Tag Archives: DNA

Disinfectant for backyard pools could be key to new nanomaterials

Research from McGill University (Québec, Canada) focuses on cyanuric acid, one of the chemicals used to disinfect backyard pools. according to a March 1, 2016 McGill University news release (received by email; it can also be found in a March 1, 2016 news item on Nanowerk *and on EurekAlert*),

Cyanuric acid is commonly used to stabilize chlorine in backyard pools; it binds to free chlorine and releases it slowly in the water. But researchers at McGill University have now discovered that this same small, inexpensive molecule can also be used to coax DNA into forming a brand new structure: instead of forming the familiar double helix, DNA’s nucleobases — which normally form rungs in the DNA ladder — associate with cyanuric acid molecules to form a triple helix.

The discovery “demonstrates a fundamentally new way to make DNA assemblies,” says Hanadi Sleiman, Canada Research Chair in DNA Nanoscience at McGill and senior author of the study, published in Nature Chemistry. “This concept may apply to many other molecules, and the resulting DNA assemblies could have applications in a range of technologies.”

The DNA alphabet, composed of the four letters A, T, G and C, is the underlying code that gives rise to the double helix famously discovered by Watson and Crick more than 60 years ago. The letters, or bases, of DNA can also interact in other ways to form a variety of DNA structures used by scientists in nanotechnology applications – quite apart from DNA’s biological role in living cells.

For years, scientists have sought to develop a larger, designer alphabet of DNA bases that would enable the creation of more DNA structures with unique, new properties. For the most part, however, devising these new molecules has involved costly and complex procedures.

The road to the McGill team’s discovery began some eight years ago, when Sleiman mentioned to others in her lab that cyanuric acid might be worth experimenting with because of its properties. The molecule has three faces with the same binding features as thymine (T in the DNA alphabet), the natural complement to adenine (A).  “One of my grad students tried it,” she recalls, “and came back and said he saw fibres” through an atomic force microscope.

The researchers later discovered that these fibres have a unique underlying structure. Cyanuric acid is able to coax strands composed of adenine bases into forming a novel motif in DNA assembly. The adenine and cyanuric acid units associate into flower-like rosettes; these form the cross-section of a triple helix.  The strands then combine to form long fibres.

“The nanofibre material formed in this way is easy to access, abundant and highly structured,” says Nicole Avakyan, a PhD student in Sleiman’s lab and first author of the study. “With further development, we can envisage a variety of applications of this material, from medicinal chemistry to tissue engineering and materials science.”

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

Reprogramming the assembly of unmodified DNA with a small molecule by Nicole Avakyan, Andrea A. Greschner, Faisal Aldaye, Christopher J. Serpell, Violeta Toader,    Anne Petitjean, & Hanadi F. Sleiman. Nature Chemistry (2016) doi:10.1038/nchem.2451 Published online 22 February 2016

This paper is behind a paywall.

*’also on EurekAlert’ added on March 2, 2016.

Shape-shifting nanoparticles for better chemotherapy from the University of Toronto (Canada)

A research team from the University of Toronto and its shape-shifting nanoparticles are being touted in a Feb. 19, 2016 news item on Nanowerk,

Chemotherapy isn’t supposed to make your hair fall out — it’s supposed to kill cancer cells. A new molecular delivery system created at U of T [University of Toronto] Engineering could help ensure that chemotherapy drugs get to their target while minimizing collateral damage.

Many cancer drugs target fast-growing cells. Injected into a patient, they swirl around in the bloodstream acting on fast-growing cells wherever they find them. That includes tumours, but unfortunately also hair follicles, the lining of your digestive system, and your skin.

U of T Engineering Professor Warren Chan has spent the last decade figuring out how to deliver chemotherapy drugs into tumours — and nowhere else. Now his lab has designed a set of nanoparticles attached to strands of DNA that can change shape to gain access to diseased tissue.

