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The question about TATA sequence flexibility

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The question about TATA sequence flexibility

Postby Fantomas » Sat Aug 31, 2013 10:57 am

Good day :)
We know that:
The TATA box is the sequence in DNA found in the promoter region of genes in archaea and eukaryotes that is responsible for recognizing the RNA-polymerase.

http://en.wikipedia.org/wiki/TATA_box
I read this article about TATA-Binding Protein:
Second, the protein uses specially-placed amino acids to interact with DNA bases. As shown in the lower picture, four phenylalanine amino acids jam into the DNA minor groove and form the kinks that bend the DNA. There are also two symmetrical asparagine amino acids that form hydrogen bonds at the very center. The combination of the unusual flexibility of TATA DNA sequences and these specific hydrogen bonds allows TATA-binding protein to recognize the proper sequence.

http://www.rcsb.org/pdb/101/motm.do?momID=67
I would like to find out that does it mean? Why the TATA box is flexible? Because of two hydrogen bonds in A-T base pairs or maybe because of some other reason? It is easier to bend DNA at that places where there are two hydrogen bonds? But why? I looked at DNA molecule but I do not know where exactly it bends, does each bond bend itself? Or maybe the phosphodiester bonds are stretched and contracted when bending the DNA molecule (in case of circular DNAs)?
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Postby Fantomas » Mon Sep 02, 2013 6:21 pm

Does not anybody know the answer? :roll:
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