Forum for Science, Industry and Business

Sponsored by:     3M 
Search our Site:

 

Simple twists of fate

30.09.2008
Brandeis researchers use advanced scientific techniques -- as well as binder clips and tape -- to reveal how gene regulation works

A novel Brandeis University study this week in PLoS Biology reports on some of the molecular gymnastics performed by a protein involved in regulating DNA transcription. Using state-of-the art tools, researchers observed the shape and behavior of individual DNA molecules bent into tight loops by Lac repressor, a protein from the bacterium E.coli that switches on and off individual genes.

The study brings scientists an important step closer to understanding the phenomenon of gene regulation, a process elemental to biology from maintaining cell stability in bacteria such as E. coli to helping facilitate the most complex processes of human development and disease. The research was carried out by former Brandeis Ph.D. student Oi Kwan Wong in collaboration with scientists from Wake Forest University and the University of North Carolina.

To switch some genes on or off, a protein has to bind to two different places on the gene simultaneously, creating a loop from the DNA. Although such loops are common, many of their features are poorly understood. Using atomic force microscopy and tethered particle motion (TPM), a technique pioneered at Brandeis, the researchers were able to look at single molecules of DNA to infer the shape of the loop, which is not visible. They discovered that many earlier models of loops were probably wrong because they required the DNA to bend and twist in ways incompatible with the behaviors the scientists observed in the single DNA molecules.

Atomic force microscopy enabled the researchers to view the shape of the DNA molecules, while TPM revealed the behavior of the DNA molecules. In the TPM experiments, a tiny plastic bead only a millionth of inch in diameter was attached to the end of a DNA molecule. By computer analysis of the bead movements seen in a microscope, the scientists were able to monitor the DNA as it looped and unlooped, revealing the details of the molecule's behavior.

But in addition to these sophisticated techniques, the researchers found a simple yet ingenious way to visualize just how the protein bent and twisted DNA: by creating three-dimensional models of the DNA loops using binder clips and tape. That simple trick helped the scientists determine which models were possible and which were unlikely.

"What we demonstrated in this paper is that, contrary to what many scientists thought, the structure of the protein is flexible and can take on different shapes, helping to minimize DNA bending or twisting in loops, and thus, maximize stable gene regulation," explained Wong's Ph.D. advisor, biochemistry professor Jeff Gelles. "We believe the protein has the ability to change its shape to accommodate different sized loops and different amounts of DNA, helping cells maintain genes in a switched on or switched off state."

"We think it is possible that the characteristics of this genetic switch are examples of a general phenomenon that helps explain gene regulation," said Gelles. Poor gene regulation is implicated in many diseases and cancers, and understanding how it works in even a simple bacterium may pave the way for the development of antibiotics.

"The key is that the protein can change shape "on the fly" to accommodate different kinds of loops, or different spacing between different parts of the DNA. This is the way that the protein may have evolved to make gene regulation more reliable," said Gelles.

Laura Gardner | EurekAlert!
Further information:
http://www.brandeis.edu

Further reports about: Brandeis DNA DNA molecules E.coli Regulation behavior loop molecular gymnastics single molecule technique twist

More articles from Life Sciences:

nachricht Dissolving protein traffic jam at the entrance of mitochondria
23.05.2019 | Albert-Ludwigs-Universität Freiburg im Breisgau

nachricht Producing tissue and organs through lithography
23.05.2019 | Goethe-Universität Frankfurt am Main

All articles from Life Sciences >>>

The most recent press releases about innovation >>>

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

Im Focus: The geometry of an electron determined for the first time

Physicists at the University of Basel are able to show for the first time how a single electron looks in an artificial atom. A newly developed method enables them to show the probability of an electron being present in a space. This allows improved control of electron spins, which could serve as the smallest information unit in a future quantum computer. The experiments were published in Physical Review Letters and the related theory in Physical Review B.

The spin of an electron is a promising candidate for use as the smallest information unit (qubit) of a quantum computer. Controlling and switching this spin or...

Im Focus: Self-repairing batteries

UTokyo engineers develop a way to create high-capacity long-life batteries

Engineers at the University of Tokyo continually pioneer new ways to improve battery technology. Professor Atsuo Yamada and his team recently developed a...

Im Focus: Quantum Cloud Computing with Self-Check

With a quantum coprocessor in the cloud, physicists from Innsbruck, Austria, open the door to the simulation of previously unsolvable problems in chemistry, materials research or high-energy physics. The research groups led by Rainer Blatt and Peter Zoller report in the journal Nature how they simulated particle physics phenomena on 20 quantum bits and how the quantum simulator self-verified the result for the first time.

Many scientists are currently working on investigating how quantum advantage can be exploited on hardware already available today. Three years ago, physicists...

Im Focus: Accelerating quantum technologies with materials processing at the atomic scale

'Quantum technologies' utilise the unique phenomena of quantum superposition and entanglement to encode and process information, with potentially profound benefits to a wide range of information technologies from communications to sensing and computing.

However a major challenge in developing these technologies is that the quantum phenomena are very fragile, and only a handful of physical systems have been...

Im Focus: A step towards probabilistic computing

Working group led by physicist Professor Ulrich Nowak at the University of Konstanz, in collaboration with a team of physicists from Johannes Gutenberg University Mainz, demonstrates how skyrmions can be used for the computer concepts of the future

When it comes to performing a calculation destined to arrive at an exact result, humans are hopelessly inferior to the computer. In other areas, humans are...

All Focus news of the innovation-report >>>

Anzeige

Anzeige

VideoLinks
Industry & Economy
Event News

SEMANTiCS 2019 brings together industry leaders and data scientists in Karlsruhe

29.04.2019 | Event News

Revered mathematicians and computer scientists converge with 200 young researchers in Heidelberg!

17.04.2019 | Event News

First dust conference in the Central Asian part of the earth’s dust belt

15.04.2019 | Event News

 
Latest News

Plumbene, graphene's latest cousin, realized on the 'nano water cube'

23.05.2019 | Materials Sciences

New flatland material: Physicists obtain quasi-2D gold

23.05.2019 | Materials Sciences

New Boost for ToCoTronics

23.05.2019 | Physics and Astronomy

VideoLinks
Science & Research
Overview of more VideoLinks >>>