A Feb. 18, 2016 University of Toronto news release (also on EurekAlert), which originated the news item, expands on the theme,

“Your body is basically a series of compartments,” says Chan. “Think of it as a giant house with rooms inside. We’re trying to figure out how to get something that’s outside, into one specific room. One has to develop a map and a system that can move through the house where each path to the final room may have different restrictions such as height and width.”

One thing we know about cancer: no two tumours are identical. Early-stage breast cancer, for example, may react differently to a given treatment than pancreatic cancer, or even breast cancer at a more advanced stage. Which particles can get inside which tumours depends on multiple factors such as the particle’s size, shape and surface chemistry.

Chan and his research group have studied how these factors dictate the delivery of small molecules and nanotechnologies to tumours, and have now designed a targeted molecular delivery system that uses modular nanoparticles whose shape, size and chemistry can be altered by the presence of specific DNA sequences.

“We’re making shape-changing nanoparticles,” says Chan. “They’re a series of building blocks, kind of like a LEGO set.” The component pieces can be built into many shapes, with binding sites exposed or hidden. They are designed to respond to biological molecules by changing shape, like a key fitting into a lock.

These shape-shifters are made of minuscule chunks of metal with strands of DNA attached to them. Chan envisions that the nanoparticles will float around harmlessly in the blood stream, until a DNA strand binds to a sequence of DNA known to be a marker for cancer. When this happens, the particle changes shape, then carries out its function: it can target the cancer cells, expose a drug molecule to the cancerous cell, tag the cancerous cells with a signal molecule, or whatever task Chan’s team has designed the nanoparticle to carry out.

“We were inspired by the ability of proteins to alter their conformation — they somehow figure out how to alleviate all these delivery issues inside the body,” says Chan. “Using this idea, we thought, ‘Can we engineer a nanoparticle to function like a protein, but one that can be programmed outside the body with medical capabilities?’”

Applying nanotechnology and materials science to medicine, and particularly to targeted drug delivery, is still a relatively new concept, but one Chan sees as full of promise. The real problem is how to deliver enough of the nanoparticles directly to the cancer to produce an effective treatment.

“Here’s how we look at these problems: it’s like you’re going to Vancouver from Toronto, but no one tells you how to get there, no one gives you a map, or a plane ticket, or a car — that’s where we are in this field,” he says. “The idea of targeting drugs to tumours is like figuring out how to go to Vancouver. It’s a simple concept, but to get there isn’t simple if not enough information is provided.”

“We’ve only scratched the surface of how nanotechnology ‘delivery’ works in the body, so now we’re continuing to explore different details of why and how tumours and other organs allow or block certain things from getting in,” adds Chan.

He and his group plan to apply the delivery system they’ve designed toward personalized nanomedicine — further tailoring their particles to deliver drugs to your precise type of tumour, and nowhere else.

Here are links to and citations for the team’s two published papers,

DNA-controlled dynamic colloidal nanoparticle systems for mediating cellular interaction by Seiichi Ohta, Dylan Glancy, Warren C. W. Chan. Science  19 Feb 2016: Vol. 351, Issue 6275, pp. 841-845 DOI: 10.1126/science.aad4925

Tailoring nanoparticle designs to target cancer based on tumor pathophysiology by Edward A. Sykes, Qin Dai, Christopher D. Sarsons, Juan Chen, Jonathan V. Rocheleau, David M. Hwang, Gang Zheng, David T. Cramb, Kristina D. Rinker, and Warren C. W. Chan. PNAS     doi: 10.1073/pnas.1521265113 published online Feb. 16, 2016.

Both papers are behind paywalls.

A nanoparticle ‘printing press’

This research comes from Montréal, Canada via a Jan. 7, 2016 McGill University news release (also on EurekAlert*),

Gold nanoparticles have unusual optical, electronic and chemical properties, which scientists are seeking to put to use in a range of new technologies, from nanoelectronics to cancer treatments.

