Tag Archives: biomolecules

Controlling the nanostructure of inorganic materials with tumor suppressor proteins

A May 3, 2017 news item on Nanowerk announces research from Japan on using tumor suppressor proteins to control nanostructures,

A new method combining tumor suppressor protein p53 and biomineralization peptide BMPep successfully created hexagonal silver nanoplates, suggesting an efficient strategy for controlling the nanostructure of inorganic materials.

Precise control of nanostructures is a key factor to form functional nanomaterials. Biomimetic approaches are considered effective for fabricating nanomaterials because biomolecules are able to bind with specific targets, self-assemble, and build complex structures. Oligomerization, or the assembly of biomolecules, is a crucial aspect of natural materials that form higher-ordered structures.

A May 3,2017 Hokkaido University research press release, which originated the news item, delves into the details,

Some peptides are known to bind with a specific inorganic substance, such as silver, and enhance its crystal formation. This phenomenon, called peptide-mediated biomineralization, could be used as a biomimetic approach to create functional inorganic structures. Controlling the spatial orientation of the peptides could yield complex inorganic structures, but this has long been a great challenge.

A team of researchers led by Hokkaido University Professor Kazuyasu Sakaguchi has succeeded in controlling the oligomerization of the silver biomineralization peptide (BMPep) which led to the creation of hexagonal silver nanoplates.

The team utilized the well-known tumor suppressor protein p53 which has been known to form tetramers through its tetramerization domain (p53Tet). “The unique symmetry of the p53 tetramer is an attractive scaffold to be used in controlling the overall oligomerization state of the silver BMPep such as its spatial orientation, geometry, and valency,” says Sakaguchi.

In the experiments, the team successfully created silver BMPep fused with p53Tet. This resulted in the formation of BMPep tetramers which yielded hexagonal silver nanoplates. They also found that the BMPep tetramers have enhanced specificity to the structured silver surface, apparently regulating the direction of crystal growth to form hexagonal nanoplates. Furthermore, the tetrameric peptide acted as a catalyst, controlling the silver’s crystal growth without consuming the peptide.

“Our novel method can be applied to other biomineralization peptides and oligomerization proteins, thus providing an efficient and versatile strategy for controlling nanostructures of various inorganic materials. The production of tailor-made nanomaterials is now more feasible,” Sakaguchi commented.

monomeric and tetrameric biomineralization peptides

(Left panels) Schematic illustrations of monomeric and tetrameric biomineralization peptides fused with p53Tet and electron microscopy images of silver nanostructures formed by the biomineralization peptides. Scale bar = 100 nm. (Right) The proposed model in which tetrameric biomineralization peptides regulate the direction of crystal growth and therefore its nanostructure.

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

Oligomerization enhances the binding affinity of a silver biomineralization peptide and catalyzes nanostructure formation by Tatsuya Sakaguchi, Jose Isagani B. Janairo, Mathieu Lussier-Price, Junya Wada, James G. Omichinski, & Kazuyasu Sakaguchi. Scientific Reports 7, Article number: 1400 (2017)  doi:10.1038/s41598-017-01442-8 Published online: 03 May 2017

This paper is open access.

Synthesized nanoparticles with the complexity of protein molecules

Caption: The structure of the largest gold nanoparticle to-date, Au246(SR)80, was resolved using x-ray crystallography. Credit: Carnegie Mellon University

Carnegie Mellon University (CMU) researchers synthesized a self-assembled nanoparticle of gold as they built on their 2015 work described in my April 14, 2015 posting (Nature’s patterns reflected in gold nanoparticles). Here’s the latest from the team in a Jan. 23, 2017 news item on phys.org,

Chemists at Carnegie Mellon University have demonstrated that synthetic nanoparticles can achieve the same level of structural complexity, hierarchy and accuracy as their natural counterparts – biomolecules. The study, published in Science, also reveals the atomic-level mechanisms behind nanoparticle self-assembly.

The findings from the lab of Chemistry Professor Rongchao Jin provide researchers with an important window into how nanoparticles form, and will help guide the construction of nanoparticles, including those that can be used in the fabrication of computer chips, creation of new materials, and development of new drugs and drug delivery devices.

