Computer scientists create reprogrammable molecular computing system – “Nano DNA Apps”


 

“Biology is proof that chemistry is inherently information-based and can store information that can direct algorithmic behavior at the molecular level,” he says.

Computer scientists at Caltech have designed DNA molecules that can carry out reprogrammable computations, for the first time creating so-called algorithmic self-assembly in which the same “hardware” can be configured to run different “software.”

In a paper published in Nature on March 21, a team headed by Caltech’s Erik Winfree (PhD ’98), professor of computer science, computation and neural systems, and bioengineering, showed how the DNA computations could execute six-bit algorithms that perform simple tasks. The system is analogous to a computer, but instead of using transistors and diodes, it uses molecules to represent a six-bit binary number (for example, 011001) as input, during computation, and as output. One such algorithm determines whether the number of 1-bits in the input is odd or even, (the example above would be odd, since it has three 1-bits); while another determines whether the input is a palindrome; and yet another generates random numbers.

 

“Think of them as nano apps,” says Damien Woods, professor of computer science at Maynooth University near Dublin, Ireland, and one of two lead authors of the study. “The ability to run any type of software program without having to change the hardware is what allowed computers to become so useful. We are implementing that idea in molecules, essentially embedding an algorithm within chemistry to control chemical processes.”

The system works by self-assembly: small, specially designed DNA strands stick together to build a logic circuit while simultaneously executing the circuit algorithm. Starting with the original six bits that represent the input, the system adds row after row of molecules–progressively running the algorithm.

 

Modern digital electronic computers use electricity flowing through circuits to manipulate information; here, the rows of DNA strands sticking together perform the computation. The end result is a test tube filled with billions of completed algorithms, each one resembling a knitted scarf of DNA, representing a readout of the computation. The pattern on each “scarf” gives you the solution to the algorithm that you were running. The system can be reprogrammed to run a different algorithm by simply selecting a different subset of strands from the roughly 700 that constitute the system.

 

“We were surprised by the versatility of programs we were able to design, despite being limited to six-bit inputs,” says David Doty, fellow lead author and assistant professor of computer science at the University of California, Davis.

“When we began experiments, we had only designed three programs. But once we started using the system, we realized just how much potential it has. It was the same excitement we felt the first time we programmed a computer, and we became intensely curious about what else these strands could do. By the end, we had designed and run a total of 21 circuits.”

 

The researchers were able to experimentally demonstrate six-bit molecular algorithms for a diverse set of tasks. In mathematics, their circuits tested inputs to assess if they were multiples of three, performed equality checks, and counted to 63. Other circuits drew “pictures” on the DNA “scarves,” such as a zigzag, a double helix, and irregularly spaced diamonds.

Probabilistic behaviors were also demonstrated, including random walks, as well as a clever algorithm (originally developed by computer pioneer John von Neumann) for obtaining a fair 50/50 random choice from a biased coin.

 

Both Woods and Doty were theoretical computer scientists when beginning this research, so they had to learn a new set of “wet lab” skills that are typically more in the wheelhouse of bioengineers and biophysicists.

“When engineering requires crossing disciplines, there is a significant barrier to entry,” says Winfree. “Computer engineering overcame this barrier by designing machines that are reprogrammable at a high level–so today’s programmers don’t need to know transistor physics. Our goal in this work was to show that molecular systems similarly can be programmed at a high level, so that in the future, tomorrow’s molecular programmers can unleash their creativity without having to master multiple disciplines.”

“Unlike previous experiments on molecules specially designed to execute a single computation, reprogramming our system to solve these different problems was as simple as choosing different test tubes to mix together,” Woods says. “We were programming at the lab bench.”

Although DNA computers have the potential to perform more complex computations than the ones featured in the Nature paper, Winfree cautions that one should not expect them to start replacing the standard silicon microchip computers. That is not the point of this research.

“These are rudimentary computations, but they have the power to teach us more about how simple molecular processes like self-assembly can encode information and carry out algorithms. Biology is proof that chemistry is inherently information-based and can store information that can direct algorithmic behavior at the molecular level,” he says.

 

Diverse and robust molecular algorithms using reprogrammable DNA self-assembly

Damien Woods, David Doty, Cameron Myhrvold, Joy Hui, Felix Zhou, Peng Yin & Erik Winfree
Naturevolume 567, pages366–372 (2019)

 

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NEW NANOTECH DRIVES HEALING BY “TALKING” TO WOUNDS


A Time To Heal

Researchers from Imperial College London have created a new molecule that can “talk” to the cells in the area near injured tissues to encourage wound healing.

“This intelligent healing is useful during every phase of the healing process, has the potential to increase the body’s chance to recover, and has far-reaching uses on many different types of wounds,” lead researcher Ben Almquist said in a news release.

Setting A TrAP

The Imperial team describes the wound-healing molecules, which it calls traction force-activated payloads (TrAPs), in a study published Monday in the journal Advanced Materials.

The first step to creating TrAPs was folding segments of DNA into aptamers, which are three-dimensional shapes that latch tightly to proteins. The researchers then added a “handle” to one end of the aptamer.