Some of the most interesting properties of nanoparticles emerge when they are brought close together – either in clusters of just a few particles or in crystals made up of millions of them. Yet particles that are just millionths of an inch in size are too small to be manipulated by conventional lab tools, so a major challenge has been finding ways to assemble these bits of gold while controlling the three-dimensional shape of their arrangement.

One approach that researchers have developed has been to use tiny structures made from synthetic strands of DNA to help organize nanoparticles. Since DNA strands are programmed to pair with other strands in certain patterns, scientists have attached individual strands of DNA to gold particle surfaces to create a variety of assemblies. But these hybrid gold-DNA nanostructures are intricate and expensive to generate, limiting their potential for use in practical materials. The process is similar, in a sense, to producing books by hand.

Enter the nanoparticle equivalent of the printing press. It’s efficient, re-usable and carries more information than previously possible. In results reported online in Nature Chemistry, researchers from McGill’s Department of Chemistry outline a procedure for making a DNA [deoxyribonucleic acid] structure with a specific pattern of strands coming out of it; at the end of each strand is a chemical “sticky patch.”  When a gold nanoparticle is brought into contact to the DNA nanostructure, it sticks to the patches. The scientists then dissolve the assembly in distilled water, separating the DNA nanostructure into its component strands and leaving behind the DNA imprint on the gold nanoparticle. …

The researchers have made an illustration of their concept available,

Credit: Thomas Edwardson

Credit: Thomas Edwardson

“These encoded gold nanoparticles are unprecedented in their information content,” says senior author Hanadi Sleiman, who holds the Canada Research Chair in DNA Nanoscience. “The DNA nanostructures, for their part, can be re-used, much like stamps in an old printing press.”

The news release includes suggestions for possible future applications,

From stained glass to optoelectronics

Some of the properties of gold nanoparticles have been recognized for centuries.  Medieval artisans added gold chloride to molten glass to create the ruby-red colour in stained-glass windows – the result, as chemists figured out much later, of the light-scattering properties of tiny gold particles.

Now, the McGill researchers hope their new production technique will help pave the way for use of DNA-encoded nanoparticles in a range of cutting-edge technologies. First author Thomas Edwardson says the next step for the lab will be to investigate the properties of structures made from these new building blocks. “In much the same way that atoms combine to form complex molecules, patterned DNA gold particles can connect to neighbouring particles to form well-defined nanoparticle assemblies.”

These could be put to use in areas including optoelectronic nanodevices and biomedical sciences, the researchers say. The patterns of DNA strands could, for example, be engineered to target specific proteins on cancer cells, and thus serve to detect cancer or to selectively destroy cancer cells.

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

Transfer of molecular recognition information from DNA nanostructures to gold nanoparticles by Thomas G. W. Edwardson, Kai Lin Lau, Danny Bousmail, Christopher J. Serpell, & Hanadi F. Sleiman. Nature Chemistry (2016)  doi:10.1038/nchem.2420 Published online 04 January 2016

This paper is behind a paywall.

*’also on EurekAlert’ added on Jan. 8, 2016.

Enzymatic fuel cells with ultrasmall gold nanocluster

Scientists at the US Department of Energy’s Los Alamos National Laboratory have developed a DNA-templated gold nanocluster (AuNC) for more efficient biofuel cell design (Note: A link has been removed). From a Sept. 24, 2015 news item on ScienceDaily,

With fossil-fuel sources dwindling, better biofuel cell design is a strong candidate in the energy field. In research published in the Journal of the American Chemical Society (“A Hybrid DNA-Templated Gold Nanocluster For Enhanced Enzymatic Reduction of Oxygen”), Los Alamos researchers and external collaborators synthesized and characterized a new DNA-templated gold nanocluster (AuNC) that could resolve a critical methodological barrier for efficient biofuel cell design.