Caption: By resolving the structure of Au246, Carnegie Mellon researchers were able to visualize its hierarchical assembly into artificial solid. Credit: Carnegie Mellon University

A Jan.  23, 2017 CMU news release on EurekAlert, which originated the news item, expands on the theme,

“Most people think that nanoparticles are simple things, because they are so small. But when we look at nanoparticles at the atomic level, we found that they are full of wonders,” said Jin.

Nanoparticles are typically between 1 and 100 nanometers in size. Particles on the larger end of the nanoscale are harder to create precisely. Jin has been at the forefront of creating precise gold nanoparticles for a decade, first establishing the structure of an ultra-small Au25 nanocluster and then working on larger and larger ones. In 2015, his lab used X-ray crystallography to establish the structure of an Au133 nanoparticle and found that it contained complex, self-organized patterns that mirrored patterns found in nature.

In the current study, they sought to find out the mechanisms that caused these patterns to form. The researchers, led by graduate student Chenjie Zeng, established the structure of Au246, one of the largest and most complex nanoparticles created by scientists to-date and the largest gold nanoparticle to have its structure determined by X-ray crystallography. Au246 turned out to be an ideal candidate for deciphering the complex rules of self- assembly because it contains an ideal number of atoms and surface ligands and is about the same size and weight as a protein molecule.

Analysis of Au246’s structure revealed that the particles had much more in common with biomolecules than size. They found that the ligands in the nanoparticles self-assembled into rotational and parallel patterns that are strikingly similar to the patterns found in proteins’ secondary structure. This could indicate that nanoparticles of this size could easily interact with biological systems, providing new avenues for drug discovery.

The researchers also found that Au246 particles form by following two rules. First, they maximize the interactions between atoms, a mechanism that had been theorized but not yet seen. Second the nanoparticles match symmetric surface patterns, a mechanism that had not been considered previously. The matching, which is similar to puzzle pieces coming together, shows that the components of the particle can recognize each other by their patterns and spontaneously assemble into the highly ordered structure of a nanoparticle.

“Self-assembly is an important way of construction in the nanoworld. Understanding the rules of self-assembly is critical to designing and building up complex nanoparticles with a wide-range of functionalities,” said Zeng, the study’s lead author.

In future studies, Jin hopes to push the crystallization limits of nanoparticles even farther to larger and larger particles. He also plans to explore the particles’ electronic and catalytic power.

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

Emergence of hierarchical structural complexities in nanoparticles and their assembly by Chenjie Zeng, Yuxiang Chen, Kristin Kirschbaum, Kelly J. Lambright, Rongchao Jin. Science  23 Dec 2016: Vol. 354, Issue 6319, pp. 1580-1584 DOI: 10.1126/science.aak9750

This paper is behind a paywall.

Electrochemical measurements of biomolecules

This work comes from Finland and features some new nano shapes. From a Nov. 10, 2016 news item on phys.org,

Tomi Laurila’s research topic has many quirky names.

“Nanodiamond, nanohorn, nano-onion…,” lists off the Aalto University Professor, recounting the many nano-shapes of carbon. Laurila is using these shapes to build new materials: tiny sensors, only a few hundred nanometres across, that can achieve great things due to their special characteristics.

For one, the sensors can be used to enhance the treatment of neurological conditions. That is why Laurila, University of Helsinki Professor Tomi Taira and experts from HUS (the Hospital District of Helsinki and Uusimaa) are looking for ways to use the sensors for taking electrochemical measurements of biomolecules. Biomolecules are e.g. neurotransmitters such as glutamate, dopamine and opioids, which are used by nerve cells to communicate with each other.

A Nov. 10, 2016 Aalto University press release, which originated the news item, expands on the theme,

Most of the drugs meant for treating neurological diseases change the communication between nerve cells that is based on neurotransmitters. If we had real time and individual information on the operation of the neurotransmitter system, it would make it much easier to for example plan precise treatments’, explains Taira.

Due to their small size, carbon sensors can be taken directly next to a nerve cell, where the sensors will report what kind of neurotransmitter the cell is emitting and what kind of reaction it is inducing in other cells.

‘In practice, we are measuring the electrons that are moving in oxidation and reduction reactions’, Laurila explains the operating principle of the sensors.

‘The advantage of the sensors developed by Tomi and the others is their speed and small size. The probes used in current measurement methods can be compared to logs on a cellular scale – it’s impossible to use them and get an idea of the brain’s dynamic’, summarizes Taira.