As cells navigated the area near a wound during lab testing, they would pull on this handle, causing the aptamer to open and release proteins that encouraged wound healing. By changing the handle, the researchers found they could control which cells activated the TrAPs.

According to Almquist, “TrAPs provide a flexible method of actively communicating with wounds, as well as key instructions when and where they are needed.”

To The Clinic

It can take a long time for research to move from the laboratory to the clinical trial stage, but the TrAPs team might be able to speed along the path. That’s because aptamers are already used for drug delivery, meaning they’re already considered safe for human use.

TrAPs are also fairly straightforward to create, meaning it wouldn’t be difficult to scale the technology to industrial levels. According to the researchers’ paper, doctors could then deliver the TrAPs via anything from collagen sponges to polyacrylamide gels. So if future testing goes well, the molecules could soon change how we heal a variety of wounds.

READ MORE: New Material Could ‘Drive Wound Healing’ Using the Body’s Inbuilt Healing System [Imperial College London]

More on aptamers: New Nanobots Kill Cancerous Tumors by Cutting off Their Blood Supply

Story Source:

Materials provided by Imperial College London. Original written by Caroline Brogan. Note: Content may be edited for style and length.


Journal Reference:

  1. Anna Stejskalová, Nuria Oliva, Frances J. England, Benjamin D. Almquist. Biologically Inspired, Cell‐Selective Release of Aptamer‐Trapped Growth Factors by Traction Forces. Advanced Materials, 2018 DOI: 10.1002/adma.201806380

Synthetic organisms are about to challenge what ’being’ and ‘alive’ really means


We need to begin a serious debate about whether artificially evolved humans are our future, and if we should put an end to these experiments before it is too late.

In 2016, Craig Venter and his team at Synthetic Genomics announced that they had created a lifeform called JCVI-syn3.0, whose genome consisted of only 473 genes.

This stripped-down organism was a significant breakthrough in the development of artificial life as it enabled us to understand more fully what individual genes do. (In the case of JCVI-syn3.0, most of them were used to create RNA and proteins, preserve genetic fidelity during reproduction and create the cell membrane.

The functions of about a third remain a mystery.)

Venter’s achievement followed an earlier breakthrough in 2014, when Floyd Romesberg at Romesberg Lab in California succeeded in creating xeno nucleic acid (XNA), a synthetic alternative to DNA, using amino acids not found among the naturally occurring four nucleotides: adenine, cytosine, guanine and thymine. 

And, most recently we have seen huge advances in the use of CRISPR, a gene-editing tool that allows substitution or injection of DNA sequences at chosen locations in a genome.

Read More: Why Bill Gates is Betting on this Synthetic Biology Start-Up

Together, these developments mean that in 2019 we will have to take seriously the possibility of our developing multicellular artificial life, and we will need to start thinking about the ethical and philosophical challenges such a possibility brings up.

In the near future we can reasonably anticipate that a large number of unnatural single-cell life forms will be created using artificially edited genomes to correct for genetic defects or to add new features to an organism’s phenotype.

It is already possible to design bacterial forms, for example, that can metabolise pollutants or produce particular substances.

We can also anticipate that new life forms may be created that have never existed in nature through the use of conventional and perhaps artificially arranged codons (nucleotide sequences that manage protein synthesis).

These are likely to make use of the conventional machinery of mitotic cell reproduction and of conventional ribosomes, creating proteins through RNA or XNA interpretation.

And there will be increasing pressures to continue this research. We may need to accelerate the evolution of terrestrial life forms, for example, including homo sapiens, so that they carry traits and capabilities needed for life in space or even on our own changing planet. 

All of this will bring up serious issues as to how we see ourselves – and behave – as a species.

While the creation of multicellular organisms that are capable of sexual reproduction is still a long way off, in 2019 we will need to begin a serious debate about whether artificially evolved humans are our future, and if we should put an end to these experiments before it is too late.

 Vint Cerf of ‘Wired’

MIT Team invents method to shrink objects to the nanoscale – “Implosion Manufacturing” – Applications from Optics to Medicine to Robotics – Materials from Quantum Dots, Metals and DNA


MIT Implosion mfg mitteaminvenAccording to professor Ed Boyden, many research labs are already stocked with the equipment required for this kind of fabrication. Credit: The researchers

” … These tiny structures could have applications in many fields, from optics to medicine to robotics, the researchers say.”

MIT researchers have invented a way to fabricate nanoscale 3-D objects of nearly any shape. They can also pattern the objects with a variety of useful materials, including metals, quantum dots, and DNA.

“It’s a way of putting nearly any kind of material into a 3-D pattern with nanoscale precision,” says Edward Boyden, an associate professor of biological engineering and of brain and cognitive sciences at MIT.

Using the , the researchers can create any shape and structure they want by patterning a  with a laser. After attaching other useful materials to the scaffold, they shrink it, generating structures one thousandth the volume of the original.

