Vital cues for cancer prevention through DNA repairing gene

Naveen Kumar, TNN, Mar 6, 2010, 10.23pm IST

VARANASI: Now, the study of DNA repairing gene using single nucleotide polymorphism (SNP) marker would provide vital cue for cancer prevention, especially neck and head that comprises of as many as seven different types of cancer in the facial region. In addition, the study would also enable early prediction of much feared breast cancer in women.

While a team of scientists is studying the genomics in cancer, especially the squamous cell carcinoma in neck, head and breast region under the Hap Map project, the case studies in the last five years have revealed interesting contribution of DNA repairing genes including P53 associated genes, where SNP can be used as a marker for prompt diagnostic purpose.

Senior scientist Central Drug Research Institute Lucknow Dr SK Rath told TOI on Saturday, “The studies have shown that P53 associated genes play a vital role in DNA repair and act as tumour suppressor. It changes the DNA repair scene and plays pivotal role in protection against mutagenic and cytotoxic effects of DNA damage that also prevents cancer.” Similarly, SNP could also provide vital cue for DNA repairing in BRAC 1 and 2 genes that are believed to cause breast cancer in women, he added.

It is to be mentioned here that Dr Rath is a key member of the team that studied genotype of cancerous and non-cancerous cells under the project in the Xth five-year plan. Now, the team is researching on SNP of different people including smokers and non-smokers, drinkers and non-drinkers, where the cause of cancer

could not be ascertained.

Saying that million of SNPs exist in human genome that occur in gene within the regulatory region, Dr Rath emphasised that the method detects the most common type of variation in the genome, as it cater to small alteration, providing better scope for prediction. The SNP markers are preferred for population genomic disease association and are good indicators of squamous cell carcinoma in neck and head region that includes cancers of oral cavity, pharynx, nasopharynx, oropharynx, hypopharynx and tongue, he added.

Stressing that cancers of neck and head region are growing at alarming rate in states like UP, he said the case studies in Lucknow revealed that out of 100 cancer patients, the number of patients with cancer in the neck and head region increased from 30 to 49 (150 per cent increase) in the last five years. Worldwide, it is the fifth most common type of cancer affecting over one million population annually, he concluded.

DNAWellnessinfo.com Resource:  http://timesofindia.indiatimes.com/city/varanasi/-Vital-cues-for-cancer-prevention-through-DNA-repairing-gene/articleshow/5648729.cms

A First: Diagnosis By DNA

Matthew Herper, 02.25.10, 11:20 AM EST
Forbes Magazine dated March 15, 2010

Last year a five-month-old boy in Turkey stopped gaining weight and became dehydrated despite getting plenty of liquids. Specialists in Istanbul suspected Bartter’s syndrome, a potentially fatal kidney disorder that afflicts one in 100,000 babies, causing dangerously low levels of potassium and salt.

To confirm their hunch they sent a blood sample to Yale Medical School geneticist Richard Lifton. They asked him to determine whether the baby had the gene defect implicated in Bartter’s. But Lifton thought that Bartter’s might not be the culprit. So he did something that would have been prohibitively expensive a few years ago. He deciphered the DNA letters for all the baby’s genes. The gene scan revealed that the baby’s problem was not Bartter’s but something else called congenital chloride diarrhea, which also lowers salt levels. The result means that the baby, now doing better on a special diet, could be treated with drugs if his condition gets worse.

The case, published in the Proceedings of the National Academies of the Sciences in October, may be the first in which the results of DNA sequencing have altered treatment of a patient. Does this herald the beginning of a new kind of medicine in which patients with unexplained symptoms get their DNA sequenced? Yes, says Lifton: “This will be a court of last resort to try and identify causes of disease.”

Gene researchers have talked for years about how sequencing will transform medicine. Now that sequencing is cheap this transformation is under way. The cost of deciphering all 6 billion letters in the human genome has dropped from $1 million in 2007 to less than $20,000 today. Lifton used a two-step method to extract and sequence only the 1% of those letters that contain known genes, lowering the price to $2,500. New DNA sequencers just introduced by Illumina ( ILMN – news – people ) (whose model Lifton used) and Life Technologies ( LIFE – news – people ) could lower the cost of sequencing a whole genome to below $3,000 by year-end.

