NICHOLAS WADE
Published: August 9, 2010
nytimes.com

A new generation of DNA tests for colon cancer seems likely to improve the detection both of cancers and of the precancerous polyps that precede them. The tests, if validated, could reduce the burden of disease substantially by detecting tumors at an early stage, including those not picked up by a colonoscopy.

Colorectal cancers tend to grow slowly and are easily removed if caught early. But many people over 50 do not comply with the recommendation to have a colonoscopy — a time-consuming procedure in which a tube is threaded up the intestine — and even colonoscopies do not catch everything. Colorectal cancer has become the second most common cancer in the United States; each year it causes more than 50,000 deaths and costs about $14 billion to treat.

Colon tumors provide considerable evidence of their presence by shedding blood and cells that are detectable in the stool. Tests for blood have reduced deaths from colorectal cancer only modestly, because they are not very sensitive to precancerous polyps, the stage at which cancer is best prevented.

Researchers turned to measuring mutations in DNA after Dr. Bert Vogelstein of Johns Hopkins University discovered the series of mutations by which a colon polyp advances to full cancer. But no single mutation predicts a patient’s risk, and the mutation tests, though more accurate than the blood tests, have not been a decisive improvement.

By 2004 it was clear that looking for the Vogelstein mutations was “neat biology but not a home run,” said Dr. David Ransohoff, an expert on colon cancer screening at the University of North Carolina.

A new generation of tests being developed depends on a different process in cancer cells. All cells switch off the genes they do not need by attaching small chemicals called methyl groups to certain sites along their DNA. In cancer cells, there is generally less methylation than usual, except for certain regions of DNA where the methylation process is taken to excess, perhaps because the cells need to shut down tumor suppressor genes. These and other genes are highly methylated in colon tumors and other kinds of cancer.

Exact Sciences, a company based in Madison, Wis., is developing a colon cancer test based on highly methylated DNA. Its researchers reported last month that by testing for methylated DNA at four markers, pieces of DNA drawn from specific genes, they could detect colon tumors and polyps, distinguishing them from normal tissue with 100 percent sensitivity and with no false positives.

The tests of methylated DNA were performed directly on tumors and are expected to be less accurate in the real world, in which they would have to work in stool samples. Almost all of the DNA in stool is from bacteria, and the methylated DNA is a fraction of the 0.01 percent that is human DNA.

Still, Kevin T. Conroy, chief executive of Exact Sciences, said he expected that the four-marker test, when applied to stool samples, would detect at least half of all precancerous polyps and 85 percent of actual cancers. Results of a trial now under way in 1,600 patients will be reported in October, he said.

The test would cost less than $300, and samples could be collected at home. Patients would be advised to take the test every three years. People with a positive result would then have a colonoscopy to verify and remove any polyps, with the result that colonoscopies could be focused on high-risk patients instead of the population at large.

Exact Sciences’ test is based on work by Dr. Vogelstein, Dr. Sanford Markowitz at Case Western Reserve University and Dr. David A. Ahlquist of the Mayo Clinic. Dr. Ahlquist, who is a scientific adviser to the company, identified some of the highly methylated genes the company is testing as markers for colon cancer.

Dr. Ahlquist said that if the test worked as well as hoped on stool samples, “this will be the first noninvasive test that will reliably detect malignant lesions.” Cervical cancer has been virtually eliminated by the Pap test, he said, and “we feel that colon cancer could be eliminated to the same extent.”

The four-marker test can pick up a kind of precancerous tissue called a serrated polyp which is often missed by colonoscopies, Dr. Ahlquist said. It also ignores most innocuous small polyps.

Using different sets of four markers, other kinds of cancer can be detected. “We can detect all of the cancers above the colon — pancreas, esophagus, stomach, bile duct,” Dr. Ahlquist said. Thus in principle, all the cancers of the gastrointestinal tract, which account for nearly a quarter of all cancer deaths in the United States, should be detectable from stool samples.