These tiny structures could have applications in many fields, from optics to medicine to robotics, the researchers say. The technique uses equipment that many biology and materials science labs already have, making it widely accessible for researchers who want to try it.

Boyden, who is also a member of MIT’s Media Lab, McGovern Institute for Brain Research, and Koch Institute for Integrative Cancer Research, is one of the senior authors of the paper, which appears in the Dec. 13 issue of Science. The other senior author is Adam Marblestone, a Media Lab research affiliate, and the paper’s lead authors are graduate students Daniel Oran and Samuel Rodriques.

MIT-Implosion-Fabrication-01Implosion fabrication

Existing techniques for creating nanostructures are limited in what they can accomplish. Etching patterns onto a surface with light can produce 2-D nanostructures but doesn’t work for 3-D structures. It is possible to make 3-D nanostructures by gradually adding layers on top of each other, but this process is slow and challenging. And, while methods exist that can directly 3-D print nanoscale objects, they are restricted to specialized materials like polymers and plastics, which lack the functional properties necessary for many applications. Furthermore, they can only generate self-supporting structures. (The technique can yield a solid pyramid, for example, but not a linked chain or a hollow sphere.)

To overcome these limitations, Boyden and his students decided to adapt a technique that his lab developed a few years ago for high-resolution imaging of brain tissue. This technique, known as expansion microscopy, involves embedding tissue into a hydrogel and then expanding it, allowing for high resolution imaging with a regular microscope. Hundreds of research groups in biology and medicine are now using expansion microscopy, since it enables 3-D visualization of cells and tissues with ordinary hardware.

By reversing this process, the researchers found that they could create large-scale objects embedded in expanded hydrogels and then shrink them to the nanoscale, an approach that they call “implosion fabrication.”

As they did for , the researchers used a very absorbent material made of polyacrylate, commonly found in diapers, as the scaffold for their nanofabrication process. The scaffold is bathed in a solution that contains molecules of fluorescein, which attach to the scaffold when they are activated by laser light.

Using two-photon microscopy, which allows for precise targeting of points deep within a structure, the researchers attach fluorescein molecules to specific locations within the gel. The fluorescein molecules act as anchors that can bind to other types of molecules that the researchers add.

“You attach the anchors where you want with light, and later you can attach whatever you want to the anchors,” Boyden says. “It could be a quantum dot, it could be a piece of DNA, it could be a gold nanoparticle.”

“It’s a bit like film photography—a latent image is formed by exposing a sensitive material in a gel to light. Then, you can develop that latent image into a real image by attaching another material, silver, afterwards. In this way implosion fabrication can create all sorts of structures, including gradients, unconnected structures, and multi-material patterns,” Oran says.

Once the desired molecules are attached in the right locations, the researchers shrink the entire structure by adding an acid. The acid blocks the negative charges in the polyacrylate gel so that they no longer repel each other, causing the gel to contract. Using this technique, the researchers can shrink the objects 10-fold in each dimension (for an overall 1,000-fold reduction in volume). This ability to shrink not only allows for increased resolution, but also makes it possible to assemble materials in a low-density scaffold. This enables easy access for modification, and later the material becomes a dense solid when it is shrunk.

“People have been trying to invent better equipment to make smaller nanomaterials for years, but we realized that if you just use existing systems and embed your  in this gel, you can shrink them down to the nanoscale, without distorting the patterns,” Rodriques says.

Currently, the researchers can create objects that are around 1 cubic millimeter, patterned with a resolution of 50 nanometers. There is a tradeoff between size and resolution: If the researchers want to make larger objects, about 1 cubic centimeter, they can achieve a resolution of about 500 nanometers. However, that resolution could be improved with further refinement of the process, the researchers say.

Better optics

The MIT team is now exploring potential applications for this technology, and they anticipate that some of the earliest applications might be in optics—for example, making specialized lenses that could be used to study the fundamental properties of light. This technique might also allow for the fabrication of smaller, better lenses for applications such as cell phone cameras, microscopes, or endoscopes, the researchers say. Farther in the future, the researchers say that this approach could be used to build nanoscale electronics or robots.

“There are all kinds of things you can do with this,” Boyden says. “Democratizing nanofabrication could open up frontiers we can’t yet imagine.”

Many research labs are already stocked with the equipment required for this kind of fabrication. “With a laser you can already find in many biology labs, you can scan a pattern, then deposit metals, semiconductors, or DNA, and then shrink it down,” Boyden says.

 Explore further: High-resolution imaging with conventional microscopes

More information: D. Oran el al., “3D nanofabrication by volumetric deposition and controlled shrinkage of patterned scaffolds,” Science (2018). science.sciencemag.org/cgi/doi … 1126/science.aau5119

T.E. Long el al., “Printing nanomaterials in shrinking gels,” Science (2018). science.sciencemag.org/cgi/doi … 1126/science.aav5712

 

‘Swiss army knife’ Nanovaccine carries multiple weapons to battle tumors – cancer


Swiss Army Knife of Nano Ps 171129163851_1_540x360
Source: National Institute of Biomedical Imaging and Bioengineering
Summary: Researchers have developed a synergistic cancer nanovaccine packing DNA and RNA sequences that modulate the immune response, along with anti-tumor antigens, into one small nanoparticle.
(Above) Large particles (left) containing the DNA and RNA components are coated with electronically charged molecules that shrink the particle. The tumor-specific neoantigen is then complexed with the surface to complete construction of the nanovaccine. Upper left: electron micrograph of large particle. Credit: Zhu, et al. Nat Comm.