Here’s an image illustrating the DNA-templated gold nanoclusters,

Caption: Gold nanoclusters (~1 nm) are efficient mediators of electron transfer between co-self-assembled enzymes and carbon nanotubes in an enzyme fuel cell. The efficient electron transfer from this quantized nano material minimizes the energy waste and improves the kinetics of the oxygen reduction reaction, toward a more efficient fuel cell cycle. Credit: Los Alamos National Laboratory

Caption: Gold nanoclusters (~1 nm) are efficient mediators of electron transfer between co-self-assembled enzymes and carbon nanotubes in an enzyme fuel cell. The efficient electron transfer from this quantized nano material minimizes the energy waste and improves the kinetics of the oxygen reduction reaction, toward a more efficient fuel cell cycle.
Credit: Los Alamos National Laboratory

A Sept. 24, 2015 Los Alamos National Laboratory news release, which originated the news item, provides more details,

“Enzymatic fuel cells and nanomaterials show great promise and as they can operate under environmentally benign neutral pH conditions, they are a greener alternative to existing alkaline or acidic fuel cells, making them the subject of worldwide research endeavors,” said Saumen Chakraborty, a scientist on the project. “Our work seeks to boost electron transfer efficiency, creating a potential candidate for the development of cathodes in enzymatic fuel cells.”

Ligands, molecules that bind to a central metal atom, are necessary to form stable nanoclusters. For this study, the researchers chose single-stranded DNA as the ligand, as DNA is a natural nanoscale material having high affinity for metal cations and can be used to assembly the cluster to other nanoscale material such as carbon nanotubes.

In enzymatic fuel cells, fuel is oxidized on the anode, while oxygen reduction reactions take place on the cathode, often using multi copper oxidases. Enzymatic fuel cell performance depends critically on how effectively the enzyme active sites can accept and donate electrons from the electrode by direct electron transfer (ET). However, the lack of effective ET between the enzyme active sites, which are usually buried ~10Å from their surface, and the electrode is a major barrier to their development. Therefore, effective mediators of this electron transfer are needed.

The team developed a new DNA-templated gold nanocluster (AuNC) that enhanced electron transfer. This novel role of the AuNC as enhancer of electron transfer at the enzyme-electrode interface could be effective for cathodes in enzymatic fuel cells, thus removing a critical methodological barrier for efficient biofuel cell design.

Possessing many unique properties due to their discrete electron state distributions, metal nanoclusters (<1.5 nm diameter; ~2-144 atoms of gold, silver, platinum, or copper) show application in many fields.

Hypothesizing that due to the ultra-small size (the clusters are ~7 atoms, ~0.9 nm in diameter), and unique electrochemical properties, the AuNC can facilitate electron transfer to an oxygen-reduction reaction enzyme-active site and therefore, lower the overpotential of the oxygen reaction. Overpotential is the extra amount of energy required to drive an electrochemical reaction.

Ideally, it is desirable that all electrochemical reactions have minimal to no overpotential, but in reality they all have some. Therefore, to design an efficient electrocatalyst (for reduction or oxidation) we want to design it so that the reaction can proceed with a minimal amount of extra, applied energy.

When self assembled with bilirubin oxidase and carbon nanotubes, the AuNC acts to enhance the electron transfer, and it lowers the overpotential of oxygen reduction by a significant ~15 mV (as opposed to ~1-2 mV observed using other types of mediators) compared to the enzyme alone. The AuNC also causes significant enhancement of electrocatalytic current densities. Proteins are electronically insulating (they are complex, greasy and large), so the use of carbon nanotubes helps the enzyme stick to the electrode as well as to facilitate electron transfer.

Although gold nanoclusters have been used in chemical catalysis, this is the first time that we demonstrate they can also act as electron relaying agents to enzymatic oxygen reduction reaction monitored by electrochemistry.

Finally, the presence of AuNC does not perturb the mechanism of enzymatic O2 reduction. Such unique application of AuNC as facilitator of ET by improving thermodynamics and kinetics of O2 reduction is unprecedented.