Feedback system and memory traces

For the sensors, the journey from in vitro tests conducted in glass dishes and test tubes to in vivo tests and clinical use is long. However, the researchers are highly motivated.

‘About 165 million people are suffering from various neurological diseases in Europe alone. And because they are so expensive to treat, neurological diseases make up as much as 80 per cent of health care costs’, tells Taira.

Tomi Laurila believes that carbon sensors will have applications in fields such as optogenetics. Optogenetics is a recently developed method where a light-sensitive molecule is brought into a nerve cell so that the cell’s electric operation can then be turned on or off by stimulating it with light. A few years ago, a group of scientists proved in the scientific journal Nature that they had managed to use optogenetics to activate a memory trace that had been created previously due to learning. Using the same technique, researchers were able to demonstrate that with a certain type of Alzheimer’s, the problem is not that there are no memory traces being created, but that the brain cannot read the traces.

‘So the traces exist, and they can be activated by boosting them with light stimuli’, explains Taira but stresses that a clinical application is not yet a reality. However, clinical applications for other conditions may be closer by. One example is Parkinson’s disease. In Parkinson’s disease, the amount of dopamine starts to decrease in the cells of a particular brain section, which causes the typical symptoms such as tremors, rigidity and slowness of movement. With the sensors, the level of dopamine could be monitored in real time.

‘A sort of feedback system could be connected to it, so that it would react by giving an electric or optical stimulus to the cells, which would in turn release more dopamine’, envisions Taira.

‘Another application that would have an immediate clinical use is monitoring unconscious and comatose patients. With these patients, the level of glutamate fluctuates very much, and too much glutamate damages the nerve cell – online monitoring would therefore improve their treatment significantly.

Atom by atom

Manufacturing carbon sensors is definitely not a mass production process; it is slow and meticulous handiwork.

‘At this stage, the sensors are practically being built atom by atom’, summarises Tomi Laurila.

‘Luckily, we have many experts on carbon materials of our own. For example, the nanobuds of Professor Esko Kauppinen and the carbon films of Professor Jari Koskinen help with the manufacturing of the sensors. Carbon-based materials are mainly very compatible with the human body, but there is still little information about them. That’s why a big part of the work is to go through the electrochemical characterisation that has been done on different forms of carbon.’

The sensors are being developed and tested by experts from various fields, such as chemistry, materials science, modelling, medicine and imaging. Twenty or so articles have been published on the basic properties of the materials. Now, the challenge is to build them into geometries that are functional in a physiological environment. And taking measurements is not simple, either.

‘Brain tissue is delicate and doesn’t appreciate having objects being inserted in it. But if this were easy, someone would’ve already done it’, conclude the two.

I wish the researchers good luck.

A DNA origami-based nanoscopic force clamp

Nanoclamp made of DNA strands. Illustration: Christoph Hohmann

Nanoclamp made of DNA strands. Illustration: Christoph Hohmann

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

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

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

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

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

A feather-light touch

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

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

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

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

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

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

This paper is behind a paywall.

Medical nanobots (nanorobots) and biocomputing; an important step in Russia

Russian researchers have reported a technique which can make logical calculations from within cells according to an Aug. 19, 2014 news item on ScienceDaily,

Researchers from the Institute of General Physics of the Russian Academy of Sciences, the Institute of Bioorganic Chemistry of the Russian Academy of Sciences and MIPT [Moscow Institute of Physics and Technology] have made an important step towards creating medical nanorobots. They discovered a way of enabling nano- and microparticles to produce logical calculations using a variety of biochemical reactions.

An Aug. 19 (?), 2014 MIPT press release, which originated the news item, provides a good beginner’s explanation of bioengineering in the context of this research,

For example, modern bioengineering techniques allow for making a cell illuminate with different colors or even programming it to die, linking the initiation  of apoptosis [cell death] to the result of binary operations.

Many scientists believe logical operations inside cells or in artificial biomolecular systems to be a way of controlling biological processes and creating full-fledged micro-and nano-robots, which can, for example, deliver drugs on schedule to those tissues where they are needed.

