Biologists Get First Look At DNA-Protein Binding Structure In An Archaeon

CHAMPAIGN, Ill. -- Biologists have answered a fundamental how-does-it-work question, involving the binding of DNA and protein, that eventually may lead to the ability to forge DNA into specific shapes for specific purposes. The researchers identified the binding structure of DNA and protein in ancient organisms -- hyperthermophilic archaeons -- pulled from the fiery, acidic mud of Yellowstone National Park. Their findings, reported in the March 12 issue of the journal Nature, shed light on how proteins attach to DNA to stabilize and protect it in harsh environments.

"The DNA has to store the genomic information, so the shape of its surface is variable," said Howard H. Robinson, a cell and structural biologist at the University of Illinois. "We've discovered that protein and DNA bind together in a more interesting way than was ever imagined. This research gives scientists a new avenue for looking at DNA-protein interactions."

In this case, the chromosomal protein Sac7d -- which to the DNA of a hyperthermophile archaeon is as abundant as the binding protein histone is to human DNA -- sticks itself snugly into small grooves between the rungs of DNA and causes the DNA to bend at a 72-degree angle.

"By knowing how this protein binds to DNA, we now understand which amino acids on the surface of the protein interact with the DNA," said Andrew H.-J. Wang, a professor of cell and structural biology. "The DNA-protein binding structure has been elusive. The way this protein binds to DNA, and how it distorts the DNA, is a very new finding. The protein kinks the DNA so that the DNA is sharply bent and stabilized."

To get this new view, the researchers formed a single crystal of the protein with pieces of DNA from the archaeons Sulfolobus acidocaldarius and S. solfataricus. After freezing the crystal with liquid nitrogen at minus 150 degrees Celsius, they were able to determine the three-dimensional structure of the binding complex using X-ray diffracti

Contact: Jim Barlow, Life Sciences Editor
University of Illinois at Urbana-Champaign

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