NanoComputer

Take a swab of saliva from your mouth and within minutes your DNA could be ready for analysis and genome sequencing with the help of a new device. Now University of Washington engineers and NanoFacture, a Bellevue, Wash., company, have created a device that can extract human DNA from fluid samples in a simpler, more efficient and environmentally friendly way than conventional methods. The device will give hospitals and research labs a much easier way to separate DNA from human fluid samples, which will help with genome sequencing, disease diagnosis and forensic investigations.

Hand-held device for extracting DNA
“It’s very complex to extract DNA,” said Jae-Hyun Chung, a UW associate professor of mechanical engineering who led the research. “When you think of the current procedure, the equivalent is like collecting human hairs using a construction crane.”
The small, box-shaped kit now is ready for manufacturing, then eventual distribution to hospitals and clinics.

Source:http://www.washington.edu/

A research team lead by Dr Peixuan Guo from the University of Kentucky (USA) have cracked a 35-year-old mystery about the workings of the natural motors that are serving as models for development of a futuristic genre of synthetic nanomotors that pump therapeutic DNA, RNA or drugs into individual diseased cells.

The importance of nanomotors in nanotechnology is akin to that of mechanical engines to daily life. The AAA+ superfamily is a class of nanomotors performing various functions. Their hexagonal arrangement facilitates bottom-up assembly for stable structures. Bacteriophage phi29 DNA-translocation motor contains three co-axial rings and viral DNA-packaging motor has been believed to be a rotational machine. However, the researchers found a revolution mechanism without rotation. By analogy, the earth revolves around the sun while rotating on its own axis.
Click here to enjoy the video

Source University of Kentucky: http://nanobio.uky.edu/
AND
ACS Nano: http://pubs.acs.org

A diagnostic “cocktail” containing a single drop of blood, a dribble of water, and a dose of DNA powder with gold particles could mean rapid diagnosis and treatment of the world’s leading diseases in the near future. The cocktail diagnostic is a homegrown brew being developed by University of Toronto’s Institute of Biomaterials and Biomedical Engineering (IBBME) PhD student Kyryl Zagorovsky and Professor Warren Chan that could change the way infectious diseases, from HPV and HIV to malaria, are diagnosed. And it involves the same technology used in over-the-counter pregnancy tests.

“There’s been a lot of emphasis in developing simple diagnostics,” says IBBME Professor and Canada Research Chair in Nanobiotechnology, Warren Chan. “The question is, how do you make it simple enough, portable enough?” Zagorovsky’s rapid diagnostic biosensor will allow technicians to test for multiple diseases at one time with one small sample, and with high accuracy and sensitivity. The biosensor relies upon gold particles in much the same vein as your average pregnancy test. With a pregnancy test, gold particles turn the test window red because the particles are linked with an antigen that detects a certain hormone in the urine of a pregnant woman. “Gold is the best medium,” explains Chan, “because it’s easy to see. It emits a very intense colour.”
source: http://ibbme.utoronto.ca/

Chad A. Mirkin, a researcher from Northwestern University, has developed a completely new set of building blocks that is based on nanoparticles and DNA. Using these tools, scientists will be able to build — from the bottom up, just as nature does — new and useful structures. Using nanoparticles and DNA, Mirkin has built more than 200 different crystal structures with 17 different particle arrangements. Some of the lattice types can be found in nature, but he also has built new structures that have no naturally occurring mineral counterpart.

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

Mirkin has presented his research in a session titled “Nucleic Acid-Modified Nanostructures as Programmable Atom Equivalents: Forging a New Periodic Table” at the American Association for the Advancement of Science (AAAS) annual meeting in Boston.
Source: http://www.eurekalert.org/

If you want to understand a novel, it helps to start from the beginning rather than trying to pick up the plot from somewhere in the middle. The same goes for analyzing a strand of DNA. The best way to make sense of it is to look at it head to tail. Luckily, according to a new study by physicists at Brown University, DNA molecules have a convenient tendency to cooperate. The research, published in the journal Physical Review Letters, looks at the dynamics of how DNA molecules are captured by solid-state nanopores, tiny holes that soon may help sequence DNA at lightning speed. The study found that when a DNA strand is captured and pulled through a nanopore, it’s much more likely to start the journey at one of its ends, rather than being grabbed somewhere in the middle and pulled through in a folded configuration.