Calculations using biomolecules inside cells, a.k.a. biocomputing, are a very promising and rapidly developing branch of science, according to the leading author of the study, Maxim Nikitin, a 2010 graduate of MIPT’s Department of Biological and Medical Physics. Biocomputing uses natural cellular mechanisms. It is far more difficult, however, to do calculations outside cells, where there are no natural structures that could help carry out calculations. The new study focuses specifically on extracellular biocomputing.

The study paves the way for a number of biomedical technologies and differs significantly from previous works in biocomputing, which focus on both the outside and inside of cells. Scientists from across the globe have been researching binary operations in DNA, RNA and proteins for over a decade now, but Maxim Nikitin and his colleagues were the first to propose and experimentally confirm a method to transform almost any type of nanoparticle or microparticle into autonomous biocomputing structures that are capable of implementing a functionally complete set of Boolean logic gates (YES, NOT, AND and OR) and binding to a target (such as a cell) as result of a computation. This method allows for selective binding to target cells, as well as it represents a new platform to analyze blood and other biological materials.

The prefix “nano” in this case is not a fad or a mere formality. A decrease in particle size sometimes leads to drastic changes in the physical and chemical properties of a substance. The smaller the size, the greater the reactivity; very small semiconductor particles, for example, may produce fluorescent light. The new research project used nanoparticles (i.e. particles of 100 nm) and microparticles (3000 nm or 3 micrometers).

Nanoparticles were coated with a special layer, which “disintegrated” in different ways when exposed to different combinations of signals. A signal here is the interaction of nanoparticles with a particular substance. For example, to implement the logical operation “AND” a spherical nanoparticle was coated with a layer of molecules, which held a layer of spheres of a smaller diameter around it. The molecules holding the outer shell were of two types, each type reacting only to a particular signal; when in contact with two different substances small spheres separated from the surface of a nanoparticle of a larger diameter. Removing the outer layer exposed the active parts of the inner particle, and it was then able to interact with its target. Thus, the team obtained one signal in response to two signals.

For bonding nanoparticles, the researchers selected antibodies. This also distinguishes their project from a number of previous studies in biocomputing, which used DNA or RNA for logical operations. These natural proteins of the immune system have a small active region, which responds only to certain molecules; the body uses the high selectivity of antibodies to recognize and neutralize bacteria and other pathogens.

Making sure that the combination of different types of nanoparticles and antibodies makes it possible to implement various kinds of logical operations, the researchers showed that cancer cells can be specifically targeted as well. The team obtained not simply nanoparticles that can bind to certain types of cells, but particles that look for target cells when both of two different conditions are met, or when two different molecules are present or absent. This additional control may come in handy for more accurate destruction of cancer cells with minimal impact on healthy tissues and organs.

Maxim Nikitin said that although this is just as mall step towards creating efficient nanobiorobots, this area of science is very interesting and opens up great vistas for further research, if one draws an analogy between the first works in the creation of nanobiocomputers and the creation of the first diodes and transistors, which resulted in the rapid development of electronic computers.

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

Biocomputing based on particle disassembly by Maxim P. Nikitin, Victoria O. Shipunova, Sergey M. Deyev, & Petr I. Nikitin. Nature Nanotechnology (2014) doi:10.1038/nnano.2014.156 Published online 17 August 2014

This paper is behind a paywall.

Extracting biomolecules from live cells with carbon nanotubes

Being able to extract biomolecules from living cells means nondestruction of the rest of the cell and the ability to observe the consequences of the extraction. From a July 18, 2014 news item on Azonano,

University of Houston researchers have devised a new method for extracting molecules from live cells without disrupting cell development, work that could provide new avenues for the diagnosis of cancer and other diseases.

The researchers used magnetized carbon nanotubes to extract biomolecules from live cells, allowing them to retrieve molecular information without killing the individual cells. A description of the work appears this week in the Proceedings of the National Academy of Sciences.

A July 16, 2014 University of Houston news release by Jeannie Kever, which originated the news item, provides more detail,

Most current methods of identifying intracellular information result in the death of the individual cells, making it impossible to continue to gain information and assess change over time, said Zhifeng Ren, M.D. Anderson Chair professor of physics and principal investigator at the Center for Superconductivity at UH and lead author of the paper. The work was a collaboration between Ren’s lab and that of Paul Chu, T.L.L. Temple Chair of Science and founding director of the Texas Center for Superconductivity.