 

 

Scientists are using their increasing knowledge of the complex interaction between cancer and the immune system to engineer increasingly potent anti-cancer vaccines. The nanovaccine produced an immune response that specifically killed tumor tissue, while simultaneously inhibiting tumor-induced immune suppression to block lung tumor growth in a mouse model of metastatic colon cancer.

Now researchers at the National Institute of Biomedical Imaging and Bioengineering (NIBIB) have developed a synergistic nanovaccine packing DNA and RNA sequences that modulate the immune response, along with anti-tumor antigens, into one small nanoparticle. The nanovaccine produced an immune response that specifically killed tumor tissue, while simultaneously inhibiting tumor-induced immune suppression. Together this blocked lung tumor growth in a mouse model of metastatic colon cancer.

The molecular dance between cancer and the immune system is a complex one and scientists continue to identify the specific molecular pathways that rev up or tamp down the immune system. Biomedical engineers are using this knowledge to create nanoparticles that can carry different molecular agents that target these pathways. The goal is to simultaneously stimulate the immune system to specifically attack the tumor while also inhibiting the suppression of the immune system, which often occurs in cancer patients. The aim is to press on the gas pedal of the immune system while also releasing the emergency brake.

A key hurdle is to design a system to reproducibly and efficiently create a nanoparticle loaded with multiple agents that synergize to mount an enhanced immune attack on the tumor. Engineers at the NIBIB report the development and testing of such a nanovaccine in the November issue of Nature Communications.

Making all the parts fit

Guizhi Zhu, Ph.D., a post-doctoral fellow in the NIBIB Laboratory of Molecular Imaging and Nanomedicine (LOMIN) and lead author on the study, explains the challenge. “We are very excited about putting multiple cooperating molecules that have anti-cancer activity into one nanovaccine to increase effectiveness. However, the bioengineering challenge is fitting everything in to a small particle and designing a way to maintain its structural integrity and biological activity.”

Zhu and his colleagues have created what they call a “self-assembling, intertwining DNA-RNA nanocapsule loaded with tumor neoantigens.” They describe it as a synergistic vaccine because the components work together to stimulate and enhance an immune attack against a tumor.

The DNA component of the vaccine is known to stimulate immune cells to work with partner immune cells for antitumor activation. The tumor neoantigens are pieces of proteins that are only present in the tumor; so, when the DNA attracts the immune cells, the immune cells interact with the tumor neoantigens and mount an expanded and specific immune response against the tumor. The RNA is the component that inhibits suppression of the immune system. The engineered RNA binds to and degrades the tumor’s mRNA that makes a protein called STAT3. Thus, the bound mRNA is blocked from making STAT3, which may suppress the immune system. The result is an enhanced immune response that is specific to the tumor and does not harm healthy tissues.

In addition to engineering a system where the DNA, RNA and tumor neoantigens self-assemble into a stable nanoparticle, an important final step in the process is shrinking the particle. Zhu explains: “Shrinking the particle is a critical step for activating an immune response. This is because a very small nanoparticle can more readily move through the lymphatic vessels to reach the parts of the immune system such as lymph nodes. A process that is essential for immune activation.”

The method for shrinking also had to be engineered. This was achieved by coating the particle with a positively charged polypeptide that interacts with the negatively charged DNA and RNA components to condense it to one-tenth of its original size.

Testing the nanovaccine

To create a model of metastatic colon cancer, the researchers injected human colon cancer cells into the circulation of mice. The cells infiltrate different organs and grow as metastatic colon cancer. One of the prime sites of metastasis is the lung.

The nanovaccine was injected under the skin of the mice 10, 16, and 22 days after the colon cancer cells were injected. To compare to the nanovaccine, two control groups of mice were analyzed; one group was injected with just the DNA and the neoantigen in solution but not formed into a nanovaccine particle, and the second control group was injected with an inert buffer solution.

At 40 days into the experiment, lung tumors from the nanovaccine-treated and the control groups were assessed by PET-CT imaging, and then removed and weighed. In mice treated with the nanovaccine, tumors were consistently one tenth the size of the tumors that were found in mice in both control groups.

Further testing revealed that mice receiving the nanovaccine had a significant increase in circulating cytotoxic T lymphocytes (CTLs) that specifically targeted the neoantigen on the colon cancer cells. CTLs are cells that attack and kill virus-infected cells and those damaged in other ways, such as cancerous cells.

An important aspect of the nanovaccine approach is that it mounts an anti-tumor immune response that circulates through the system, and therefore is particularly valuable for finding and inhibiting metastatic tumors growing throughout the body.

