This illustration shows how a DNA origami nanoplate with a central aperture can serve as a smart lid or "gatekeeper" for a solid-state nanopore sensor. Researchers at the Technische Universitaet Muenchen have demonstrated that this arrangement can be used to filter biomolecules by size or to "fish" for specific target molecules by placing single-strand DNA receptors inside the aperture as "bait." With further research, they suggest, it might be possible to use such single-molecule sensors as the basis of a novel DNA sequencing system. Credit: TU Muenchen

The latest advance in solid-state nanopore sensors devices that are made with standard tools of the semiconductor industry yet can offer single-molecule sensitivity for label-free protein screening expands their bag of tricks through bionanotechnology. Researchers at the Technische Universitaet Muenchen have enhanced the capabilities of solid-state nanopores by fitting them with cover plates made of DNA. These nanoscale cover plates, with central apertures tailored to various "gatekeeper" functions, are formed by so-called DNA origami the art of programming strands of DNA to fold into custom-designed structures with specified chemical properties.

The results are published in Angewandte Chemie International Edition.

Over the past few years, Prof. Hendrik Dietz's research group at TUM has been refining control over DNA origami techniques and demonstrating how structures made in this way can enable scientific investigations in diverse fields. Meanwhile, Dr. Ulrich Rant's research group has been doing the same for solid-state nanopore sensors, where the basic working principle is to urge biomolecules of interest, one at a time, through a nanometer-scale hole in a thin slab of semiconductor material. When biomolecules pass through or linger in such a sensor, minute changes in electrical current flowing through the nanopore translate into information about their identity and physical properties. Now Dietz and Rant, who are both Fellows of the TUM Institute for Advanced Study, have begun to explore what these two technologies can accomplish together.

The new device concept purely hypothetical before this series of experiments begins with the placement of a DNA origami "nanoplate" over the narrow end of a conically tapered solid-state nanopore. "Tuning" the size of the central aperture in the DNA nanoplate should allow filtering of molecules by size. A further refinement, placing single-stranded DNA receptors in the aperture as "bait," should allow sequence-specific detection of "prey" molecules. Conceivable applications include biomolecular interaction screens and detection of DNA sequences. In principle, such a device could even serve as the basis of a novel DNA sequencing system.

Step by step, the researchers investigated each of these ideas. They were able to confirm the self-assembly of custom-designed DNA origami nanoplates, and then their placement after being electrically guided into position over solid-state nanopores. They were able to demonstrate both size-based filtering of biomolecules and bait/prey detection of specific target molecules. "We're especially excited about the selective potential of the bait/prey approach to single-molecule sensing," Dietz says, "because many different chemical components beyond DNA could be attached to the appropriate site on a DNA nanoplate."

High-resolution sensing applications such as DNA sequencing will face some additional hurdles, however, as Rant explains: "By design, the nanopores and their DNA origami gatekeepers allow small ions to pass through. For some conceivable applications, that becomes an unwanted leakage current that would have to be reduced, along with the magnitude of current fluctuations."

More information: DNA Origami Gatekeepers for Solid-State Nanopores, Ruoshan Wei, Thomas G. Martin, Ulrich Rant, and Hendrik Dietz, Angewandte Chemie International Edition online, April 4, 2012. DOI: 10.1002/anie.201200688

Provided by Technische Universitaet Muenchen

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DNA origami puts a smart lid on solid-state nanopore sensors

Polar bears were previously thought to have split from brown bears some 150,000 years ago. But a study of the bears' mitochondrial DNA indicates that they became a distinct species about 600,000 years ago.

Polar bears have been chilling on the ice far longer than is generally thought, new research suggests, and they probably interbred with brown bears at one point after the two species separated.

The new German study contradicts data from a study published last July in the journal Current Biology that suggested polar bearsseparated from brown bears150,000 years ago. The new study analyzed the bears' mitochondrial DNA, a special "additional genome" that lives in the cell's energy factories and is passed down only from the mother. The new study concludes that the bears became separate species closer to 600,000 years ago.

If the polar bears were only 150,000 years old, as suggested by the previous study, they would have had to evolve many specialized traits in a curiously brief time, the German researchers said.

"I've been long puzzled by the suggestion that the polar bears would have been such a miraculous and rapidly evolving species," Frank Hailer of the Senckenberg Nature Research Society in Frankfurt told LiveScience. "I had this lingering question: Is it really true?"

Hailer and his colleagues looked at the polar bear's nuclear DNA, which comes from both parents and is much larger than the mitochondrial genome. [Fun Facts About Polar Bears]

They compared 9,000 base-pair sequences (the chemicals that make up the "rungs" of DNA's ladderlike molecule) from the nuclear DNA of 45 polar, brown and black bears. This comparison let the researchers build a family tree, with the idea that the greater the genetic differences between the species, the farther they were apart in evolutionary time. They were able to estimate when the polar bears and brown bears separated.

"We found that polar bears are much older than we previously knew from other studies; their appearance dated to about 600,000 years ago," Hailer said. "That would make sense around that time for something like apolar bear to evolve, because Arctic habitats were much larger than they are today, so there would have been much larger habitats that would have been suitable for a species like a polar bear."

The researchers say the mitochondrial DNA data could have come from a hybridization event between polar and brown bears 150,000 years ago during the last warm interglacial period. During that time, sea ice melted and polar bears took to the shores, where they came intocontact with brown bears.

The researchers say this hybridization (similar to the hybrid "grolar" or "pizzly" bears seen in recent years in Canada) would have introduced the brown bear mitochondrial DNA into the polar bear population. If the DNA from the brown bears helped the polar bears survive the warm period, it's possible it could have easily spread throughout the population.

