Forum for Science, Industry and Business

Sponsored by:     3M 
Search our Site:

 

Preventing cells from getting the kinks out of DNA

25.05.2010
New action mechanism for topoisomerases could help improve antibiotics, anticancer drugs

Many standard antibiotics and anti-cancer drugs block the enzymes that snip the kinks and knots out of DNA – DNA tangles are lethal to cells – but the drugs are increasingly encountering resistant bacteria and tumors.

A new discovery by University of California, Berkeley, biochemists could pave the way for new research into how to re-design these drugs to make them more effective poisons for cancer cells and harmful bacteria.

"The development of the anti-bacterial and anti-tumor agents that target these enzymes thus far has been done entirely in the absence of any visualization of how these drugs actually interact with the protein itself. And they have done remarkably well," said James Berger, UC Berkeley professor of molecular and cell biology. "But we have increasing problems of resistance to these drugs. Being able to see how these drugs can interact with the enzyme and DNA is going to be critical to developing the next generation of therapeutics that can be used to overcome these resistance problems."

Berger and colleagues at Emerald BioStructues of Bainbridge Island, Wash., and Vanderbilt University in Nashville, Tenn., report their new findings in a paper to be printed in the journal Nature and made available last week as an advance online publication at http://www.nature.com.

The tangles in DNA, like those in a string of holiday lights, are a result of packing some six feet of DNA into a cell nucleus so small that it is invisible to the naked eye. Every time a cell divides, it has to unpack, duplicate and repack its DNA, generating about a million tangles among the newly-copied chromosomes in the process.

As Berger has shown in previous work, enzymes called topoisomerases home in on the sharp turns in a knot and then progressively snip the DNA, unloop it, and restitch it flawlessly. If, however, the enzyme slips up, that one snip can turn into a potentially mutagenic or cell-killing DNA break.

While the protein structure of these topoisomerases is known, the details of the chemical reactions that take place between the enzyme and DNA, and their reaction with the drugs that bind both, remain a mystery, Berger said. In fact, one of the main puzzles is why antibiotics like ciprofloxacin (Cipro) and anti-cancer drugs like etoposide, which vary widely in structure, have the same effect: jamming the enzyme and causing a break in the double-stranded DNA helix.

Berger and his colleagues found a way to obtain a picture that shows the interaction of the protein bound to DNA. The next step is to do the same for a drug bound to the protein/DNA complex, getting an image of exactly how these drugs interfere with the knot elimination machinery.

"The technique we used to trap this complex so that we could actually crystallize it and image it we think now gives us a handle on how to go after drug-bound complexes of human topoisomerases that have long eluded the field," said Berger, who also is a staff scientist at Lawrence Berkeley National Laboratory (LBNL).

The scientists' new picture of the enzyme bound to DNA also turned up something totally unexpected. Most enzymes that bind DNA to snip or stitch it together use two metal ions – typically two magnesium ions – to catalyze the reaction. Berger found that type II topoisomerases, which target double-stranded DNA, make use of only one of their two magnesium ions and instead use the amino acid arginine as their second catalytic center. The second magnesium merely provides structural integrity to the protein.

"We stumbled upon a new kind of cleavage mechanism for DNA, an example of a protein that uses a completely new approach for the same mechanism," Berger said. "It speaks to the evolutionary plasticity and adaptability of nature that continuously amazes us with finding new ways to carry out reactions that it needs to perform."

Berger now plans to use his trick to trap the enzyme on a short segment of DNA, allowing him to collect enough to crystallize and analyze in an X-ray beam from LBNL's Advanced Light Source, to trap both drug and enzyme on DNA. Once crystallized and imaged, he will have the first full picture of a topoisomerase interacting the way it does in a real cancer cell or microbe.

Berger's co-authors are UC Berkeley graduate student Bryan H. Schmidt; chemist Alex B. Burgin of Emerald BioStructures; and biochemists Joseph E. Deweese and Neil Osheroff of Vanderbilt University School of Medicine. The X-ray crystallography of the protein/DNA complex was conducted in Stanley Hall at the UC Berkeley branch of the California Institute for Quantitative Biosciences (QB3), with which Berger is affiliated.