Dr. Vogelstein said tests for DNA mutations would be better in theory than tests for DNA methylation because “mutations are entirely specific and they are what is driving the tumor”; the methylation is less causative and increases naturally with age.

But the DNA methylation tests are promising in principle, he said, and it seems feasible for Exact Sciences to get a sensitivity of better than 90 percent and a false positive rate of only 5 to 10 percent. “We can tolerate 5 to 10 percent false positives because those people will just get colonoscopies,” he said.

For cancers above the colon, there are many enzymes that digest DNA, so whether such cancers can be detected efficiently can be answered only with experiments, Dr. Vogelstein said. And false positives would be more of a problem, since for these cancers there is no easy verification method like colonoscopy. “That’s when these false positives really start to be the devil,” he said.

Dr. Ransohoff said the Exact Sciences test was still at a preliminary point. “This is neat and it’s promising,” he said. “But we’ve been down this road before and we need to be hopeful without being carried away.”

DNAWellnessinfo.com Resource:  http://www.nytimes.com/2010/08/10/health/10cancer.html?_r=1

DNA Test May Speed Colon Cancer Diagnosis is a post from: dnawellnessinfo.com

WSJ’s blog on health and the business of health – July 23, 2010, 11:30 AM ET

By Katherine Hobson

Direct-to-consumer genetic-testing companies were in the hot seat this week, with scrutiny from both the FDA and Congress. Fodder for some of the discussion was a new GAO report that focused on the scientific accuracy and marketing efforts of tests by companies including 23andMe, Pathway Genomics, deCODE genetics and Navigenics.

You can read about the GAO report in this story from today’s WSJ. And here’s the GAO report itself.

Investigators from the independent agency, which works on behalf of Congress, sent DNA samples for assessment of the risk of different diseases and conditions. The report found analyses of the same samples varied, in many cases wildly; the companies say they use different genetic markers, which means results won’t be uniform — though some agreed that there is a need for some common standards.

But for some Friday fun, listen to or read the transcripts of undercover calls to unnamed genetic-testing companies made by GAO investigators. (Undercover contact was made with 15 companies, including the four listed above.)

One fake customer asked a company rep, “So if I’m high risk, does that mean I’ll definitely get breast cancer?”

Rep: “You … you’d be in the high risk of, you know, pretty much getting it so …”

(The GAO notes these tests are not diagnostic and that this company didn’t even test for the BRCA gene variations that are linked to a higher chance — but by no means a certainty — of getting breast cancer. Experts consulted by the GAO called the rep’s response “horrifying.”)

Another marketing rep told a fake customer that “we can repair DNA damage.”

Fake customer: “You can, really?”

Rep: “Oh yeah, it’s called epigenetics and …”

Fake customer: “That’s repairing DNA?”

Rep: “Yeah … The genes are considered now not to be the source of our biology, they’re a symptom.”

(Experts told the GAO there was “no scientific basis for these claims.”)

The transcript also features company reps agreeing to process a DNA sample obtained surreptitiously, for a “surprise” analysis ordered by a woman for her fiancé (in most states, that’s an illegal breach of privacy); falsely claiming Lance Armstrong as a celebrity endorser, and claiming supplements can cure disease.

DNAWellnessinfo.com Resource: http://blogs.wsj.com/health/2010/07/23/listen-to-consumer-dna-test-company-sales-reps-behaving-badly/

Listen to Consumer DNA Test Company Sales Reps Behaving Badly! is a post from: dnawellnessinfo.com

foxnews.com
Thursday, July 22, 2010

Public swimming pools are more dangerous than you might think, a new study suggests. When sweat and urine, among other organics, mix with the disinfectants in pool water, the result can be hazardous to health.

The findings, announced this week, link the application of disinfectants in recreational pools to genetic cell damage that has been shown to be linked with adverse health outcomes such as asthma and bladder cancer.