See the original post here:
Polar bears emerged far earlier than thought, DNA study indicates

Polar bears were previously thought to have split from brown bears some 150,000 years ago. But a study of the bears' mitochondrial DNA indicates that they became a distinct species about 600,000 years ago.

Polar bears have been chilling on the ice far longer than is generally thought, new research suggests, and they probably interbred with brown bears at one point after the two species separated.

The new German study contradicts data from a study published last July in the journal Current Biology that suggested polar bearsseparated from brown bears150,000 years ago. The new study analyzed the bears' mitochondrial DNA, a special "additional genome" that lives in the cell's energy factories and is passed down only from the mother. The new study concludes that the bears became separate species closer to 600,000 years ago.

If the polar bears were only 150,000 years old, as suggested by the previous study, they would have had to evolve many specialized traits in a curiously brief time, the German researchers said.

"I've been long puzzled by the suggestion that the polar bears would have been such a miraculous and rapidly evolving species," Frank Hailer of the Senckenberg Nature Research Society in Frankfurt told LiveScience. "I had this lingering question: Is it really true?"

Hailer and his colleagues looked at the polar bear's nuclear DNA, which comes from both parents and is much larger than the mitochondrial genome. [Fun Facts About Polar Bears]

They compared 9,000 base-pair sequences (the chemicals that make up the "rungs" of DNA's ladderlike molecule) from the nuclear DNA of 45 polar, brown and black bears. This comparison let the researchers build a family tree, with the idea that the greater the genetic differences between the species, the farther they were apart in evolutionary time. They were able to estimate when the polar bears and brown bears separated.

"We found that polar bears are much older than we previously knew from other studies; their appearance dated to about 600,000 years ago," Hailer said. "That would make sense around that time for something like apolar bear to evolve, because Arctic habitats were much larger than they are today, so there would have been much larger habitats that would have been suitable for a species like a polar bear."

The researchers say the mitochondrial DNA data could have come from a hybridization event between polar and brown bears 150,000 years ago during the last warm interglacial period. During that time, sea ice melted and polar bears took to the shores, where they came intocontact with brown bears.

The researchers say this hybridization (similar to the hybrid "grolar" or "pizzly" bears seen in recent years in Canada) would have introduced the brown bear mitochondrial DNA into the polar bear population. If the DNA from the brown bears helped the polar bears survive the warm period, it's possible it could have easily spread throughout the population.

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Polar bears emerged far earlier than thought, DNA study indicates (+video)

By Robert Langreth - Thu Apr 19 18:00:00 GMT 2012

Scientists moved a step closer to synthesizing new life forms in the laboratory after researchers showed that artificial genetic material called XNA can be replicated in the test tube much like real DNA.

Researchers at the Medical Research Council Laboratory of Molecular Biology in the U.K. demonstrated for the first time a way to extract information from the artificial genetic molecules and mass produce copies of them. The finding, published today in the journal Science, shows that DNA and its sister molecule RNA may not be the only chemical structures upon which a living unit can be based.

Life is based on this amazing ability of DNA and RNA to store and propagate information, said Philipp Holliger, a Medical Research Council molecular biologist and senior author on the study. We have shown that the basic functions of DNA and RNA can be recapitulated with new artificial molecules.

The scientists invented a lab method for making copies of synthetic DNA. They also developed a way to make XNA fragments that evolve with desired properties. In particular, they created XNA fragments that could bind with great specificity to a molecular target in the HIV virus. The discovery could create a new platform for devising targeted drugs to treat a variety of diseases, researchers said.

This brings us one big step closer to artificial life, said Gerald Joyce, a biochemist at Scripps Research Institute in San Diego, in a telephone interview. The heart of what life is, is the replication of genetic information, he said. Joyce wrote a commentary accompanying the study.

DNA, deoxyribonucleic acid, is the hereditary molecule at the center of our cells. It contains code, in the form of chemical letters A, T, C and G, that tells the body how to make proteins that perform numerous bodily functions such as regulating blood sugar or fighting infections.

XNAs, or xeno-nucleic acids, maintain the same four-letter chemical code while altering the backbone of the DNA double helix molecule to add properties such as acid resistance.

While XNAs arent new, chemists have always had to make them one at a time, limiting their utility, Joyce said. With the new work, if I give you a few XNAs in the morning, I can come back in the afternoon and you can give me trillions of copies.

The work may give scientists a new method for creating designer drugs and diagnostic tools. There are a whole host of opportunities in biotechnology which now become possible, Holliger said.

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Artificial DNA Can Replicate in Lab, Researchers Find

19 April 2012 Last updated at 19:57 ET By Helen Briggs BBC News

The polar bear is much older than previously thought, according to new genetic evidence.

DNA studies suggest the Arctic predator split from its ancestor, the brown bear, about 600,000 years ago.

Previous estimates put the polar bear at about 150,000 years old, suggesting the mammal adapted very rapidly to Arctic life.

Conservationists say the new study, published in Science, has implications for bear conservation.

Polar bears are listed as threatened under the US Endangered Species Act.

Conservationists say their survival is at risk, mainly due to the loss of the Arctic sea ice on which they spend much of their lives.

Dr Frank Hailer of the German Biodiversity and Climate Research Centre in Frankfurt, who led the international study, said the genetic information shed new light on conservation issues.

"It fundamentally changes our understanding of polar bears and their conservation today," he told BBC News.

"They have survived previous warm phases but they carry scars from these times - they must have been close to extinction at times."

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DNA reveals polar bear's origins