promoter binding site searching-why both strands?

[gocha_ada]

Hello !!!

I want to analyse promoters of a few genes. I never done something like that before. I found several programms sutaible for me. Most of them search transcription factors on both strands. Could somebody explaine me why?

Thanks in adavance

[moleculardude]

Hello there Gocha_ada!

Both strands are very important for promoter evaluation. This is because many transcriptional factors including enhancer elements (DNA binding factors) have been shown to bind to the sense AND anti-sense strands!

This is true especially with enhancer elements which can function on both strands due to looping mechanisms even up to several kb away!

cheers
Moleculardude

[cyberpostdoc]

Yes, some transcription factors help to separate the two strand before transcription start, therefore, binding motif they recognize might be on both strands.

[dharmanivi9@yahoo.com]

HI..i want to develop a tool tht can find promoter binding sites in E.coli??i have found several programs for tht but i couldn't find the specific pattern with which i can develop a tool?? can u please suggest me how i can found those patterns???