DNA sequencers haven’t been approved for use in medical testing, and insurers don’t pay for sequencing. But peering into DNA is becoming an option for wealthy patients with rare and scary diseases. Knome, a privately held company in Cambridge, Mass., started out in 2008 charging $350,000 to arrange sequencing and interpret the data for wealthy patrons as a vanity project. Now it offers the scans for as little as $25,000. Chief Executive Jorge Conde says several patients hoping to improve their care are among his customers.

The $600 million annual market for DNA sequencers is still all about research, with Illumina holding a 60% market share. But numerous companies are already jockeying for position in anticipation of a big future medical-test market.

Cancer patients may be among the first to benefit from DNA sequencing technology. In one early example of how this may work, Marco Marra, a researcher at the Michael Smith Genome Sciences Centre in Vancouver, last year sequenced the genes from a tumor that had spread from an 80-year-old patient’s tongue to his lungs. There is no standard therapy for this type of tumor. But the gene scan found the tumor was making large amounts of a growth-promoting protein called RET. When the patient’s medicine was switched to Pfizer ( PFE – news – people )’s Sutent, a drug that blocks this protein, the tumor shrank, according to a report in Nature.

A looming question is how the Food & Drug Administration will regulate sequencing technology. It could treat DNA sequencing like genetic tests and require separate approvals for each use. Some equipment makers hope for a faster path in which doctors practicing a new medical specialty emerge to evaluate and interpret gene scans, as radiologists do with X-rays. Clifford Reid, chief executive of Complete Genomics, which has finished 50 genomes, is skeptical that it will be that easy. “The FDA has been very quiet up until now,” he says. “We all have to expect the FDA to be intimately involved with these new tests.”

DNAWellnessinfo.com Resource:  http://www.forbes.com/forbes/2010/0315/health-illumina-genome-cancer-diagnosis-by-dna.html

Scientists develop universal DNA reader to advance faster, cheaper sequencing efforts

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

A new theory of how low doses of antibioitics create antibiotic resistance

Feb 11, 2010 – usatoday.com

E.coli bacteria is seen under a microscope.

CAPTION

By Centers for Disease Control

Exposure to low levels of antibiotics increases mutations in E. coli and Staphylococcus bacteria hundreds of time more than normal, making the creation of drug-resistance strains more likely, says a paper in today’s edition of the journal Molecular Cell.

This finding adds to concerns about antibiotic resistance brought on by poor prescriptions practices among doctors, patients who don’t take all their medicine and even low doses of antibiotics given to help animals grow faster.

The researchers found that while low levels of antibiotics may not be enough to kill off the bacteria, they still stress them. That stress causes them to produce free radicals, says James Collins, a biomedical engineer at Boston University and one of the paper’s authors.

Those free radicals are produced by oxidation, a process that’s known to damage cells. In the case of bacteria, the free radicals damage the bacteria’s DNA, causing some of the affected bugs to mutate.

Two and a half years ago Collins’ group began looking at how bacteria respond to antibiotics. It was then that they discovered that antibiotics can stimulate the pathways that create free radicals in bacteria.

A year ago they started considering what other implications their discovery might have.

“We wondered whether sub-lethal levels still produce free radicals. We know the cells wouldn’t die, but we know that free radicals can damage DNA, and that increases mutenigenesis,” he says.

And that’s exactly what they found. Basically, if the antibiotic dose isn’t high enough to kill every bacteria in sight, “you could be creating a zoo with a wide range of mutations,” he says.

The  finding is important “within the context of our understanding — or lack of understanding — of how bacteria become resistant to antibiotics,” says Deborah Hung, a molecular biologist at Massachusetts General Hospital, who wrote an accompanying Perspective piece on the article.

The  truth is that no one really knows exactly how bacteria become resistant to antibiotics, says Hung. So knowing that low levels of antibiotics might potentially increase the random chance that bacteria might mutate into resistant forms could have important implications for medicine.

By Elizabeth Weise

DNAWellnessinfo.com Resource:  http://content.usatoday.com/communities/sciencefair/post/2010/02/a-new-theory-of-how-low-doses-of-antibioitics-create-antibiotic-resistance/1

Living fast? Scientists show lifespan is linked to DNA

Ian Sample, science correspondent
guardian.co.uk, Sunday 7 February 2010 19.55 GMT

Scientists have isolated a gene sequence that appears to determine how fast our bodies age, the first time a link between DNA and human lifespan has been found.