Pool water represents extreme cases of disinfection that differ from the disinfection of drinking water as pools are continuously exposed to disinfectants. But with so many people cooling off and exercising in pools and water parks (339 million visits across the United States each year), the disinfectants are a must to prevent outbreaks of infectious disease.

Chlorine and Pee Don’t Mix

The problem occurs when the sanitizers mix with organic matter.

“All sources of water possess organic matter that comes from decaying leaves, microbes and other dead life forms,” said study researcher Michael Plewa, University of Illinois professor of genetics. “In addition to organic matter and disinfectants, pool waters contain sweat, hair, skin, urine and consumer products such as cosmetics and sunscreens from swimmers.”
These consumer products are often nitrogen-rich, and when mixed with disinfectants, these products may become chemically modified and converted into more toxic agents.

Long-term exposure to these disinfection byproducts can mutate genes, induce birth defects, accelerate the aging process, cause respiratory ailments, and even induce cancer, according to the researchers. While the new study did not examine actual effects on humans, it suggests such research might be warranted.

Pool Samples

In this study, researchers evaluated water samples from public pools and a control sample of tap water. They tested whether the byproduct chemicals in the samples could induce gene mutations using a so-called systematic mammalian cell genotoxicity analysis.

This sensitive DNA technology can detect genomic damage in mammalian cells, allowing researchers to investigate damage at the level of each nucleus within each cell.

Results proved that all disinfected pool samples had more genomic DNA damage than the source tap water, Plewa said.

The findings are published in the journal Environmental Science & Technology. The work was supported by grants from the National Science Foundation.
Cleaner Pools

All this doesn’t mean you need to ditch your pool plans. Plewa offers recommendations for pool operators and swimmers to reduce hazardous chemicals and make for safer pool water.

“Care should be taken in selecting disinfectants to treat recreational pool water,” Plewa advised.

“The data suggest that brominating agents should be avoided as disinfectants of recreational pool water. The best method
to treat pool waters is a combination of UV treatment with chlorine as compared to chlorination alone.”

In addition, organic carbon should be removed prior to disinfection when the pool water is being recycled, Plewa said.

Swimmers can also help by showering before entering the water, which would mean fewer organics and so reduce the genotoxicity of the pool water. One recommendation that may seem obvious: Don’t pee in the pool. Plewa suggests pool owners remind patrons about the potential harm caused by urinating in a pool.

DNAWellnessinfo.com Resource: http://www.foxnews.com/story/0,2933,597467,00.html

Urine in Public Pools Could Cause Cell Damage is a post from: dnawellnessinfo.com

By ACT court reporter Katherine Pohl

Updated Mon May 31, 2010 8:27am AEST

The use of DNA evidence in criminal court cases is under the spotlight with state and territory attorneys-general backing a review into collecting and testing procedures.

Questions have been raised about contamination and the risks of convicting someone on DNA evidence alone.

“Those two areas are of critical concern, not only to defence lawyers but to prosecutors as well,” New South Wales Deputy Senior Public Defender Andrew Haesler said.

Those issues have been recently examined by the High Court.

Benjamin Forbes was found guilty of sexually assaulting a Canberra teenager in 2005 as she walked home from work.

DNA was the only evidence linking him to the crime scene.

The High Court ruled that it was not a suitable test case on which to base a DNA challenge.

But Mr Haesler predicts it will not be long before such a case comes along.

“Judges and juries have to be very critical when evidence is presented that identifies an offender solely on the basis of DNA,” he said.

Contamination of DNA evidence is also a major issue.

Simon Walsh from the Australian Federal Police admits DNA evidence can be a double-edged sword.

“One of the advantages of the testing progress and technology is that it allows us to test very small amounts of DNA,” he said.

“The corollary of that is that it makes it potentially more susceptible to contamination.”

Contamination issues were at the centre of a case in Victoria earlier this month in which a man was wrongly convicted of rape because of tainted DNA evidence.

The case has prompted all state and territory attorneys-general to back a review of DNA collection and analysis.

