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.