The discovery could have a profound impact on public health and raises the best hope yet for drugs that prevent the biological wear and tear behind common age-related conditions such as heart disease and certain cancers.

The work is expected to pave the way for screening programmes to spot people who are likely to age fast and be more susceptible to heart problems and other conditions early in life. People who test positive for the gene variant in their 20s could be put on cholesterol-lowering statin drugs and encouraged to exercise, eat healthily and avoid smoking.

The breakthrough is unlikely to lead to drugs that dramatically extend lifespan, but doctors say it may help prolong the lives of patients whose genes make them susceptible to dying young.

The research gives the kind of insight into the biology of ageing that has not emerged from work on other strategies that claim to extend lifespan, such as consuming vast quantities of antioxidants or pursuing a severely calorie-restricted diet.

“This may help us identify patients who are at a greater risk of developing common age-related diseases so we can focus more attention on them,” said Professor Nilesh Samani, a cardiologist at the University of Leicester, who led the research.

The research highlights the difference between chronological age and biological age, the latter of which is determined by our genetic makeup and lifestyle factors, such as diet and smoking. Two people of the same age can have biological ages that differ by more than 10 years.

A team led by Samani and Professor Tim Spector at King’s College, London found a common sequence of DNA was strongly linked to a person’s biological age. In a study of nearly 3,000 people, around 38% inherited one copy of the gene variant and were biologically three to four years older than those who did not carry the sequence.

A minority of 7% inherited two copies of the DNA sequence and were on average six to seven biological years older. The majority of the population, 55%, do not carry any copies of the variant.

The study, published in the journal Nature Genetics, was prompted by the huge variability in the age at which people develop medical problems that are often considered diseases of the elderly.

“I see patients in their 80s with high blood pressure who have healthy coronary arteries and I see people in their 40s who don’t seem to have any risk factors yet have advanced heart disease,” Samani said. “We think this kind of variability must have something to do with premature ageing.”

Most of the cells in our bodies contain long molecules of DNA called chromosomes that have protective caps at either end called telomeres. Every time a cell divides, the telomeres shorten, like plastic tips fraying on a shoelace. When the telomeres become very short, the cell starts to malfunction and show signs of ageing.

From blood samples, Samani and Spector found a particular gene sequence was more common in people who had unusually short telomeres for their age. The section of DNA was found on chromosome three, next to a gene called TERC, which makes an enzyme that repairs telomeres when they shorten.

People who carry one or two copies of the genetic sequence probably make less of the enzyme, called telomerase, when they are growing in the womb. This means they are born with shorter telomeres, and so are prone to ageing more quickly.

“The effect may be built in at a very early stage in life. If you’re born with shorter telomeres, there’s evidence you will be prone to heart disease and other age-related diseases,” Samani said.

Scientists are unlikely to reverse the ageing process by boosting telomerase in people’s bodies. Telomerase is almost completely deactivated after birth, but is switched back on in cancer cells so they can divide endlessly without dying. “Introducing telomerase might protect you from heart disease, but if you turn it on willy nilly you could cause cancer instead,” Samani said.

DNAWellnessinfo.com Resource:  http://www.guardian.co.uk/science/2010/feb/07/ageing-genetics

Premature birth gene clue found

Friday, 5 February 2010 – bbc news

DNA differences which appear to affect the risk of giving birth early have been found by US scientists.

The US National Institutes of Health study found the variants in both babies and mothers, a US conference was told.

It is thought they may play a role in controlling immune responses which could theoretically trigger labour if they become too powerful.

Premature birth – which accounts for 7% of UK births – is one of the biggest threats to a baby’s future health.

The causes of premature birth are poorly understood, although infections and other medical complications are blamed in some cases.

The study looked at 700 DNA variants in 190 genes in women who delivered early, and those who carried their baby to term.

The cord blood of the babies was also tested for these variations.

They narrowed the search down to a handful of gene variations found more often in the women who gave birth prematurely, and their babies.

In particular, babies who carried the gene for the “Interleukin 6 receptor” were more likely to be born early.