Chu, a co-author of the paper, said the new technique will allow researchers to draw fundamental information from a single cell.The researchers said the steps outlined in the paper offer proof of concept. Ren said the next step “will be more study of the biological and chemical processes of the cell, more analysis.”

The initial results hold promise for biomedicine, he said.  “This shows how nanoscience and nanoengineering can help the medical field.”

Cai said the new method will be helpful for cancer drug screening and carcinogenesis study, as well as for studies that allow researchers to obtain information from single cells, replacing previous sampling methods that average out cellular diversity and obscure the specificity of the biomarker profiles.

In the paper, the researchers explain their rationale for the work – most methods for extracting molecular information result in cell death, and those that do spare the cell carry special challenges, including limited efficiency.

This method is relatively straightforward, requiring the use of magnetized carbon nanotubes as the transporter and a polycarbonate filter as a collector, they report. Cells from a human embryonic kidney cancer cell line were used for the experiment.

The work builds on a 2005 paper published by Ren’s group in Nature Methods, which established that magnetized carbon nanotubes can deliver molecular payloads into cells. The current research takes that one step further to move molecules out of cells by magnetically driving them through the cell walls.

The carbon nanotubes were grown with a plasma-enhanced chemical vapor deposition system, with magnetic nickel particles enclosed at the tips. A layer of nickel was also deposited along the surface of individual nanotubes in order to make the nanotubes capable of penetrating a cell wall guided by a magnet.

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

Molecular extraction in single live cells by sneaking in and out magnetic nanomaterials by Zhen Yang, Liangzi Deng, Yucheng Lan, Xiaoliu Zhang, Zhonghong Gao, Ching-Wu Chu, Dong Cai, and Zhifeng Ren. PNAS 2014 ; published ahead of print July 16, 2014, doi:10.1073/pnas.1411802111

This paper is behind a paywall.

Similarities between biological molecules and synthetic nanocrystals extend beyond size

Researchers at the University of Illinois at Urbana-Champaign have determined that there are more similarities between biological molecules and synthetic nanocrystals than formerly believed, according to a Dec. 17, 2013 news item on Nanowerk (Note: A link has been removed),

Researchers have long thought that biological molecules and synthetic nanocrystals were similar only in size. Now, University of Illinois at Urbana-Champaign chemists have found that they can add reactivity to the list of shared traits. Atoms in a nanocrystal can cooperate with each other to facilitate binding or switching, a phenomenon widely found in biological molecules.

The finding could catalyze manufacturing of nanocrystals for smart sensors, solar cells, tiny transistors for optical computers, and medical imaging. Led by chemistry professor Prashant Jain, the team published its findings in the journal Nature Communications (“Co-operativity in a nanocrystalline solid-state transition”).

A Dec. 16, 2013 University of Illinois at Urbana-Champaign news release, which originated the news item, explains why the scientists are so interested and how they went about their investigation,

“In geological, industrial and domestic environments, the nanoscale grains of any material undergo chemical transitions when they are put under reactive conditions,” Jain said. “Iron rusting over time and diamond forming from carbon are examples of two commonly occurring transitions. Understanding how these transitions occur on the scale of the tiniest grains of the material is a major motivation of our work.”

Scientists can exploit such transitions to make nanocrystals that conform to a particular structure. They can make a nanocrystal of one material and transform it into another material, essentially using the original nanocrystal framework as a template for creating a nanocrystal of the new material with the same size and shape. This lets researchers create nanocrystals of new materials in shapes and structures they may not be able to otherwise.

In the new study, the researchers transformed tiny crystals of the material cadmium selenide to crystals of copper selenide. Copper selenide nanocrystals have a number of interesting properties that can be used for solar energy harvesting, optical computing and laser surgery. Transformation from cadmium selenide creates nanocrystals with a purity difficult to attain from other methods.

The researchers, including graduate student Sarah White, used advanced microscopy and spectroscopy techniques to determine the dynamics of the atoms within the crystals during the transformation and found that the transformation occurs not as a slow diffusion process, but as a rapid switching thanks to co-operativity.