ACT Attorney General Simon Corbell says there is a lot to learn from that particular case and he is encouraging prudent collection and testing procedures.

A working group is examining the issues.

DNAWellnessinfo.com Resource: http://www.abc.net.au/news/stories/2010/05/31/2913474.htm

DNA handling under the microscope is a post from: dnawellnessinfo.com

ntimes.com
By SABIN RUSSELL
Published: May 28, 2010

Still in fine fettle at the age of 87, Ruth Young, a retired Oakland school nurse, jumped at the chance, she said, to “spit for the cause.”

Mrs. Young is one of more than 130,000 members of Kaiser Permanente in Northern California who have volunteered to have their DNA scanned by robotic, high-speed gene-reading machines as part of the largest human genome study of its kind ever attempted.

The goal of the study they are participating in is to help scientists uncover the genetic roots of chronic disease and, perhaps, to find out why some people live longer than others.

This month, researchers at Kaiser Permanente in Oakland and the University of California, San Francisco began the highly automated, large-scale process of analyzing that DNA, which is being extracted from tens of thousands of saliva samples donated by Kaiser members in Northern California since 2008.

Each sample of ordinary spit is laden with cells containing the volunteer’s entire set of genes, their genomes, which carry in sequences of DNA the coded instructions for building and maintaining life. The hope for this so-called genome-wide association study is that, when the genes of people with diseases like cancer and multiple sclerosis are compared with the genes of those in good health, computer analysis will pinpoint genes responsible for the illnesses.

With a speed that would have seemed preposterous to contemplate a decade ago, the work of collecting, purifying and digitizing billions of discrete bits of chemical information will be finished in less than 18 months, providing a rich resource for scientists to analyze for decades to come.

Winifred K. Rossi, who is managing the project for the National Institute on Aging, said most genome-wide association studies scan between 5,000 and 8,000 participants, although data from multiple, smaller studies can be pooled to form a larger group. What makes the Kaiser study unique is that members of a single, colossal cohort will have their genomes scanned uniformly, then paired with their medical histories. “It is absolutely the largest study of its kind, and it has enormous statistical power.” Ms. Rossi said.

Mrs. Young, a Kaiser member for 63 years, suffers from arthritic knees and Type II diabetes, which took her father’s life at an early age. “I’m conscientious about my diet, but I do love sweets,” she said.

She had originally been one of nearly two million patients asked in 2007 about participating in the Kaiser study. A huge group of volunteers, ranging in age from 18 to 107, filled out questionnaires. Tens of thousands of them, like Mrs. Young, were asked for specimens.

Following instructions found in a kit mailed to her Oakland home, Mrs. Young deposited the requested spit into a special plastic cup. She sealed it with a blue lid fitted with a built-in preservative and sent it back to Kaiser. Along with her saliva, the samples from the other 130,000 people began arriving in Kaiser’s mailbox.

Experiments like this one underscore how quickly gene-scanning technology is moving from the lab to the home. Last week, officials of the University of California, Berkeley, disclosed that 6,000 incoming freshman and transfer students will be asked to swab their cheeks at home for DNA, to participate in a collective lesson in genetics and a preview of the predicted era when medicine will be tailored to each person’s genetic makeup.

Each student who agrees to participate will be able to tap in a security code on a laptop and check whether they carry gene variants that might affect their ability to process lactose, alcohol or folate, a vitamin found in leafy greens. The Kaiser study participants will not have the same option. Their names are scrubbed from their samples, and only researchers — working with codes instead of names — will be able to link the gene scans to medical histories. Their goal is to discern the larger picture, hoping to spot associations between genes and health that would not show up until very large numbers of individuals are compared at once.

Although this vast experiment has been contemplated for years, it was given a boost last year when Kaiser and the university won a $25 million grant from the National Institutes of Health as part of the stimulus package.

However, the study has begun just as some scientists have started to question the value of these experiments, and when private ventures, like 23andMe, are struggling to find a consumer market for gene tests.