“We think this is an important advance for understanding how DNA molecules interact with these nanopores,” said Derek Stein, assistant professor of physics at Brown, who performed the research with graduate student Mirna Mihovilovic and undergraduate Nick Hagerty. “If you want to do sequencing or some other analysis, you want the molecule going through the pore head to tail.”
Source: http://news.brown.edu/

A research team from the City University of New York -CUNY-, has developped a method to detect a single virus particle, which is in the size range of a nanoparticle. (About 80,000 nanoparticles side by side would have the same width as a human hair). Their work has made it possible, for the first time, to detect the smallest virus particle. Since even one viral particle can represent a deadly threat, the research likely will make an important contribution to ongoing research on early detection of such diseases as AIDS and cancer. The team’s breakthrough involved adding a nano-antenna to the light-sensing device to enhance the signal.

“The idea that light can ‘sense’ the presence of nanoparticles and respond to their arrival was groundbreaking,” Dr. Kolchenko from CUNY says. “Since all the deadliest viruses and most interesting biological molecules – proteins and DNA — belong to the nano world, our research proved truly innovative, and its promise is almost unlimited in terms of detecting pretty much everything of interest in life sciences,” he adds.
Let’ds remind that a Norwegian team has found one month ago a way to measure individual particle in the blood. SEE former article : http://www.nanocomputer.com/?p=4393
Source: http://www1.cuny.edu/

University of Illinois physics team discovered how a DNA-repair protein matches up a broken DNA strand with an intact region of double-stranded DNA. Every time a human or bacterial cell divides it first must copy its DNA. Specialized proteins unzip the intertwined DNA strands while others follow and build new strands, using the originals as templates. Whenever these proteins encounter a break – and there are many – they stop and retreat, allowing a new cast of molecular players to enter the scene. Scientists have long sought to understand how one of these players, a repair protein known as RecA in bacterial cells, helps broken DNA find a way to bridge the gap. They knew that RecA guided a broken DNA strand to a matching sequence on an adjoining bit of double-stranded DNA, but they didn’t know how. In a new study, researchers report they have identified how the RecA protein does its job.

“The puzzle for scientists has been: How does the damaged DNA look for and find its partner, the matching DNA, so that it can repair itself?” said University of Illinois physics professor Taekjip Ha, who led the study. “Because the genomic DNA is millions of bases long, this task is much like finding a needle in a haystack. We found the answer to how the cell does this so quickly.”
Source: http://news.illinois.edu/

The claim that nanopore technology is on the verge of making DNA analysis so fast and cheap that a person’s entire genome could be sequenced in just minutes and at a fraction of the cost of available commercial methods, has resulted in overwhelming academic, industrial, and global interest. But a review by Northeastern University – Boston – physicist Meni Wanunu, published in a special issue on nanopore sequencing in Physics of Life Reviews, questions whether the remaining technical hurdles can be overcome to create a workable, easily produced commercial device.

Earlier this year Oxford Nanopore Technologies, one of the pioneering companies of sequencing discoveries, announced that they expect nanopore strand sequencing to achieve a 15-minute genome by 2014 at a cost of $1,500. This is a far cry from the $10 million it cost to sequence an entire genome just 5 years ago. Since the idea of nanopore sequencing was first proposed in the mid 1990s, huge advances have been made. The basic idea is exceedingly simple: a single thread of DNA is passed through a tiny molecule-sized hole—or nanopore—and the various DNA bases are identified in sequence as they move through the pore.

But according to Wanunu, the reality of manipulating technology based on pores so tiny that 25,000 of them can fit side by side on a human hair has proved a daunting task. The main challenge has been to slow the process down and control the movement of the DNA strand through the pore at a rate slow enough to make individual DNA bases readable and usable. A new approach using enzyme-controlled movement, developed to overcome this problem, has its own drawbacks including poor enzyme activity resulting in limited processivity and uncontrolled forward-reverse motion.
Source:
- http://www.elsevier.com/wps/find/authored_newsitem.cws_home
/companynews05_02508?navopenmenu=3
- http://www.northeastern.edu/news/2012/09/nanopores-promise-cost-savings-in-gene-sequencing/

In order to assemble novel biomolecular machines, individual protein molecules must be installed at their site of operation with nanometer precision. Researchers from the Ludwig Maximilian Universitat Munchen – LMU – Germany – have now found a way to do just that. Green light on protein assembly! In a major step towards this goal, the LMU team has modified the method to allow them to take proteins from a storage site and place them at defined locations within a construction area with nanometer precision. “In liquid medium at room temperature, the “weather conditions” at the nanoscale are comparable to those in a hurricane,” says Mathias Strackharn, first author of the new study. Hence, the molecules being manipulated must be firmly attached to the tip of the AFM and held securely in place in the construction area.