This was a good candidate gene because Interleukin 6 is produced by cells in response to infection and is involved in inflammation.

High levels of Interleukin 6 in the amniotic fluid and foetal blood have been linked to the onset of premature labour.

Baby threat

Dr Roberto Romero, who led the study, said: “Our hypothesis is that the mother and/or the foetus signal the onset of preterm labour when the environment inside the uterus is unfavourable and threatens the survival of the maternal-foetal pair.

“When there is an infection in the uterus, the onset of premature labour appears to have survival value – it would allow the mother to rid herself of infected tissue and preserve her ability to have future pregnancies.”

The chief executive of charity Bliss, Andy Cole, welcomed the study results.

“In England alone, 54,000 babies are born prematurely each year, a third of these for no known reason,” he said.

“The development of a reliable test for identifying these mothers is vital in ensuring our most vulnerable babies have the best possible outcomes.”

DNAWellnessinfo.com Resource:  http://news.bbc.co.uk/2/hi/health/8498712.stm

Crash-Test Reveals DNA Traffic Control

1/29/10 – HHMI News

Enzymes that copy DNA don’t travel on a lonely highway, but instead ply their trade on crowded interstates. Now, Howard Hughes Medical Institute researchers have discovered that when those DNA-copying machines run head-on into oncoming traffic, they kick the obstacles out of their way.

DNAi_replication_354.mov

A detailed view of DNA replication showing both strands of the DNA double helix acting as templates for the new DNA strands.

Video: HHMI Biointeractive

“Losing an RNA transcript is no big deal. But the consequences would be dire if the replisome fell apart every time it met an RNA polymerase. ”
Michael E. O’Donnell

The finding, reported in the January 29, 2010, issue of Science, reveals new details about the “rules of the road” that help ensure that cells make accurate copies of their genetic material – essential for producing healthy new cells.

In preparation for cell division, cells rely on complex protein machines to pull apart and untwist opposing strands of DNA. Once the double helix is untwisted, both strands are copied to produce two complete sets of the genome. The replisome is a protein complex that moves at high speed for long distances on DNA, wrenching the helix apart as it goes. The replisome shares its tracks with other proteins that transcribe DNA into messenger RNA, which is then used to produce proteins. Sometimes these convoys move in opposite directions – and collisions are unavoidable. HHMI investigator Michael O’Donnell of Rockefeller University wondered what happens to the machines when they collide.

To find out, O’Donnell and his colleague Richard Pomerantz reconstructed a cellular traffic accident in a test tube. To do that, they first had to assemble the replisome on DNA in a test tube, an endeavor that required years of effort in O’Donnell’s lab. Once his group had successfully reconstructed a replisome from the relatively simple bacteria E. coli, they were ready to begin their experiments.

They set an RNA polymerase—the enzyme that transcribes DNA into RNA—in motion on a piece of DNA and then stalled it. Next, they assembled the components that make up the DNA replication machine at the opposite end of the DNA and nudged this complex into action. Then they analyzed the aftermath of the resulting collision.

They found that the DNA replication machine managed to copy the full length of the DNA molecule, indicating that it had traveled the full distance and somehow got past the RNA polymerase. Further analysis suggested that the DNA replication machine stops when it encounters the RNA polymerase, shoves the RNA polymerase off the DNA, and then proceeds.

Researchers knew that a protein called Mfd kicks RNA polymerase off DNA when it has stalled out because a section of DNA is damaged. In the current experiment, RNA polymerase was stalled by another means. But O’Donnell and Pomerantz wondered whether Mfd would help the DNA replication machinery move through RNA polymerase faster even in this case.

O’Donnell and Pomerantz repeated the crash test, this time including Mfd in the mix. With Mfd present, the replisome made even more full-length copies of the DNA than it did without Mfd, suggesting that Mfd helps give RNA polymerase the boot.

Scientists have reported conflicting observations about whether replisomes fall apart when they hit a road block, and O’Donnell’s results provide additional evidence that the replisome is hearty. “The replisome is very stable,” says O’Donnell. “It just sits there until it finally wins.”

It makes sense biologically to give the replisome priority, he adds. “Losing an RNA transcript is no big deal. But the consequences would be dire if the replisome fell apart every time it met an RNA polymerase. These collisions are probably common in the cell, so keeping the replisome moving ensures that DNA replication proceeds neatly and rapidly.”

