacy in form, therefore, I shall define to be that peculiarity in the lines, which compose it, that leads the eye a wanton kind of chace, and from the pleasure that gives the mind, intitles it to the name of beautiful…” William Hogarth “The Analysis of Beauty” 1753

In 1753 the Georgian artist William Hogarth self-published his magnum-opus, “The Analysis of Beauty” – the book in which Hogarth expounded an aesthetic system based on analysing the virtues of the Serpentine, S-shaped, waving and snake-like lines. The Serpentine Line that William Hogarth discussed is identical to what modern nomenclature refers to as the sine-wave – the mathematical function whose geometry finds physical expression in oscillatory motion of musical strings, in pure musical notes, and in many phenomena of engineering, physics and communications science, signal processing and information technology.

In context of the architect William Playfair’s design for the Georgian Gallery at Talbot Rice, sonic and visual arts project Disinformation presents a minutely-tuned assemblage of pure musical sine-waves, which extend and extrapolate the visual aesthetics of Hogarth’s analyses, manifesting throughout the Georgian Gallery as a gently-hypnotic, immersive and dream-like sound-world. The installation is created using signals from laboratory oscillators, which manifest in-situ as standing-waves (the audio equivalent of stationary pond-ripples), through which visitors move as they explore and interact with the architectural acoustics of the exhibition space.

Here’s a video featuring a version of Disinformation’s ‘Analysis of Beauty’,

The Nov. 6, 2014 email announcement describes some of what you may have seen (if you’ve watched the video) and gives a summarized history for this installation,

“The Analysis of Beauty” sound installation is accompanied at Talbot Rice by the video of the same name, in which musical sine-waves are fed into and displayed on the screen of a laboratory oscilloscope. These signals visually manifest as a slowly rotating rope-like pattern of phosphorescent green lines, strongly reminiscent of the geometry of DNA. This earliest version of “The Analysis of Beauty” installation was exhibited at Kettle’s Yard gallery in Cambridge, in 2000, where the Disinformation exhibit was set-up alongside works by Umberto Eco, Marc Quinn and the artist project Art & Language, and directly alongside one of Francis Crick & James Watson’s earliest working-models of DNA.

Joe Banks offers a more comprehensive history in a post titled “Disinformation and “The Analysis of Beauty” A Project History“on the slashseconds.org website,

“The Analysis of Beauty” is an optokinetic sound and light installation, created by the art project Disinformation1 , which takes its title from the book of the same name written by the painter, engraver and satyrist William Hogarth in 1753. The installation was conceived in December 1999 and first exhibited in January 2000, in the “Noise” exhibition at Kettle’s Yard gallery (curated by Adam Lowe and by the Cambridge historian of science Professor Simon Schaffer)2 . “The Analysis of Beauty” was exhibited alongside work by artists Marc Quinn and Art and Language, semiotician and author Umberto Eco, and the Elizabethan polymath (mathematician, astronomer, geographer and occultist) John Dee. On account of the (subjective, but strong) similarity between the imagery produced by this installation and DNA, this work was (recent controversies notwithstanding) exhibited at Kettle’s Yard directly opposite one of Francis Crick and James Watson’s original models of DNA.

The entry does not appear to have been updated since 2007 at the latest.

Coincidentally or not, I received a Nov. 8, 2014 email announcement about an installation in Rennes (France) by an artist who seems to be associated with the ‘Disinformation’ group,

 “Babylone Electrifiée” Joshua Bonnetta + Disinformation

Exhibition continues until 22 Nov 2014

Le Bon Accueil – Lieu d’Art Contemporain
74 Canal Saint-Martin
35700 Rennes
France

The “Babylone Electrifiée” exhibition (image below) features “The Analysis of Beauty”, “National Grid” and “Blackout” (Sound Mirrors) by Disinformation, plus “Strange Lines & Distances” by Joshua Bonnetta

Here’ s the image,

[downloaded from http://bon-accueil.org/]

[downloaded from http://bon-accueil.org/]

You can find out more about

the ‘gap in the air: a festival of sonic art’ here

University of Edinburgh’s Talbot Rice Gallery exhibitions here

Le Bon Accuei exhibitions here

Joshua Bonnetta here

Happy Listening! And, to whomever came up with the idea of emails from William Hogarth, Bravo!

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.