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

A Hybrid DNA-Templated Gold Nanocluster For Enhanced Enzymatic Reduction of Oxygen by Saumen Chakraborty, Sofia Babanova, Reginaldo C. Rocha, Anil Desireddy, Kateryna Artyushkova, Amy E. Boncella, Plamen Atanassov, and Jennifer S. Martinez. J. Am. Chem. Soc., 2015, 137 (36), pp 11678–11687 DOI: 10.1021/jacs.5b05338 Publication Date (Web): August 19, 2015

Copyright © 2015 American Chemical Society

This paper is behind a paywall.

What’s in your DNA (deoxyribonucleic acid)? an art auction at Christies

For this item, I have David Bruggeman’s Sept. 24, 2015 posting on his Pasco Phronesis blog to thank,

As part of a fundraising project for a building at the Francis Crick Institute, Christie’s will hold an auction for 30 double-helix sculptures on September 30 (H/T ScienceInsider).

David has embedded a video featuring some of the artists and their works in his posting. By contrast, here are a few pictures of the DNA (deoxyribonucleic acid) art objects from the Cancer Research UK’s DNA Trail page,

For our London Art trail, which ran from 29 June – 6 September 2015, we asked internationally renowned artists to design a beautiful double helix sculpture inspired by the question: What’s in your DNA? Take a look at their sculptures and find out more about the artists’ inspirations.

This one is called The Journey and is by Gary Portell,

DNA_The Journey

His inspiration is: “My design is based on two symbols, the swallow who shares my journey from Africa to England and the hand print. The hand print as a symbol of creation and the swallow reflects the traveller.

This one by Thiery Noir is titled Double Helix Noir.


The inspiration is: For this sculpture, Noir wanted to pay tribute to the memory of his former assistant, Lisa Brown, who was affected by breast cancer and who passed away in July 2001, at the young age of 31 years old.

Growing Stem is by Orla Kiely,


The inspiration is: I find inspiration in many things, but especially love nature with the abundance of colourful flowers, leaves, and stems. Applying our multi stem onto the DNA spiral seemed a natural choice as it represents positivity and growth: qualities that are so relevant for cancer research.

Double Dutch Delftblue DNA is by twins, Chris and Xand van Tulleken.


The inspiration is: The recurrent motifs of Delft tiles reference those of DNA. Our inspiration was the combination of our family’s DNA, drawing on Dutch and Canadian origins, and the fact that twins have shared genomes.  (With thanks to Anthony van Tulleken)

Ted Baker’s Ted’s Helix of Haberdashery,


Inspiration is: Always a fan of spinning a yarn, Ted Baker’s Helix of Haberdashery sculpture unravels the tale of his evolution from shirt specialist to global lifestyle brand. Ted’s DNA is represented as a cascading double helix of pearlescent buttons, finished with a typically playful story-telling flourish.

Finally, What Mad Pursuit is by Kindra Crick,


Inspiration is: What Mad Pursuit explores the creative possibilities achievable through the intermingling of art, science and imagination in the quest for knowledge. The piece is inspired by my family’s contribution to the discovery of the structure of DNA.

Aparna Vidyasagar interviewed Kindra Crick in a Sept. 24, 2015 Q&A for ScienceInsider (Note: Links have been removed),

Kindra Crick, granddaughter of Francis Crick, the co-discoverer of DNA’s structure, is one of more than 20 artists contributing sculptures to an auction fundraiser for a building at the new Francis Crick Institute. The auction is being organized by Cancer Research UK and will be held at Christie’s in London on 30 September. The auction will continue online until 13 October.

The new biomedical research institute, named for the Nobel laureate who died in 2004, aims to develop prevention strategies and treatments for diseases including cancer. It is a consortium of six partners, including Cancer Research UK.

Earlier this year, Cancer Research UK asked about two dozen artists—including Chinese superstar Ai Weiwei—to answer the question “What’s in your DNA?” through a sculpture based on DNA’s double helix structure. …

Q: “What’s in your DNA?” How did you build your sculpture around that question?

