I don't understand this sentence: "the NF-kB p65/RelA homodimer optimally recognizes a nine-base-pair target sequence containing two 5'-GGPuN 3'half sites and a central A:T base pair."(Cold Spring Harb Perspect Biol2009;1:a000075）
What is the sequence of this sentence describe?
Can anyone give me an explanation in detail?
Thank you
Hi Li,
DNA half sites are generally identification and binding sites of DNA binding Proteins like enhancers, Transcription factors etc. These cis sites in DNA are also called Half Sites because the base pairs are symmetrically identical e.g. 3'...ATTCGGTAGGCTTA..5' will be called as 3'ATTCGG5' Half site and a central T:A because after this half the base pair arrangement is symmetrical.
This type of arrangement is found probably to bind both sub units of Dimer.
Do let me know, if I explained you satisfactorily and let me know if you have more query
Hi Li,
DNA half sites are generally identification and binding sites of DNA binding Proteins like enhancers, Transcription factors etc. These cis sites in DNA are also called Half Sites because the base pairs are symmetrically identical e.g. 3'...ATTCGGTAGGCTTA..5' will be called as 3'ATTCGG5' Half site and a central T:A because after this half the base pair arrangement is symmetrical.
This type of arrangement is found probably to bind both sub units of Dimer.
Do let me know, if I explained you satisfactorily and let me know if you have more query
Hi Li,
Two half sites form the complete binding site on the DNA strands. So, two half sites constitute that region, usually upstream from a gene, where a DNA binding protein such as an intracellular receptor or transcription factor in this case will bind and eventually activate a gene. The two half sites can be palindromic (mirrored) or direct repeats, and are often separated by 3 or so base pairs. In this case, there is just a single, central A:T base pair on either side of which the two half sites are arranged. In the case you describe these are palindromic because the Nf-kB is a homodimer, i. e., symmetrical, each monomer recognizing and binding to its separate half site.
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