“We demonstrated the method’s feasibility by bringing hundreds of fluorescent GFP molecules together to form a little green man, like the traffic-light figure that signals to pedestrians to cross the road, but only some micro micrometers high,” Strackharn explains.

Traffic signals prove the efficiency
The forces that tether the proteins during transport and assembly must also be weak enough not to cause damage, and must be tightly controlled. To achieve these two goals, the researchers used a combination of antibodies, DNA-binding “zinc-finger” proteins, and DNA anchors. Source:
http://www.en.uni-muenchen.de/news/newsarchiv/2012/2012_strackharn.html

Molecular biologists at The University of Texas at Austin have solved one of the mysteries of how double-stranded RNA is remodeled inside cells in both their normal and disease states. The discovery will have great implications for treating cancer and viruses in humans. They use chemical energy to clamp down and pry open RNA strands, thereby enabling the formation of new structures. This remodeling of RNA is essential to the basic functioning of cells.

“If you want to couple fuel energy to mechanical work to drive strand separation, this is a very versatile mechanism,” said co-author Alan Lambowitz, the Nancy Lee and Perry R. Bass Regents Chair in Molecular Biology in the College of Natural Sciences and director of the Institute for Cellular and Molecular Biology. “These findings could have far-reaching implications for our ability to control the activities of proteins in this class when their functions go awry in disease states,” comments Michael Bender, program director in the Division of Genetics and Developmental Biology at the National Institutes of Health, which partially funded the work.
Source: http://web5.cns.utexas.edu/news/2012/09/ancient-enzymes-function-like-nanopistons-to-unwind-rna/

Our genetic code packs billions of gigabytes into a single gram. A mere milligram of the molecule could encode the complete text of every book in the Library of Congress and have plenty of room to spare. All of this has been mostly theoretical —until now. In a new study, researchers from Harvard University stored an entire genetics textbook in less than a picogram of DNA—one trillionth of a gram— an advance that could revolutionize our ability to save data.

“A device the size of your thumb could store as much information as the whole Internet,” said Harvard University molecular geneticist George Church, the project’s senior researcher.

Source: http://online.wsj.com/article/SB10000872396390444233104577593291643488120.html?mod=WSJUK_hpp_MIDDLELSMini

University of Illinois chemists found that DNA can shape gold nanoparticle growth similarly to the way it shapes protein synthesis, with different letters of the genetic code producing gold circles, stars and hexagons. DNA holds the genetic code for all sorts of biological molecules and traits. But University of Illinois researchers have found that DNA’s code can similarly shape metallic structures. DNA segments can direct the shape of gold nanoparticles – tiny gold crystals that have many applications in medicine, electronics and catalysis. Led by Yi Lu, the Schenck Professor of Chemistry at the U. of I., the team published its surprising findings in the journal Angewandte Chemie.

“DNA-encoded nanoparticle synthesis can provide us a facile but novel way to produce nanoparticles with predictable shape and properties,” Lu said. “Such a discovery has potential impacts in bio-nanotechnology and applications in our everyday lives such as catalysis, sensing, imaging and medicine.”

Source: http://news.illinois.edu/news/12/0808nanoparticles_YiLu.html

Scientists from the University of Utah have adapted the “nanopore” method to find DNA damage that can lead to mutations and disease. Indeed sequencing DNA – decipher genetic blueprints – is faster and cheaper by passing strands of the genetic material through molecule-sized pores. Strands of DNA are made of “nucleotide bases” known as A, T, G and C. Some stretches of DNA strands are genes.The new method looks for places where a base is missing, known as an “abasic site,” one of the most frequent forms of damage in the 3-billion-base human genome or genetic blueprint. This kind of DNA damage happens 18,000 times a day in a typical cell as we are exposed to everything from sunlight to car exhaust. Most of the damage is repaired, but sometimes it leads to a gene mutation and ultimately disease.

“We’re using this technique and synthetic organic chemistry to be able to see a damage site as it flies through the nanopore,” says Henry White, distinguished professor and chair of chemistry at the University of Utah and senior coauthor of the new study.