A: When I was given the theme, I thought this was a wonderful project for me, considering my family history. Also, in my own art practice I try to express the wonder and the process of scientific inquiry. This draws on my backgrounds; in molecular biology from when I was at Princeton [University], and in art while going to the School of the Art Institute of Chicago.

I was influenced by my grandparents, Francis Crick and Odile Crick. He was the scientist and she was the artist. My grandfather worked on elucidating the structure of DNA, and my grandmother, Odile, was the one to draw the first image of DNA. The illustration was used for the 1953 paper that my grandfather wrote with James Watson. So, there’s a rich history there that I can draw from, in terms of what’s in my DNA.

Should you be interested in bidding on one of the pieces, you can go to Christie’s What’s in your DNA webpage,

ONLINE AUCTION IS LIVE: 30 September – 13 October 2015

Good luck!

David Bruggeman has put in a request (from his Sept. 24, 2015 posting),

… if you become aware of human trials for 3D bioprinting, please give a holler.  I may now qualify.

Good luck David!

Science cakery

I have to thank Dean Burnett for his science cake extravagance on the Guardian science blogs. Here’s a few pictures of cake to tantalize you from Burnett’s Aug. 12, 2015 posting,

An evolution-of-life cake from @OxUniEarthSci Palaeontology Group. Bizarre how this life-sciences cake seems to defy physics with its structure. Photograph: @JackJMatthews

An evolution-of-life cake from @OxUniEarthSci Palaeontology Group. Bizarre how this life-sciences cake seems to defy physics with its structure.
Photograph: @JackJMatthews

A cake shaped like a subject entering an MRI scanner for @ImanovaImaging’s 1st birthday party. Because why not? Photograph: @M_Wall

A cake shaped like a subject entering an MRI scanner for @ImanovaImaging’s 1st birthday party. Because why not?
Photograph: @M_Wall

Katie Watkins created TMS coils on talking brains. For the record, it is not necessary or even helpful for the brain to be exposed during TMS. Photograph: Kate Watkins

Katie Watkins created TMS coils on talking brains. For the record, it is not necessary or even helpful for the brain to be exposed during TMS. Photograph: Kate Watkins

Katie Grifiths, posing with a DNA cake made by her sister Emma. What’s with these biology-themed cakes and their ability to overrule gravity? Do NASA know about this? Photograph: Katie Griffiths

Katie Grifiths, posing with a DNA cake made by her sister Emma. What’s with these biology-themed cakes and their ability to overrule gravity? Do NASA know about this?
Photograph: Katie Griffiths

Marilyn Audlsey produced this particles-in-a-cloud-chamber ginger cake. I’m not even going to pretend to know what that is, but it makes for a nice looking cake. Photograph: Marilyn Audsley

Marilyn Audlsey produced this particles-in-a-cloud-chamber ginger cake. I’m not even going to pretend to know what that is, but it makes for a nice looking cake. Photograph: Marilyn Audsley

And this is the last one I’m including,

Sara Barnes did this @ATLASexperiment. At last, the money spent on the Lare Hadron Collider starts to show useful results. Photograph: Sarah Barnes

Sara Barnes did this @ATLASexperiment. At last, the money spent on the Lare Hadron Collider starts to show useful results.
Photograph: Sarah Barnes

Burnett has many more areas of science memorialized in cake in his Aug. 12, 2015 posting.

I last featured science and cakes in a March 31, 2012 posting about the periodic table of elements and cupcakes. On a closely related note, I wrote about mathematics and baking in a June 28, 2013 posting.