David B. Goldstein, a Duke University researcher, said he believed “interesting and valuable information” would come from the Kaiser study, but he questioned whether it was the most efficient way to gather information about the genetic links to disease. “It’s an awfully expensive study,” Dr. Goldstein said in an e-mail message.

He added, “We have literally hundreds of genome-wide association studies for common diseases, and in most cases we are having trouble making much use of them.” While Dr. Goldstein stresses that discoveries are being made using that technique, he believes that a different approach — sequencing the entire genetic code of fewer patients rather than scanning the genome for variations — “is likely to yield more useful returns.”

For Kaiser, the federal grant is just the beginning of a long-term endeavor.

In the coming years, 400,000 more members will be asked to contribute their DNA to the project when they come in for routine blood work. Kaiser is spending $9 million to build a repository for the blood samples.

“It’s an idea whose time has come,” said Dr. Pui-Yan Kwok, an investigator at the Institute for Human Genetics at the University of California, San Francisco, where the genes are being scanned. “The genotyping technology is here, the electronic medical records are here.”

Using high-precision robots to process each sample, the genomes of 2,500 participants are being analyzed each week. The genetic information will be stored in computers for future studies by scientists all over the globe.

At the same time, Elizabeth Blackburn, a Nobel-prize winning biologist at the university, and her lab will be conducting a mass experiment on a separate set of 100,000 samples of DNA from the Kaiser patients. They will be measuring the length of telomeres — wads of DNA at the top and bottom of every chromosome that, like shoelace tips, keep them from unraveling when a cell divides. Telomere length tends to shorten with age, and shorter telomeres tend to be linked with shorter life spans.

“Telomere length is more reflective of things that happen in your life than the genetic hand you are born with,” said Dr. Blackburn.

She said that the Kaiser patients are a valuable resource for science because their detailed medical histories can be matched with the varied measurements of telomere length and matched to the gene scans that will be done for each participant as well. Her targets are the three top diseases that kill the elderly: cancer, cardiovascular disease and diabetes.

At the Kaiser research lab, a production line of robotic equipment has been set up to process the 130,000 cups of saliva that have been mailed by patients and stored, at room temperature, in racks of cardboard “pizza boxes,” 50 cups to a box. Here, the robots draw out a sample of spit, and chemically process it to extract the donor’s DNA.

One set of Mrs. Young’s DNA will be sent to Dr. Blackburn’s lab, where the length of its telomeres will be measured. A second set will arrive at Dr. Kwok’s newly equipped facility, where the genome of each Kaiser participant will be scanned using an array of robots, each costing about a quarter million dollars.

At Dr. Kwok’s ninth-floor lab, three sets of robots prepare the DNA samples shipped from Oakland. The full complement of DNA from each volunteer is washed over a custom-designed silicon chip about this size of small fingernail. Microscopic wells etched into the chip are each engineered to pluck out one of 675,000 possible gene variants.

“Our biggest fear is a power-failure,” said Dr. Kwok. Each array, filled with 96 processed DNA samples, costs $10,000.

DNAWellnessinfo.com Resource: http://www.nytimes.com/2010/05/30/science/30sfgenome.html?pagewanted=1

From Californians’ DNA, a Giant Genome Project is a post from: dnawellnessinfo.com

Last Updated: Wednesday, May 5, 2010 | 1:11 PM ET

Canadian researchers have unraveled a genetic “code within a code” that helps explain how the instructions for building complex organisms, like humans, can be found in a small number of genes.

University of Toronto scientists Brendan Frey and Benjamin Blencowe said they have found a hidden code in DNA that helps explain how a small number of genes can contain instructions for a larger number of proteins and structures.

When researchers fully sequenced the human genome in 2004, they were surprised at how few genes humans actually have.

“Human DNA has 22,000 genes. That might seem like a lot, but not when you consider that a poplar tree has 45,000,” said Frey, in a statement.

