predict RNA polymerase and promoter sequence interaction by auto dock docking

Question

[miravet65]

hi I want checking interaction between promoter sequence and RNA polymerase but i dont know what form of DNA must be select for this predict. (A,Z,B). RNA polymerase in human is including different sub unit about 12 subunit. for checking this interaction which of sub unit must be select. TBP, TAF ,TFIIH ,RpB1 i think, i must check each sub unit separately with promoter ? if you tell your idea , you can help me. thanks

Answer 1

[Carlo Yague]

The RNA polymerase itself does not have strong sequence preference for binding. After all, it reads all kind of DNA sequences. However transcription factors responsible for PIC assembly have promoter sequence specificity. I'm mostly thinking of the TBP (TATA binding protein) that binds TATA boxes. It could be a good place to start.

[miravet65]

thanks. your words are correct but some promoters have not TATAbox element for example Inr element that is a problem for me. i read a paper that mention a subunit of RNApol . RpB1 binding to promoter that isnt transcription factor

[Carlo Yague]

Do you have the reference of that paper ? I didn't know about that.