DNA (deoxyribonucleic acid) scaffolding for nonbiological construction

DNA (deoxyribonucleic acid) is being exploited in ways that would have seemed unimaginable to me when I was in high school. Earlier today (June 3, 2015), I ran a piece about DNA and data storage as imagined in an art/science project (DNA (deoxyribonucleic acid), music, and data storage) and now I have this work from the US Department of Energy’s (DOE) Brookhaven National Laboratory, from a June 1, 2015 news item on Nanowerk,

You’re probably familiar with the role of DNA as the blueprint for making every protein on the planet and passing genetic information from one generation to the next. But researchers at Brookhaven Lab’s Center for Functional Nanomaterials have shown that the twisted ladder molecule made of complementary matching strands can also perform a number of decidedly non-biological construction jobs: serving as a scaffold and programmable “glue” for linking up nanoparticles. This work has resulted in a variety of nanoparticle assemblies, including composite structures with switchable phases whose optical, magnetic, or other properties might be put to use in dynamic energy-harvesting or responsive optical materials. Three recent studies showcase different strategies for using synthetic strands of this versatile building material to link and arrange different types of nanoparticles in predictable ways.

The researchers have provided an image of the DNA building blocks,

Controlling the self-assembly of nanoparticles into superlattices is an important approach to build functional materials. The Brookhaven team used nanosized building blocks—cubes or octahedrons—decorated with DNA tethers to coordinate the assembly of spherical nanoparticles coated with complementary DNA strands.

Controlling the self-assembly of nanoparticles into superlattices is an important approach to build functional materials. The Brookhaven team used nanosized building blocks—cubes or octahedrons—decorated with DNA tethers to coordinate the assembly of spherical nanoparticles coated with complementary DNA strands.

A June 1, 2015 article (which originated the news item) in DOE Pulse Number 440 goes on to highlight three recent DNA papers published by researchers at Brookhaven National Laboratory,

The first [leads to a news release], published in Nature Communications, describes how scientists used the shape of nanoscale building blocks decorated with single strands of DNA to orchestrate the arrangement of spheres decorated with complementary strands (where bases on the two strands pair up according to the rules of DNA binding, A to T, G to C). For example, nano-cubes coated with DNA tethers on all six sides formed regular arrays of cubes surrounded by six nano-spheres. The attractive force of the DNA “glue” keeps these two dissimilar objects from self-separating to give scientists a reliable way to assemble composite materials in which the synergistic properties of different types of nanoparticles might be put to use.

In another study [leads to a news release], published in Nature Nanotechnology, the team used ropelike configurations of the DNA double helix to form a rigid geometrical framework, and added dangling pieces of single-stranded DNA to glue nanoparticles in place on the vertices of the scaffold. Controlling the code of the dangling strands and adding complementary strands to the nanoparticles gives scientists precision control over particle placement. These arrays of nanoparticles with predictable geometric configurations are somewhat analogous to molecules made of atoms, and can even be linked end-to-end to form polymer-like chains, or arrayed as flat sheets. Using this approach, the scientists can potentially orchestrate the arrangements of different types of nanoparticles to design materials that regulate energy flow, rotate light, or deliver biomolecules.

“We may be able to design materials that mimic nature’s machinery to harvest solar energy, or manipulate light for telecommunications applications, or design novel catalysts for speeding up a variety of chemical reactions,” said Oleg Gang, the Brookhaven physicist who leads this work on DNA-mediated nano-assembly.

Perhaps most exciting is a study [leads to a news release] published in Nature Materials in which the scientists added “reprogramming” strands of DNA after assembly to rearrange and change the phase of nanoparticle arrays. This is a change at the nanoscale that in some ways resembles an atomic phase change—like the shift in the atomic crystal lattice of carbon that transforms graphite into diamond—potentially producing a material with completely new properties from the same already assembled nanoparticle array. Inputting different types of attractive and repulsive reprogramming DNA strands, scientists could selectively trigger the transformation to the different resulting structures.

“The ability to dynamically switch the phase of an entire superlattice array will allow the creation of reprogrammable and switchable materials wherein multiple, different functions can be activated on demand,” Gang said.

