A promoter is a DNA sequence that is adjacent to a gene and required for transcription. Promoters contain short consensus sequences that are important in the initiation of transcription.

Initial RNA synthesis After the holoenzyme has attached to the promoter, RNA polymerase is positioned over the start site for transcription (at position +1) and has unwound the DNA to produce a single-stranded template. The orientation and spacing of consensus sequences on a DNA strand determine which strand will be the template for transcription, and thereby determine the direction of transcription.

The start site itself is not marked by a consensus sequence but often has the sequence CAT, with the start site at the A. The position of the start site is determined not by the sequences located there but by the location of the consensus sequences, which positions RNA poly-merase so that the enzyme's active site is aligned for initiation of transcription at + 1. If the consensus sequences are artificially moved upstream or downstream, the location of the starting point of transcription correspondingly changes.

To begin the synthesis of an RNA molecule, RNA polymerase pairs the base on a ribonucleoside triphos-phate with its complementary base at the start site on the DNA template strand (I Figure 13.13d). No primer is required to initiate the synthesis of the 5' end of the RNA molecule. Two of the three phosphates are cleaved from the ribonucleoside triphosphate as the nucleotide is added to the 3' end of the growing RNA molecule. However, because the 5' end of the first ribonucleoside triphosphate does not take part in the formation of a phosphodiester bond, all three of its phosphates remain. An RNA molecule therefore possesses, at least initially, three phosphates at its 5' end (< Figure 13.13e).

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