Frey said his team, including Blencowe and Yoseph Barash, found a second level of information that the cells of living organisms use to create a larger set of instructions.

“We discovered a hidden code within DNA that living cells use to turn 20,000 genes into hundreds of thousands of genetic messages, by rearranging their parts,” he said.

Barash and Frey, who is also a professor of computer science and engineering, created a computer program that analyzes DNA to find “code words” in the genome.

The code words together are called the “splicing code,” containing the biological information needed to splice together different parts of the genetic code in different orders to generate a greater number of messages.

“For example, three neurexin genes can generate over 3,000 genetic messages that help control the wiring of the brain,” said Frey.

Neurexin is a protein that glues together the connections between nerve cells in the brain.

Frey said their work is the result of a close collaboration between computer scientists and experimental biologists.

“Understanding a complex biological system is like understanding a complex electronic circuit. Our team ‘reverse-engineered’ the splicing code using large-scale experimental data generated by the group,” he said.

The research was the cover story in this week’s issue of the journal Nature.

DNAWellnessinfo.com Resource: http://www.cbc.ca/technology/story/2010/05/05/tech-dna-splicing-code.html#ixzz0n9Wn5yO0

Canadian scientists crack hidden DNA code is a post from: dnawellnessinfo.com

April 13, 2010, 16:00 EST

DNAWellnessinfo.com Resource:  http://www.businessweek.com/lifestyle/content/healthday/637947.html

DNA Test Misses Virus That Causes Hearing Loss is a post from: dnawellnessinfo.com

Feb. 22, 2010 – cbsnews.com

(CBS) This article was written by Discover’sAndrew Moseman.

Doctors who are torn over how aggressively to treat a cancer patient, not knowing whether a tumor has fully regressed or is coming back, might someday be able to find out just by testing the patient’s blood. In a study forthcoming his week in Science Translational Medicine, John Hopkins researchers say they have tested a way to spot the “fingerprint” of cancer-the changes to the

Jeffery Schloss of the National Human Genome Research Institute, who wasn’t involved in the study, likened the approach to drawing a map. Sequencing the letters of the genetic code would be akin to plotting every house in a large neighborhood. The Hopkins team was looking only for neighborhoods-in particular, neighborhoods out of place compared with where they would be in normal tissue. The researchers in the study looked at tissue from people with breast or bowel cancer, and found multiple DNA rearrangements in each of the samples of cancerous tissue.

In each patient, the genetic changes in the cancerous cells amount to a unique marker of the patient’s tumor, the researchers say. Using blood samples from two of the colorectal cancer patients, they found the test was sensitive enough to detect this marker or “fingerprint” DNA that had been shed by tumors into the bloodstream.

The study’s approach could be invaluable for tracking the progress of a tumor. When a cancer is operated on or treated with radio – or chemotherapy, the levels of the fingerprint should fall, and vanish altogether if the tumor has been eradicated. Indeed, in one of their patients, the study authors saw the cancer biomarker drop after surgery but then rise again, suggesting to them that the cancer wasn’t fully eradicated.

Because the technique requires sequencing a person’s whole genome, it’s not coming to a hospital near you in the immediate future, says study author Bert Vogelstein: “This is really personalized medicine. This is not something off the shelf…. This is something that has to be designed for each individual patient”. But with the cost of genome sequencing rapidly coming down in price, this kind of approach might not be too far away, and doctors could use it to catch a recurring cancer before it’s large enough to be visible to other methods, like CT scans.


By Andrew Moseman
Reprinted with permission from Discover

DNAWellnessinfo.com Resource: http://www.cbsnews.com/stories/2010/02/22/tech/main6232081.shtml

Blood Tests May Reveal Tumor Size is a post from: dnawellnessinfo.com

Scientists perfect quick, low-cost DNA test is a post from: dnawellnessinfo.com

2/11/10 – physorg.com

Led by ASU Regents’ Professor Stuart Lindsay, director of the Biodesign Institute’s Center for Single Molecule Biophysics, the ASU team is one of a handful that has received stimulus funds for a National Human Genome Research Initiative, part of the National Institutes of Health, to make DNA genome sequencing as widespread as a routine medical checkup.

