Gene-bender proteins may sway to DNA

Dec 04, 2006

Among the many genes packed into each cell of our body, those that get turned on, or expressed, are the ones that make us who we are. Certain proteins do the job of regulating gene expression by clasping onto key spots of DNA -- the nucleic acid that contains the genetic instructions.

How does the protein recognize a particular binding site" Structural changes in both the protein and DNA, sometimes with the DNA within the complex kinked or sharply bent, allow for the specific contacts needed for a tight DNA-protein fit.

Scientists think DNA is largely passive in this genetic tango. But new findings by Anjum Ansari, associate professor of biophysics at the University of Illinois at Chicago, suggest DNA may not be the wallflower that many had assumed.

To follow in real time the structural changes that accompany protein-DNA binding, Ansari and her UIC colleagues used a test protein from bacteria and applied a laser pulse lasting about 10 billionths of a second to heat up and disturb the protein-DNA complex. They watched the dynamics of the bound DNA in response to this perturbation.

Ansari's group was the first to apply the laser temperature-jump technique to study the dynamics of a protein-DNA complex.

The studies were done in collaboration with Donald Crothers, Sterling Professor Emeritus of chemistry at Yale University, who examined the protein-DNA interaction with the more traditional stopped-flow technique.

"While stopped-flow technique can capture dynamics of biomolecules occurring on millisecond time-scales or longer, the goal of this study was to extend the time-resolution down to sub-microseconds. It gave us a new time window on probing protein-DNA interactions," Ansari said.

That broader time window, obtained in combination with the stopped-flow measurements, provided the first direct observation of DNA bending when bound to a DNA-bending protein.

"We found that the time-scales on which DNA was bending were very similar to previously reported time-scales on which individual base-pairs that hold the two DNA strands together were transiently breaking. That led us to conclude that the DNA is able to bend or kink on its own, at weak points created by the transient opening of base-pairs, and that the protein recognizes and binds tightly to the bent DNA conformation."

Conclusions by Ansari and her colleagues deviate slightly from the conventional dogma that it is the protein that bends the DNA. She said the results raise important questions about the role that the DNA "bendability" plays in guiding the correct bending protein to the appropriate site on the DNA.

Ansari said the research adds to the basic understanding of how proteins recognize a specific binding site.

"Gaining better insights into protein-DNA interactions that control all aspects of gene regulation may prove useful for rational design of drugs to target specific sites on the DNA, whereby one can ultimately develop better gene-based therapies," she said.

Source: University of Illinois at Chicago

Explore further: How do our muscles work? Scientists reveal important new insights into muscle protein

add to favorites email to friend print save as pdf

Related Stories

Researchers find way to turn sawdust into gasoline

13 minutes ago

Researchers at KU Leuven's Centre for Surface Chemistry and Catalysis have successfully converted sawdust into building blocks for gasoline. Using a new chemical process, they were able to convert the cellulose ...

Virtual money and user's identity

14 minutes ago

Bitcoin is the new money: minted and exchanged on the Internet. Faster and cheaper than a bank, the service is attracting attention from all over the world. But a big question remains: are the transactions ...

Recommended for you

Genomes of malaria-carrying mosquitoes sequenced

4 hours ago

Nora Besansky, O'Hara Professor of Biological Sciences at the University of Notre Dame and a member of the University's Eck Institute for Global Health, has led an international team of scientists in sequencing ...

Bitter food but good medicine from cucumber genetics

4 hours ago

High-tech genomics and traditional Chinese medicine come together as researchers identify the genes responsible for the intense bitter taste of wild cucumbers. Taming this bitterness made cucumber, pumpkin ...

New button mushroom varieties need better protection

8 hours ago

A working group has recently been formed to work on a better protection of button mushroom varieties. It's activities are firstly directed to generate consensus among the spawn/breeding companies to consider ...

User comments : 0

Please sign in to add a comment. Registration is free, and takes less than a minute. Read more

Click here to reset your password.
Sign in to get notified via email when new comments are made.