The researchers view their nanovaccine as an important part of eventual therapies combining immunotherapy with other cancer killing approaches.

Story Source:

Materials provided by National Institute of Biomedical Imaging and BioengineeringNote: Content may be edited for style and length.


Journal Reference:

  1. Guizhi Zhu, Lei Mei, Harshad D. Vishwasrao, Orit Jacobson, Zhantong Wang, Yijing Liu, Bryant C. Yung, Xiao Fu, Albert Jin, Gang Niu, Qin Wang, Fuwu Zhang, Hari Shroff, Xiaoyuan Chen. Intertwining DNA-RNA nanocapsules loaded with tumor neoantigens as synergistic nanovaccines for cancer immunotherapyNature Communications, 2017; 8 (1) DOI: 10.1038/s41467-017-01386-7

DNA and Nanotechnology: Protein ‘Rebar’ could help make Error-Free Nanostructures: NIST


DNA proteinrebarThe protein RecA (purple units), wraps around and fortifies double-stranded DNA, enabling scientists to build large structures with the genetic material. Credit: NIST

DNA is the stuff of life, but it is also the stuff of nanotechnology. Because molecules of DNA with complementary chemical structures recognize and bind to one another, strands of DNA can fit together like Lego blocks to make nanoscale objects of complex shape and structure.

But researchers need to work with much larger assemblages of DNA to realize a key goal: building durable miniature devices such as biosensors and drug-delivery containers. That’s been difficult because long chains of DNA are floppy and the standard method of assembling long chains is prone to error.

Using a DNA-binding protein called RecA as a kind of nanoscale rebar, or reinforcing bar, to support the floppy DNA scaffolding, researchers at the National Institute of Standards and Technology (NIST) have constructed several of the largest rectangular, linear and other shapes ever assembled from DNA. The structures can be two to three times larger than those built using standard DNA self-assembly techniques.

In addition, because the new method requires fewer chemically distinct pieces to build organized structures than the standard technique, known as DNA origami, it is likely to reduce the number of errors in constructing the shapes. That’s a big plus for the effort to produce reliable DNA-based devices in large quantities, said NIST researcher Alex Liddle.

Although RecA’s ability to bind to double-stranded DNA has been known for years, the NIST team is the first to integrate filaments of this protein into the assembly of DNA structures. The addition of RecA offers a particular advantage: Once one unit of the protein binds to a small segment of double-stranded DNA, it automatically attracts other units to line up alongside it, in the same way that bar magnets will join end-to-end. Like bricks filling out a foundation, RecA lines the entire length of the DNA strand, stretching, widening and strengthening it. A floppy, 2-nanometer-wide strand of DNA can transform into a rigid structure more than four times as wide.

“The RecA method greatly extends the ability of DNA self-assembly methods to build larger and more sophisticated structures,” said NIST’s Daniel Schiffels.

Schiffels, Liddle and their colleague Veronika Szalai describe their work in a recent article in ACS Nano.

The new method incorporates the DNA origami technique and goes beyond it, according to Liddle. In DNA origami, short strands of DNA that have a specific sequence of four base pairs are used as staples to tie together long sections of DNA. To make the skinny DNA skeleton stronger and thicker, the strand may loop back on itself, quickly using up the long string.

If DNA origami is all about the folding, Liddle likened his team’s new method to building a room, starting with a floor plan. The location of the short, single-stranded pieces of DNA that act as staples mark the corners of the room. Between the corners lies a long, skinny piece of single-stranded DNA. The enzyme DNA polymerase transforms a section of the long piece of single-stranded DNA into the double-stranded version of the molecule, a necessary step because RecA only binds strongly to double-stranded DNA. Then RecA assembles all along the double strand, reinforcing the DNA  and limiting the need for extra staples to maintain its shape.

With fewer staples required, the RecA  is likely able to build organized structures with fewer errors than DNA origami, Liddle said.

 Explore further: The promise of nanomanufacturing using DNA origami

More information: Daniel Schiffels et al. Molecular Precision at Micrometer Length Scales: Hierarchical Assembly of DNA–Protein Nanostructures, ACS Nano (2017). DOI: 10.1021/acsnano.7b00320

 

Arizona State University ~ ‘Living Computers’ from RNA for Nanotechnology


RNA Nano 2 bd1d43755f5067d16cb5985bd7de8ea1a3a38212

Researchers from Arizona State University have demonstrated that living cells can be induced to carry out complex computations in the manner of tiny robots or computers.