The broad goal of this “$1000 genome” initiative is to develop a next-generation DNA sequencing technology to usher in the age of personalized medicine, where knowledge of an individual’s complete, 3 billion-long code of DNA information, or genome, will allow for a more tailored approach to disease diagnosis and treatment. With current technologies taking almost a year to complete at a cost of several hundreds of thousands of dollars, less than 20 individuals on the planet have had their whole genomes sequenced to date.

To make their research dream a reality, Lindsay’s team has envisioned building a tiny, nanoscale DNA reader that could work like a supermarket checkout scanner, distinguishing between the four chemical letters of the DNA genetic code, abbreviated by A, G, C, and T, as they rapidly pass by the reader.

To do so, they needed to develop the nanotechnology equivalent of threading the eye of a needle. In this case, the DNA would be the thread that could be recognized as it moved past the reader ‘eye.’ During the past few years, Lindsay’s team has made steady progress, and first demonstrated the ability to read individual DNA sequences in 2008—but this approach was limited because they had to use four separate readers to recognize each of the DNA bases. More recently, they demonstrated the ability to thread DNA sequences through the narrow hole of a fundamental building block of nanotechnology, the carbon nanotube.

Lindsay’s team relies on the eyes of nanotechnology, scanning tunneling- (STM) and atomic force- (ATM) microscopes, to make their measurements. The microscopes have a delicate electrode tip that is held very close to the DNA sample.

In their latest innovation, Lindsay’s team made two electrodes, one on the end of microscope probe, and another on the surface, that had their tiny ends chemically modified to attract and catch the DNA between a gap like a pair of chemical tweezers. The gap between these functionalized electrodes had to be adjusted to find the chemical bonding sweet spot, so that when a single chemical base of DNA passed through a tiny, 2.5 nanometer gap between two gold electrodes, it momentarily sticks to the electrodes and a small increase in the current is detected. Any smaller, and the molecules would be able to bind in many configurations, confusing the readout, any bigger and smaller bases would not be detected.

“What we did was to narrow the number of types of bound configurations to just one per DNA base,” said Lindsay. “The beauty of the approach is that all the four bases just fit the 2.5 nanometer gap, so it is one size fits all, but only just so!”

At this scale, which is just a few atomic diameters wide, quantum phenomena are at play where the electrons can actually leak from one electrode to the other, tunneling through the DNA bases in the process.

Each of the chemical bases of the DNA genetic code, abbreviated A, C, T or G, gives a unique electrical signature as they pass between the gap in the electrodes. By trial and error, and a bit of serendipity, they discovered that just a single chemical modification to both electrodes could distinguish between all 4 DNA bases.

“We’ve now made a generic DNA sequence reader and are the first group to report the detection of all 4 DNA bases in one tunnel gap,” said Lindsay. “Also, the control experiments show that there is a certain (poor) level of discrimination with even bare electrodes (the control experiments) and this is in itself, a first too.”

“We were quite surprised about binding to bare electrodes because, like many physicists, we had always assumed that the bases would just tumble through. But actually, any surface chemist will tell you that the bases have weak chemical interactions with metal surfaces.”

Next, Lindsay’s group is hard at work trying to adapt the reader to work in water-based solutions, a critically practical step for DNA sequencing applications. Also, the team would like to combine the reader capabilities with the carbon nanotube technology to work on reading short stretches of DNA.

More information: The Nano Letters research article can be accessed online at URL: http://pubs.acs.org/doi/pdfplus/10.1021/nl1001185

Provided by Arizona State University (news : web)

DNAWellnessinfo.com Resource:  http://www.physorg.com/news185129971.html

Scientists develop universal DNA reader to advance faster, cheaper sequencing efforts is a post from: dnawellnessinfo.com