The work was funded by grants from the National Cancer Institute of the National Institutes of Health, including some funds administered through the American Recovery and Reinvestment Act (ARRA) of 2009.

Robert Sanders | EurekAlert!
Further information:
http://www.berkeley.edu

More articles from Life Sciences:

nachricht Fingerprint' technique spots frog populations at risk from pollution
27.03.2017 | Lancaster University

nachricht Parallel computation provides deeper insight into brain function
27.03.2017 | Okinawa Institute of Science and Technology (OIST) Graduate University

All articles from Life Sciences >>>

The most recent press releases about innovation >>>

Die letzten 5 Focus-News des innovations-reports im Überblick:

Im Focus: Giant Magnetic Fields in the Universe

Astronomers from Bonn and Tautenburg in Thuringia (Germany) used the 100-m radio telescope at Effelsberg to observe several galaxy clusters. At the edges of these large accumulations of dark matter, stellar systems (galaxies), hot gas, and charged particles, they found magnetic fields that are exceptionally ordered over distances of many million light years. This makes them the most extended magnetic fields in the universe known so far.

The results will be published on March 22 in the journal „Astronomy & Astrophysics“.

Galaxy clusters are the largest gravitationally bound structures in the universe. With a typical extent of about 10 million light years, i.e. 100 times the...

Im Focus: Tracing down linear ubiquitination

Researchers at the Goethe University Frankfurt, together with partners from the University of Tübingen in Germany and Queen Mary University as well as Francis Crick Institute from London (UK) have developed a novel technology to decipher the secret ubiquitin code.

Ubiquitin is a small protein that can be linked to other cellular proteins, thereby controlling and modulating their functions. The attachment occurs in many...

Im Focus: Perovskite edges can be tuned for optoelectronic performance

Layered 2D material improves efficiency for solar cells and LEDs

In the eternal search for next generation high-efficiency solar cells and LEDs, scientists at Los Alamos National Laboratory and their partners are creating...

Im Focus: Polymer-coated silicon nanosheets as alternative to graphene: A perfect team for nanoelectronics

Silicon nanosheets are thin, two-dimensional layers with exceptional optoelectronic properties very similar to those of graphene. Albeit, the nanosheets are less stable. Now researchers at the Technical University of Munich (TUM) have, for the first time ever, produced a composite material combining silicon nanosheets and a polymer that is both UV-resistant and easy to process. This brings the scientists a significant step closer to industrial applications like flexible displays and photosensors.

Silicon nanosheets are thin, two-dimensional layers with exceptional optoelectronic properties very similar to those of graphene. Albeit, the nanosheets are...

Im Focus: Researchers Imitate Molecular Crowding in Cells

Enzymes behave differently in a test tube compared with the molecular scrum of a living cell. Chemists from the University of Basel have now been able to simulate these confined natural conditions in artificial vesicles for the first time. As reported in the academic journal Small, the results are offering better insight into the development of nanoreactors and artificial organelles.

Enzymes behave differently in a test tube compared with the molecular scrum of a living cell. Chemists from the University of Basel have now been able to...

All Focus news of the innovation-report >>>

Anzeige

Anzeige

Event News

International Land Use Symposium ILUS 2017: Call for Abstracts and Registration open

20.03.2017 | Event News

CONNECT 2017: International congress on connective tissue

14.03.2017 | Event News

ICTM Conference: Turbine Construction between Big Data and Additive Manufacturing

07.03.2017 | Event News

 
Latest News

Northern oceans pumped CO2 into the atmosphere

27.03.2017 | Earth Sciences

Fingerprint' technique spots frog populations at risk from pollution

27.03.2017 | Life Sciences

Big data approach to predict protein structure

27.03.2017 | Life Sciences

VideoLinks
B2B-VideoLinks
More VideoLinks >>>