It’s an example of engineers and biologists coming together to create an innovative solution to the performing of calculations. The implications are a potential game-changer for intelligent drug design and smart drug delivery. Other fields that could be affected include green energy production, low-cost diagnostic technologies and the development of futuristic nanomachines to be used in gene-editing. ASU xximage_1.png.pagespeed.ic.dPihifYIDEThe basis of the new technology is the natural interactions between nucleic acid; in this case the predictable and programmable RNA-RNA interactions. RNA is ribonucleic acid, an important molecule with long chains of nucleotides.
A nucleotide contains a nitrogenous base, a ribose sugar, and a phosphate. RNA is involved with the coding, decoding, regulation, and expression of genes. This builds on earlier work where DNA and RNA, the molecules of life, where demonstrated as being able to perform computer-like computations by Leonard Adleman (University of Southern California) in 1994 (“Molecular Computation of Solutions To Combinatorial Problems.”)
Atomic structure of the 50S Large Subunit of the Ribosome. Proteins are colored in blue and RNA in o...

Atomic structure of the 50S Large Subunit of the Ribosome. Proteins are colored in blue and RNA in orange. RNA is central to the synthesis of proteins. Wikipedia / Vossman
From this basis, lead researcher Professor Alex Green has used computer software to design RNA sequences that behave the way researchers want them to in a cell. This makes the design process a much faster.RNA Nano 3 RNAThe output is circuit designs, which look like conventional electronic circuits, but which self-assemble inside bacterial cells. This allows the cells to sense incoming messages and respond to them by producing a computational output. To test this out, the researchers worked with specialized circuits called logic gates. The tiny circuit switches were tripped when messages (RNA fragments) which attached themselves to their complementary RNA sequences in the cellular circuit. This activated the logic gate and produced an output. A series of more complex logic gates were then designed, to respond to multiple inputs. Here logic gates known as AND, OR and NOT were designed.
The video below explains more about these switches:

From this the scientists developed the first ribocomputing devices capable of four-input AND, six-input OR and a 12-input device able to carry out a complex combination of AND, OR and NOT logic known as disjunctive normal form expression.The great strength of the new method is with its ability to perform many operations at the same time. This capacity for parallel processing allows for faster and more sophisticated computation.The example, of meshing engineering and biology together, is part of an emerging field called synthetic biology, and it is one of the fastest growing areas of scientific research. In a sense, synthetic biology is a biology-based “toolkit”. According to the European research group ERBC the science deploys abstraction, standardization, and automated construction to change how we build biological systems and expand the range of possible products. One such example of what a highly accurate platform like this could do is with diagnosing viruses the Zika virus.The research has been published in the journalNature under the title “Complex cellular logic computation using ribocomputing devices.”

 

Laser activated gold pyramids could deliver drugs, DNA into cells without harm


Harvard DNA Delivery 170323150417_1_540x360

Summary: The ability to deliver cargo like drugs or DNA into cells is essential for biological research and disease therapy but cell membranes are very good at defending their territory. Researchers have developed various methods to trick or force open the cell membrane but these methods are limited in the type of cargo they can deliver and aren’t particularly efficient. Harvard School of Engineering and Applied Sciences 

The ability to deliver cargo like drugs or DNA into cells is essential for biological research and disease therapy but cell membranes are very good at defending their territory. Researchers have developed various methods to trick or force open the cell membrane but these methods are limited in the type of cargo they can deliver and aren’t particularly efficient.

Now, researchers from the Harvard John A. Paulson School of Engineering and Applied Sciences (SEAS) have developed a new method using gold microstructures to deliver a variety of molecules into cells with high efficiency and no lasting damage. The research is published in ACS Nano.

“Being able to effectively deliver large and diverse cargos directly into cells will transform biomedical research,” said Nabiha Saklayen, a PhD candidate in the Mazur Lab at SEAS and first author of the paper. “However, no current single delivery system can do all the things you need to do at once. Intracellular delivery systems need to be highly efficient, scalable, and cost effective while at the same time able to carry diverse cargo and deliver it to specific cells on a surface without damage. It’s a really big challenge.”

In previous research, Saklayen and her collaborators demonstrated that gold, pyramid-shaped microstructures are very good at focusing laser energy into electromagnetic hotspots. In this research, the team used a fabrication method called template stripping to make surfaces — about the size of a quarter — with 10 million of these tiny pyramids.

“The beautiful thing about this fabrication process is how simple it is,” said Marinna Madrid, coauthor of the paper and PhD candidate in the Mazur Lab. “Template-stripping allows you to reuse silicon templates indefinitely. It takes less than a minute to make each substrate, and each substrate comes out perfectly uniform. That doesn’t happen very often in nanofabrication.”

Harvard DNA Delivery 170323150417_1_540x360
A scanning-electron microscope image of chemically-fixed HeLa cancer cells on the substrate. The tips of the pyramids create tiny holes in the cell membranes, allowing molecular cargo to diffuse into the cells. Credit: Harvard SEAS

The team cultured HeLa cancer cells directly on top of the pyramids and surrounded the cells with a solution containing molecular cargo.

Using nanosecond laser pulses, the team heated the pyramids until the hotspots at the tips reached a temperature of about 300 degrees Celsius. This very localized heating — which did not affect the cells — caused bubbles to form right at the tip of each pyramid. These bubbles gently pushed their way into the cell membrane, opening brief pores in the cell and allowing the surrounding molecules to diffuse into the cell.