Here are links to and citation for all three papers,

Superlattices assembled through shape-induced directional binding by Fang Lu, Kevin G. Yager, Yugang Zhang, Huolin Xin, & Oleg Gang. Nature Communications 6, Article number: 6912 doi:10.1038/ncomms7912 Published 23 April 2015

Prescribed nanoparticle cluster architectures and low-dimensional arrays built using octahedral DNA origami frames by Ye Tian, Tong Wang, Wenyan Liu, Huolin L. Xin, Huilin Li, Yonggang Ke, William M. Shih, & Oleg Gang. Nature Nanotechnology (2015) doi:10.1038/nnano.2015.105 Published online 25 May 2015

Selective transformations between nanoparticle superlattices via the reprogramming of DNA-mediated interactions by Yugang Zhang, Suchetan Pal, Babji Srinivasan, Thi Vo, Sanat Kumar & Oleg Gang. Nature Materials (2015) doi:10.1038/nmat4296 Published online 25 May 2015

The first study is open access, the second is behind a paywall but there is a free preview via ReadCube Acces, and the third is behind a paywall.

DNA (deoxyribonucleic acid), music, and data storage

David Bruggeman (Pasco Phronesis blog) has written up, as he so often does, a fascinating art/science piece in his May 28, 2015 post (Note: A link has been removed),

Opening next month [June 2015] at the Dilston Grove Gallery at GDP London is Music of the Spheres, an exhibition that uses bioinformatics to record music.  Dr. Nick Goldman of the European Bioinformatics Institute has been working on new technologies for encoding large amounts of information into DNA.  Collaborating with Charlotte Jarvis, the two have worked on installations of bubbles that would contain DNA encoded with music (the DNA is suspended in soap solution).

There’s more information about the exhibit on the Music of the Spheres webpage on the CGP London website,

Music of the Spheres utilises new bioinformatics technology developed by Dr. Nick Goldman to encode a new musical recording by the Kreutzer Quartet into DNA.

The DNA has been suspended in soap solution and will be used by visual artist Charlotte Jarvis to create performances and installations filled with bubbles. The recording will fill the air, pop on visitors skin and literally bathe the audience in music.

Dr. Nick Goldman and Charlotte Jarvis have been working together for the past year to create a series of moving visual and musical experiences that explore the scope and future ubiquity of DNA technologies.

The Kreutzer Quartet’s new composition for string quartet loosely follows the traditional form of a concerto, in comprising of three musical movements. The second movement only exists in the form of a recording encoded into DNA.

For the exhibition the DNA will be suspended in soap solution and used to create silent installations filled with bubbles. The bubbles will be accompanied by a video projection showing the musicians playing in the server room of the European Bioinformatics Institute, Cambridge.

In response to the growing challenge of storing vast quantities of biological data generated by biomedical research Dr. Nick Goldman and the European Bioinformatics Institute have developed a method to encode huge amounts of information in DNA itself. Every day the huge quantities and speed of data pouring into servers gets larger. When research groups sequence DNA the file sizes are too large to be kept on local computers. It is this problem that was the motivation for Nick Goldman to develop his new technology. Their goal is a system that will safely store the equivalent of one million CDs in a gram of DNA for 10,000 years. Nick’s work was has been featured in The New York Times, The Guardian and on BBC News amongst other media outlets.

The Kreutzer Quartet will play the full-length composition live during the preview on 12 June [2015] timed with the setting of the sun through the large westerly windows. [emphasis mine] During the passage of the second movement the stage will fall silent, the music will be released into the auditorium in the form of bubbles. The performance will be accompanied by film projection and a discussion about the project.

The exhibit runs from June 12 – July 5, 2015. Hours and location can be found on the CGP website.

The Music of the Spheres DNA/music project was first mentioned here in a May 5, 2014 post about the launch of the book ‘Synthetic Aesthetics: Investigating Synthetic Biology’s Designs on Nature’. The launch featured a number of performances and events, scroll down abut 80% of the way for the then description of Music of the Spheres.

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.