An additional DNA element that binds RNA polymerase is found in some strong promoters, for example, those directing expression of the ribosomal RNA (rRNA) genes. This is called an UP-element and increases polymerase binding by providing an additional specific interaction between the enzyme and the DNA.

TLS Online TPP Program

#Id: 2302

#Unit 3. Fundamental Processes

As RNA polymerase moves along the DNA template, it unwinds the duplex at the front of the bubble (the unwinding point), and the DNA automatically reforms the double helix at the back (the rewinding point). 

1. The length of the transcription bubble is 12 to 14 bp, but the length of the RNA–DNA hybrid within the bubble is only 8 to 9 bp. 

2. As the enzyme moves along the template, the DNA duplex reforms, and the RNA is displaced as a free polynucleotide chain. 

3. The last 14 ribonucleotides in the growing RNA are complexed with the DNA and/or the enzyme at any given moment.

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#Id: 2303

#Unit 3. Fundamental Processes

Mechanism: How Polymerase Find Promoter Sequences

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#Id: 2304

#Unit 3. Fundamental Processes

Amino acids in the 2.4 a-helix of beta70 contact specific bases in the coding strand of the -10 promoter sequences.

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#Id: 2305

#Unit 3. Fundamental Processes

Initiation complex contains sigma and covers 75bp

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#Id: 2306

#Unit 3. Fundamental Processes

Initiation elongation complex forms at 10 bases, mayloses sigma, and loses contacts from -35 to -55.

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#Id: 2307

#Unit 3. Fundamental Processes

During the transition to the open complex, the conformation of both the RNA polymerase and the DNA change. 

1) 90° bend in the DNA, which allows the template strand to approach the active site of the enzyme; 

2) strand opening of the promoter DNA between -11 and +3 with respect to the transcription start site; 

3) the promoter DNA scrunches into the active channel forming the transcription bubble; and 

4) closing of the jaws of the enzyme to encircle the section of the promoter downstream section of the transcription start site.