“We found that if we made these pores very quickly, the cells would heal themselves and we could keep them alive, healthy and dividing for many days,” Saklayen said.

Each HeLa cancer cell sat atop about 50 pyramids, meaning the researchers could make about 50 tiny pores in each cell. The team could control the size of the bubbles by controlling the laser parameters and could control which side of the cell to penetrate.

The molecules delivered into the cell were about the same size as clinically relevant cargos, including proteins and antibodies.

Next, the team plans on testing the methods on different cell types, including blood cells, stem cells and T cells. Clinically, this method could be used in ex vivo therapies, where unhealthy cells are taken out of the body, given cargo like drugs or DNA, and reintroduced into the body.

“This work is really exciting because there are so many different parameters we could optimize to allow this method to work across many different cell types and cargos,” said Saklayen. “It’s a very versatile platform.”

Harvard’s Office of Technology Development has filed patent applications and is considering commercialization opportunities.

“It’s great to see how the tools of physics can greatly advance other fields, especially when it may enable new therapies for previously difficult to treat diseases,” said Eric Mazur, the Balkanski Professor of Physics and Applied Physics and senior author of the paper.

This research was supported by the National Science Foundation and the Howard Hughes Medical Institute. It was coauthored by Marinus Huber, Marinna Madrid, Valeria Nuzzo, Daryl Inna Vulis, Weilu Shen, Jeffery Nelson, Arthur McClelland and Alexander Heisterkamp.


Story Source:

Materials provided by Harvard School of Engineering and Applied Sciences. Note: Content may be edited for style and length.


Journal Reference:

  1. Nabiha Saklayen, Marinus Huber, Marinna Madrid, Valeria Nuzzo, Daryl I. Vulis, Weilu Shen, Jeffery Nelson, Arthur A. McClelland, Alexander Heisterkamp, Eric Mazur. Intracellular Delivery Using Nanosecond-Laser Excitation of Large-Area Plasmonic Substrates. ACS Nano, 2017; DOI: 10.1021/acsnano.6b08162

Switched-on DNA: Sparking nano-electronic applications


DNA, the stuff of life, may very well also pack quite the jolt for engineers trying to advance the development of tiny, low-cost electronic devices. Credit: ASU

Switched-on DNA

DNA, the stuff of life, may very well also pack quite the jolt for engineers trying to advance the development of tiny, low-cost electronic devices.

Much like flipping your light switch at home—-only on a scale 1,000 times smaller than a human hair—-an ASU-led team has now developed the first controllable DNA switch to regulate the flow of electricity within a single, atomic-sized molecule. 

The new study, led by ASU Biodesign Institute researcher Nongjian Tao, was published in the advanced online journal Nature Communications.

“It has been established that charge transport is possible in DNA, but for a useful device, one wants to be able to turn the charge transport on and off. We achieved this goal by chemically modifying DNA,” said Tao, who directs the Biodesign Center for Bioelectronics and Biosensors and is a professor in the Fulton Schools of Engineering. 

“Not only that, but we can also adapt the modified DNA as a probe to measure reactions at the single-molecule level. This provides a unique way for studying important reactions implicated in disease, or photosynthesis reactions for novel renewable energy applications.”

Engineers often think of electricity like water, and the research team’s new DNA switch acts to control the flow of electrons on and off, just like water coming out of a faucet.

Previously, Tao’s research group had made several discoveries to understand and manipulate DNA to more finely tune the flow of electricity through it. They found they could make DNA behave in different ways—and could cajole electrons to flow like waves according to quantum mechanics, or “hop” like rabbits in the way electricity in a copper wire works —creating an exciting new avenue for DNA-based, nano-electronic applications.

Tao assembled a multidisciplinary team for the project, including ASU postdoctoral student Limin Xiang and Li Yueqi performing bench experiments, Julio Palma working on the theoretical framework, with further help and oversight from collaborators Vladimiro Mujica (ASU) and Mark Ratner (Northwestern University).

Tao’s group, modified just one of DNA’s iconic double helix chemical letters, abbreviated as A, C, T or G, with another chemical group, called anthraquinone (Aq). Anthraquinone is a three-ringed carbon structure that can be inserted in …more




To accomplish their engineering feat, Tao’s group, modified just one of DNA’s iconic double helix chemical letters, abbreviated as A, C, T or G, with another chemical group, called anthraquinone (Aq). Anthraquinone is a three-ringed carbon structure that can be inserted in between DNA base pairs but contains what chemists call a redox group (short for reduction, or gaining electrons or oxidation, losing electrons).
 

These chemical groups are also the foundation for how our bodies’ convert chemical energy through switches that send all of the electrical pulses in our brains, our hearts and communicate signals within every cell that may be implicated in the most prevalent diseases.

The modified Aq-DNA helix could now help it perform the switch, slipping comfortably in between the rungs that make up the ladder of the DNA helix, and bestowing it with a new found ability to reversibly gain or lose electrons.