O’Donnell is now searching for other factors that push the replisome through blocks. He’d also like to know whether the replisome in eukaryotic cells, such as yeast or mammalian cells, behaves similarly to the bacterial complex he and Pomerantz have studied. The replication machinery in those kinds of cells is much more complicated, and his group is still working on recreating the mammalian replisome in a test tube.

DNAWellnessinfo.com Resource:  http://www.hhmi.org/news/odonnell20100129.html

Missing DNA tied to obesity

Last Updated: Wednesday, February 3, 2010 | 6:02 PM ET
CBC News

Some severely obese people are missing a set of genes, a new study has found.

Researchers have found a small proportion of obese people are born without 30 or so of the estimated 30,000 genes in the human genome.

This deletion of genes was not found in any subjects of normal weight, the team from Imperial College London and their colleagues in Europe, the United States and Montreal reported in Wednesday’s issue of the journal Nature.

The missing genes may account for seven out of 1,000 cases of morbid obesity — people with a body mass index, or BMI, over 40, the study found. The body mass index is a tool used to determine the healthy weight range for a particular height. A BMI over 30 is considered obese and 25 to 29.9 is overweight.

The recent rise in obesity in the developed world has been attributed to an abundance of unhealthy food and too little exercise, but the way people respond to these environmental factors is often genetic, said Prof. Phillipe Froguel, lead author of the study at the School of Public Health at Imperial College London.

“It is becoming increasingly clear that for some morbidly obese people, their weight gain has an underlying genetic cause,” Froguel said in a news release.

“If we can identify these individuals through genetic testing, we can then offer them appropriate support and medical interventions, such as the option of weight-loss surgery, to improve their long-term health.”

Searched general population
In the first part of the study, researchers looked for the genes in obese teenagers and adults with learning difficulties or delayed development. They found 31 severely obese people with nearly identical deletions in one copy of their DNA.

The second part of the study looked at the genomes of 16,053 European people in the general population, reflecting a range of weights. Nineteen people in this group were missing the same set of genes, and all were morbidly obese.

Those lacking the genes tended to be normal weight as toddlers, overweight during childhood and severely obese as adults, the researchers said.

The study is the first to confirm that severe obesity in otherwise physically healthy individuals can be caused by a rare deletion of DNA, the authors said.

Until now, individual genes linked to weight gain have had a relatively modest effect of about two pounds.

“The genetic change identified in this study is much less common but leads to much more substantial changes in the body weight of the individuals that it affects,” study co-author Dr. Robert Sladek of McGill University in Montreal said in a release Wednesday.

Researchers have found a similar modest effect with genes influencing Type 2 diabetes. The approach the obesity researchers used — identifying the deletion in very obese people and then looking for the variant in a much broader population — could help to identify genetic influences on Type 2 diabetes and other diseases, the researchers said.

They now plan to study the function of the missing genes. Previous studies have suggested that deletions of these genes may be linked with delayed development, autism and schizophrenia.

DNAWellnessinfo.com Resource: http://www.cbc.ca/health/story/2010/02/03/obesity-dna-deletion.html

HIV Researchers Solve Key Puzzle After 20 Years of Trying

ScienceDaily (Jan. 31, 2010) — Researchers have made a breakthrough in HIV research that had eluded scientists for over 20 years, potentially leading to better treatments for HIV, in a study published January 30 in the journal Nature.

The researchers, from Imperial College London and Harvard University, have grown a crystal that reveals the structure of an enzyme called integrase, which is found in retroviruses like HIV. When HIV infects someone, it uses integrase to paste a copy of its genetic information into their DNA.

Prior to the new study, which was funded by the Medical Research Council and the US National Institutes of Health, many researchers had tried and failed to work out the three-dimensional structure of integrase bound to viral DNA. New antiretroviral drugs for HIV work by blocking integrase, but scientists did not understand exactly how these drugs were working or how to improve them.

Researchers can only determine the structure of this kind of molecular machinery by obtaining high quality crystals. For the new study, researchers grew a crystal using a version of integrase borrowed from a little-known retrovirus called Prototype Foamy Virus (PFV). Based on their knowledge of PFV integrase and its function, they were confident that it was very similar to its HIV counterpart.

