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Unusual twist found in protein-DNA pairing.

Cells keep the instructions for making proteins locked up in their genes. Each gene consist of DNA, which is made up of pairs of nucleotide bases strung together in a specific order. That order tells RNA what amino acids, the building blocks of proteins, to make -- but the instructions are in code. RNA molecules can read that code only if the base pairs split into strings of single nucleotides.

The locksmiths responsible fo splitting these pairs include a variety of specialized molecules, in particular one called the TATA-box binding protein (TBP). This protein gets its name from the nucleotide sequence it seeks out -- TATA, T for thymine, A for adenine.

Until now, geneticists and biochemists could only guess how TBP readied DNA pairs for unlocking. But the surprising results of two research groups working independently show that TBP kinks and stabilizes DNA in a way that makes it more receptive to other molecular locksmiths. The two teams describe their crystallization work in the Oct. 7 NATURE.

"[The results] show dramatic changes in the conformation of [DNA's] double helix, the like[s] of which have never been seen before in any DNA-protein complex," comments Aaron Klug of the Medical Research Council Laboratory of Molecular Biology in Cambridge, England. The findings set the stage for elucidating the steps that initiate the reading of the DNA code.

Shaped like a saddle, the TBP of the plant Arabidopsis thaliana causes the DNA that lies under it to arch sharply upward, conforming to the protein's concave shape, report structual biologist Joseph L. Kim and his colleagues at Rockefeller University in New York City.

Likewise, when saddle-shaped yeast TBP binds to DNA containing the TATA box, it causes that DNA to bend sharply in two places and the base pairs in between to lose their helical twist, says Paul B. Sigler, a structural biologist at Yale University.

"The structures agree very nicely," Kim says. Even though the two research teams used different DNA strands and types of TBP, both TBP molecules contain a 180-amino-acid section that links to the TATA box. No one knows what the rest of the TBP molecule does, he adds.

Scientists had thought DNA would orient along TBP much as a horse's back-bone fits under a saddle, says Sigler. Instead, eight DNA base pairs lie across the protein saddle. Amino acids sticking out of the saddle like stirrups wedge between the first and second and the seventh and eighth base pairs, causing the DNA to bend sharply there, he explains. The middle base pairs snuggle up under the saddle, helping to stabilize this new DNA configuration, adds Kim.

"You're not used to looking at such highly distorted DNA," says Kim. "It was a very unusual result, so it was probably beneficial that there were two independent results."
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Title Annotation:how TATA-box binding protein prepares DNA pairs for unlocking
Author:Pennisi, Elizabeth
Publication:Science News
Article Type:Brief Article
Date:Oct 16, 1993
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