Source: http://unews.utah.edu/news_releases/utah-chemists-use-nanopores-to-detect-dna-damage/

Using a technique known as “nucleic acid origami,” chemical engineers have built tiny particles made out of DNA and RNA that can deliver snippets of RNA directly to tumors, turning off genes expressed in cancer cells.To achieve this type of gene shutdown, known as RNA interference, many researchers have tried — with some success — to deliver RNA with particles made from polymers or lipids. However, those materials can pose safety risks and are difficult to target, says Daniel Anderson, an associate professor of health sciences and technology and chemical engineering, and a member of the David H. Koch Institute for Integrative Cancer Research at MIT. 

Researchers successfully used this nanoparticle, made from several strands of DNA and RNA, to turn off a gene in tumor cells. 

“When you think of metastatic cancer, you don’t want to just stop in the liver,” Anderson says. “You also want to get to more diverse sites.”

Source: http://web.mit.edu/newsoffice/2012/rna-interference-lightweight-nanoparticle-0604.html

Scientists at The Scripps Research Institute suggests that the replication process for DNA — the genetic instructions for living organisms that is composed of four bases (C, G, A and T) — is more open to unnatural letters than had previously been thought. An expanded "DNA alphabet" could carry more information than natural DNA, potentially coding for a much wider range of molecules and enabling a variety of powerful applications, from precise molecular probes and nanomachines to useful new life forms.

We now know that the efficient replication of our unnatural base pair isn't a fluke, and also that the replication process is more flexible than had been assumed,"" said Floyd E. Romesberg, associate professor at Scripps Research, principal developer of the new DNA bases, and a senior author of the new study. The Romesberg laboratory collaborated on the new study with the laboratory of co-senior author Andreas Marx at the University of Konstanz in Germany, and the laboratory of Tammy J. Dwyer at the University of San Diego.
Romesberg and his lab have been trying to find a way to extend the DNA alphabet since the late 1990s. In 2008, they developed the efficiently replicating bases NaM and 5SICS, which come together as a complementary base pair within the DNA helix, much as, in normal DNA, the base adenine (A) pairs with thymine (T), and cytosine (C) pairs with guanine (G).

Source:  http://www.nature.com/nchembio/journal/vaop/ncurrent/full/nchembio.966.html

Researchers at the National Institute of Standards and Technology (NIST) and the University of Massachusetts Amherst (UMass) have provided the first evidence that engineered nanoparticles are able to accumulate within plants and damage their DNA. In a recent paper, the team led by NIST chemist Bryant C. Nelson showed that under laboratory conditions, cupric oxide nanoparticles have the capacity to enter plant root cells and generate many mutagenic DNA base lesions.

The team tested the human-made, ultrafine particles between 1 and 100 nanometers in size on a human food crop, the radish, and two species of common groundcovers used by grazing animals, perennial and annual ryegrass. This research is part of NIST's work to help characterize the potential environmental, health and safety (EHS) risks of nanomaterials, and develop methods for identifying and measuring them.

Source: http://www.nist.gov/mml/biochemical/nanoparticles-041712.cfm

Researchers have devised a nanoscale sensor to electronically read the sequence of a single DNA molecule, a technique that is fast and inexpensive and could make DNA sequencing widely available. The technique could lead to affordable personalized medicine, potentially revealing predispositions for afflictions such as cancer, diabetes or addiction.

"There is a clear path to a workable, easily produced sequencing platform," said Jens Gundlach, a University of Washington physics professor who leads the research team. "We augmented a protein nanopore we developed for this purpose with a molecular motor that moves a DNA strand through the pore a nucleotide at a time."The researchers previously reported creating the nanopore by genetically engineering a protein pore from a mycobacterium. The nanopore, from Mycobacterium smegmatis porin A, has an opening 1 billionth of a meter in size, just large enough for a single DNA strand to pass through.

Source: http://www.washington.edu/news/articles/tiny-reader-makes-fast-cheap-dna-sequencing-feasible

Scientists in Duke University have managed to create a reusable DNA chip from which DNA building blocks may be photocopied and used to create unique nanoscale structures.  Ishtiaq Saaem, a biomedical engineering researcher at Duke, commented: “We found we had an “immortal” DNA chip on our hands. Essentially, we were able to do the biological copying process to release material off the chip tens of times". "The process seems to work even using a chip that we made, used, stored in -20C for a while, and brought out and used again". “I would not be surprised if this methodology is used to fabricate the next generation of microprocessors that can push Moore’s law even further.”

Duke University researchers have used an inkjet printer head to place droplets of chemicals on the plastic chip, slowly building a DNA strand of various length and composition. The researchers were surprised, subsequently discovered the chip could be reused.
http://www.duke.edu/