The researchers saw that once the cadmium-selenide nanocrystal has taken up a few initial copper “seed” impurities, atoms in the rest of the lattice can cooperate to rapidly swap out the rest of the cadmium for copper. Jain compares the crystals to hemoglobin, the molecule in red blood cells that carries oxygen. Once one oxygen molecule has bound to hemoglobin, other binding sites within hemoglobin slightly change conformation to more easily pick up more oxygen. He posits that similarly, copper impurities might cause a structural change in the nanocrystal, making it easier for more copper ions to infiltrate the nanocrystal in a rapid cascade.

The researchers reproduced the experiment with silver, in addition to copper, and saw similar, though slightly less speedy, cooperative behavior.

Now, Jain’s team is using its advanced imaging to watch transitions happen in single nanocrystals, in real time.

“We have a sophisticated optical microscope in our lab, which has now allowed us to catch a single nanocrystal in the act of making a transition,” Jain said. “This is allowing us to learn hidden details about how the transition actually proceeds. We are also learning how one nanocrystal behaves differently from another.”

Next, the researchers plan to explore biomolecule-like cooperative phenomena in other solid-state materials and processes. For example, co-operativity in catalytic processes could have major implications for solar energy or manufacturing of expensive specialty chemicals.

“In the long term, we are interested in exploiting the co-operative behavior to design artificial smart materials that respond in a switch-like manner like hemoglobin in our body does,” Jain said.

Here’s an image of the various forms of cadmium selenide used in research,

Nanocrystals of cadmium selenide, known for their brilliant luminescence, display intriguing chemical behavior resulting from positive cooperation between atoms, a behavior akin to that found in biomolecules.  Photo courtesy Prashant Jain

Nanocrystals of cadmium selenide, known for their brilliant luminescence, display intriguing chemical behavior resulting from positive cooperation between atoms, a behavior akin to that found in biomolecules. Photo courtesy
Prashant Jain

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

Co-operativity in a nanocrystalline solid-state transition by Sarah L. White, Jeremy G. Smith, Mayank Behl, & Prashant K. Jain Nature Communications 4, Article number: 2933 doi:10.1038/ncomms3933 Published 12 December 2013

This article is behind a paywall.

Watching zinc, iron, and copper molecules real-time as they interact with biomolecules

Eventually they’re hoping this work will lead to insights about diabetes and cancer. In the meantime, researchers at RIKEN Center for Life Science Technologies (Japan) have developed a new imaging technique that allows them to observe metal molecules interacting with biomolecules in real-time. From the May 2, 2013 news release on EurekAlert,

Metal elements and molecules interact in the body but visualizing them together has always been a challenge. Researchers from the RIKEN Center for Life Science Technologies in Japan have developed a new molecular imaging technology that enables them to visualize bio-metals and bio-molecules simultaneously in a live mouse. This new technology will enable researchers to study the complex interactions between metal elements and molecules in living organisms.

It’s well known we need zinc, iron, and copper in our bodies for proper functioning. Until now, no one has been able to observe the interaction in real-time, from the RIKEN May 2, 2013 press release (which originated the EurekAlert news release),

In the study, the researchers were able to visualise two radioactive agents injected in a tumor-bearing mouse, as well as an anti-tumor antibody labelled with a PET molecular probe agent, simultaneously in the live mouse.

This new revolutionary technology is expected to offer new insights into the relationships between bio-metal elements and associated bio-molecules, and the roles they play in diseases such as diabetes and cancer.

The researchers had to create a camera capable of visualizing the interactions (from the RIKEN press release),

Dr. Shuichi Enomoto, Dr. Shinji Motomura and colleagues, from the RIKEN Center for Life Science Technologies have developed a gamma-ray imaging camera enabling them to detect the gamma-rays emitted by multiple bio-metal elements in the body and study their behavior.

Their second prototype of the system, called GREI–II and presented today in the Journal of Analytical Atomic Spectrometry, enables them to visualize multiple bio-metal elements more than 10 times faster than before, and to do so simultaneously with positron emission tomography (PET).

You can find the research study here.

For those unfamiliar with RIKEN, here’s more from their About RIKEN page,

RIKEN is Japan’s largest comprehensive research institution renowned for high-quality research in a diverse range of scientific disciplines. Founded in 1917 as a private research foundation in Tokyo, RIKEN has grown rapidly in size and scope, today encompassing a network of world-class research centers and institutes across Japan.

