The Promoter reference article from the English Wikipedia on 24-Apr-2004 (provided by Fixed Reference: snapshots of Wikipedia from wikipedia.org)

Promoter

In genetics, a promoter is a DNA sequence that enables a gene to be transcribed. The promoter is recognized by RNA polymerase, which then initiates transcription.

The perfect promoter is called a canonical sequence.

Promoter sequences

Prokaryotic promoters

In prokaryotes, the promoter consists of two short sequences at -10 and -35 position upstream of the gene, that is, prior to the gene in the direction of transcription. The sequence at -10 is called the Pribnow box and usually consists of the six nucleotides TATAAT. The Pribnow box is absolutely essential to start transcription in prokaryotes. The other sequence at -35 usually consists of the six nucleotides TTGACA. Its presence allows a very high transcription rate.

   <-- upstream                                                          downstream -->

5'-XXXXXXXPPPPPXXXXXXPPPPPXXXXGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGXXXX-3'

           -35        -10     Gene to be transcribed

Probability of occurence of each nucleotide

 T    A    T    A    A    T

77%  76%  60%  61%  56%  82%

 T    T    G    A    C    A

69%  79%  61%  56%  54%  54%

Eukaryotic promoters

See Michael Levine and Robert Tjian. "Transcription regulation and animal diversity". Nature 424, 147 - 151 (10 July 2003) [1]

Binding

The binding of a promoter sequence (P) to a sigma factor-RNAP complex (R) is a two step process:

1. R+P ↔ RP(closed). K = 10E7
2. RP(closed) --> RP(open). K = 10E-2

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