Through their studies, when they sandwiched the DNA between a pair of electrodes, they careful controlled their electrical field and measured the ability of the modified DNA to conduct electricity. This was performed using a staple of nano-electronics, a scanning tunneling microscope, which acts like the tip of an electrode to complete a connection, being repeatedly pulled in and out of contact with the DNA molecules in the solution like a finger touching a water droplet.

“We found the electron transport mechanism in the present anthraquinone-DNA system favors electron “hopping” via anthraquinone and stacked DNA bases,” said Tao. In addition, they found they could reversibly control the conductance states to make the DNA switch on (high-conductance) or switch-off (low conductance). 

When anthraquinone has gained the most electrons (its most-reduced state), it is far more conductive, and the team finely mapped out a 3-D picture to account for how anthraquinone controlled the electrical state of the DNA.

For their next project, they hope to extend their studies to get one step closer toward making DNA nano-devices a reality.

“We are particularly excited that the engineered DNA provides a nice tool to examine redox reaction kinetics, and thermodynamics the single molecule level,” said Tao.

 Explore further: Scientists engineer tunable DNA for electronics applications

More information: Gate-controlled conductance switching in DNA, Nature Communications, DOI: 10.1038/ncomms14471 

Journal reference: Nature Communications  

Provided by: Arizona State University  

Silver nanoclusters inside synthetic DNA to create a programmed, tunable fluorescent array


Silver Nano DNA 0430 150423154807_1_540x360The silver used by Beth Gwinn’s research group at UC Santa Barbara has value far beyond its worth as a commodity, even though it’s used in very small amounts.

The group works with the precious metal to create nanoscale silver clusters with unique fluorescent properties. These properties are important for a variety of sensing applications including biomedical imaging.

The team’s latest research is published in a featured article in this month’s issue of ACS Nano, a journal of the American Chemical Society. The scientists positioned silver clusters at programmed sites on a nanoscale breadboard, a construction base for prototyping of photonics and electronics. “Our ‘breadboard’ is a DNA nanotube with spaces programmed 7 nanometers apart,” said lead author Stacy Copp, a graduate student in UCSB’s Department of Physics.

“Due to the strong interactions between DNA and metal atoms, it’s quite challenging to design DNA breadboards that keep their desired structure when these new interactions are introduced,” said Gwinn, a professor in UCSB’s Department of Physics. “Stacy’s work has shown that not only can the breadboard keep its shape when silver clusters are present, it can also position arrays of many hundreds of clusters containing identical numbers of silver atoms — a remarkable degree of control that is promising for realizing new types of nanoscale photonics.”

Silver Nano DNA 0430 150423154807_1_540x360

DNA nanotubes were decorated by silver clusters with DNA-programmed color.
Credit: UCSB

The results of this novel form of DNA nanotechnology address the difficulty of achieving uniform particle sizes and shapes. “In order to make photonic arrays using a self-assembly process, you have to be able to program the positions of the clusters you are putting on the array,” Copp explained. “This paper is the first demonstration of this for silver clusters.”

The colors of the clusters are largely determined by the DNA sequence that wraps around them and controls their size. To create a positionable silver cluster with DNA-programmed color, the researchers engineered a piece of DNA with two parts: one that wraps around the cluster and the other that attaches to the DNA nanotube. “Sticking out of the nanotube are short DNA strands that act as docking stations for the silver clusters’ host strands,” Copp explained.

The research group’s team of graduate and undergraduate researchers is able to tune the silver clusters to fluoresce in a wide range of colors, from blue-green all the way to the infrared — an important achievement because tissues have windows of high transparency in the infrared. According to Copp, biologists are always looking for better dye molecules or other infrared-emitting objects to use for imaging through a tissue.

“People are already using similar silver cluster technologies to sense mercury ions, small pieces of DNA that are important for human diseases, and a number of other biochemical molecules,” Copp said. “But there’s a lot more you can learn by putting the silver clusters on a breadboard instead of doing experiments in a test tube. You get more information if you can see an array of different molecules all at the same time.”

The modular design presented in this research means that its step-by-step process can be easily generalized to silver clusters of different sizes and to many types of DNA scaffolds. The paper walks readers through the process of creating the DNA that stabilizes silver clusters. This newly outlined protocol offers investigators a new degree of control and flexibility in the rapidly expanding field of nanophotonics.

The overarching theme of Copp’s research is to understand how DNA controls the size and shape of the silver clusters themselves and then figure out how to use the fact that these silver clusters are stabilized by DNA in order to build nanoscale arrays.

“It’s challenging because we don’t really understand the interactions between silver and DNA just by itself,” Copp said. “So part of what I’ve been doing is using big datasets to create a bank of working sequences that we’ve published so other scientists can use them. We want to give researchers tools to design these types of structures intelligently instead of just having to guess.”

The paper’s acknowledgements include a dedication to “those students who lost their lives in the Isla Vista tragedy and to the courage of the first responders, whose selfless actions saved many lives.”

– See more at: http://www.news.ucsb.edu/2015/015345/silver-lining#sthash.LyFLOWCO.dpuf


Story Source:

The above story is based on materials provided by University of California – Santa Barbara.