Over the course of four years, the researchers carried out over 40,000 trials, out of which they were able to grow just seven kinds of crystals. Only one of these was of sufficient quality to allow determination of the three-dimensional structure.

Dr Peter Cherepanov, the lead author of the study from the Department of Medicine at Imperial College London, said: “It is a truly amazing story. When we started out, we knew that the project was very difficult, and that many tricks had already been tried and given up by others long ago. Therefore, we went back to square one and started by looking for a better model of HIV integrase, which could be more amenable for crystallization. Despite initially painstakingly slow progress and very many failed attempts, we did not give up and our effort was finally rewarded.”

After growing the crystals in the lab, the researchers used the giant synchrotron machine at the Diamond Light Source in South Oxfordshire to collect X-ray diffraction data from these crystals, which enabled them to determine the long-sought structure. The researchers then soaked the crystals in solutions of the integrase inhibiting drugs Raltegravir (also known as Isentress) and Elvitegravir and observed for the first time how these antiretroviral drugs bind to and inactivate integrase.

The new study shows that retroviral integrase has quite a different structure to that which had been predicted based on earlier research. Availability of the integrase structure means that researchers can begin to fully understand how existing drugs that inhibit integrase are working, how they might be improved, and how to stop HIV developing resistance to them.

DNAWellnessinfo.com Resouce:  http://www.sciencedaily.com/releases/2010/01/100131142438.htm

Researchers Find New Way To Study How Enzymes Repair DNA Damage

January 28, 2010

Researchers at Ohio State University have found a new way to study how enzymes move as they repair DNA sun damage — and that discovery could one day lead to new therapies for healing sunburned skin.

Ultraviolet (UV) light damages skin by causing chemical bonds to form in the wrong places along the DNA molecules in our cells. Normally, other, even smaller molecules called photolyases heal the damage. Sunburn happens when the DNA is too damaged to repair, and cells die.

Photolyases have always been hard to study, in part because they work in tiny fractions of a second. In this week’s online edition of the Proceedings of the National Academy of Sciences, Ohio State physicist and chemist Dongping Zhong and his colleagues describe how they used ultra-fast pulses of laser light to spy on a photolyase while it was healing a strand of DNA.

This is the first time that anyone has observed this enzyme motion without first attaching a fluorescent molecule to the photolyase, which disturbs its movements. They were able to see the enzyme’s motion to help the healing process as it happens in nature.

“Now that we have accurately mapped the motions of a photolyase at the site of DNA repair, we can much better understand DNA repair at the atomic scale, and we can reveal the entire repair process with unprecedented detail,” said Zhong, the Robert Smith Associate Professor of Physics, and associate professor in the departments of chemistry and biochemistry at Ohio State.

Such small motions are very hard to study. Typically, researchers deal with the problem by attaching tiny bits of fluorescent molecules to the enzymes they are trying to study. But adding an extra molecule to an enzyme such as photolyase could change how it moves.

“Once you tag it, you can’t be sure that the motions you detect are the true motions of the molecule as it would normally function,” Zhong explained.

So instead of using tags, he and his team took laser “snapshots” of a single photolyase in action in the laboratory. They mapped the shape and position of the photolyase molecule as it broke up the harmful chemical bonds in DNA caused by UV light. The whole reaction lasted only a few billionths of a second.

In nature, DNA avoids damage by converting UV rays into heat. Sunscreen lotions protect us by reflecting sunlight away from the skin, and also by dissipating UV as heat.

Sunburn happens when the DNA absorbs the UV energy instead of converting it to heat. This is due in part to the random position of the DNA molecule within our cells when the UV hits it. When the UV energy is absorbed, it triggers chemical reactions that form lesions — errant chemical bonds — along the DNA strand.

If photolyases are unable to completely repair the lesions, the DNA can’t replicate properly. Badly damaged cells simply die — that’s what gives sunburn its sting. Scientists also believe that chronic sun damage creates mutations that lead to diseases such as skin cancer.

More information: http://www.pnas.org/

Provided by The Ohio State University (news : web)

DNAWellnessinfo.com Resource:  http://www.physorg.com/news183913344.html