Making movies of biomolecules

’tis the season for recycling news; this research about making biomolecular movies was published in Nature Protocols in June 2012 according to the Jan. 4, 2013 news item on phys.org (Note: Links have been removed),

Toshio Ando and co-workers at Kanazawa University [Japan] have developed and used HS-AFM [high-speed atomic force microscopy] to increase our understanding of several protein systems through microscopic movies of unprecedented spatial and temporal resolution. The team have now published a guide to video recording these important cell components, so that other researchers can benefit from this unique technology.

To produce an image, HS-AFM acquires information on sample height at many points by tapping the sample with the sharp tip of a tiny cantilever. Depending on the application, this might involve recording the amplitude and phase of oscillations, or the resonant frequency of the cantilever.

Ando and co-workers use very small cantilevers that afford 10 to 20 times the sensitivity of larger, conventional cantilevers. Copies of their home-made apparatus are now commercially available through the manufacturer Research Institute of Biomolecule Metrology Co., Ltd. (RIBM) in Tsukuba, and record images at least ten times more quickly than their competitors.

There are more details in the news item or for those who want to read the guide, here’s a citation and a link,

Guide to video recording of structure dynamics and dynamic processes of proteins by high-speed atomic force microscopy by Takayuki Uchihashi, Noriyuki Kodera, & Toshio Ando in Nature Protocols 7 (6), 1193–1206 (2012) doi:10.1038/nprot.2012.047

This article is behind a paywall.

Lastly, should anyone wish to purchase the apparatus developed at Kanazawa University from the Research Institute of Biomolecule Metrology Co., Ltd., here’s more about it from the company’s home page,

Dynamic Visualization of nano-scale world

HS-AFM*1.0 – Ando model – is the High-Speed Atomic Force Microscope which was developed based on the research achievements accomplished by Prof. Ando in Kanazawa University. This is the world’s first instrument that broke through the weak point of conventional AFM “low-speed”, and realized the video rate scan. The high-speed scan enables us to capture swinging molecules in solution clearly without blurring. Consequently, the strong anchoring of a sample to the substrate is unnecessary and a dynamic observation is achieved without losing the activities of soft biomolecules.

Protein cages, viruses, and nanoparticles

The Dec. 19, 2012 news release on EurekAlert about a study published by researchers at Aalto University (Finland) describes a project where virus particles are combined with nanoparticles to create new metamaterials,

Scientists from Aalto University, Finland, have succeeded in organising virus particles, protein cages and nanoparticles into crystalline materials. These nanomaterials studied by the Finnish research group are important for applications in sensing, optics, electronics and drug delivery.

… biohybrid superlattices of nanoparticles and proteins would allow the best features of both particle types to be combined. They would comprise the versatility of synthetic nanoparticles and the highly controlled assembly properties of biomolecules.

The gold nanoparticles and viruses adopt a special kind of crystal structure. It does not correspond to any known atomic or molecular crystal structure and it has previously not been observed with nano-sized particles.

Virus particles – the old foes of mankind – can do much more than infect living organisms. Evolution has rendered them with the capability of highly controlled self-assembly properties. Ultimately, by utilising their building blocks we can bring multiple functions to hybrid materials that consist of both living and synthetic matter, Kostiainen [Mauri A. Kostiainen, postdoctoral researcher] trusts.

The article which has been published in Nature Nanotechnology is free,

Electrostatic assembly of binary nanoparticle superlattices using protein cages by Mauri A. Kostiainen, Panu Hiekkataipale, Ari Laiho, Vincent Lemieux, Jani Seitsonen, Janne Ruokolainen & Pierpaolo Ceci in Nature Nanotechnology (2012) doi:10.1038/nnano.2012.220  Published online 16 December 2012

There’s a video demonstrating the assembly,

From the YouTube page, here’s a description of what the video is demonstrating,

Aalto University-led research group shows that CCMV virus or ferritin protein cages can be used to guide the assembly of RNA molecules or iron oxide nanoparticles into three-dimensional binary superlattices. The lattices are formed through tuneable electrostatic interactions with charged gold nanoparticles.

Bravo and thank  you to  Kostiainen who seems to have written the news release and prepared all of the additional materials (image and video). There are university press offices that could take lessons from Kostiainen’s efforts to communicate about the work.