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The Start Site and the Promoter Region

In prokaryotic cells, free RNA polymerase molecules are constantly colliding with DNA helices. The collision leads to a weak association between the DNA and RNA polymerase, which is soon broken. However, when the RNA polymerase binds to a specific sequence on the DNA, it binds tightly, forming a DNA/RNA polymerase complex. This specific site of binding is called the start site. The start site represents the location on the DNA that marks where the first nucleotide of an RNA chain should go; that spot is designated as the "plus one position". Positions that are designated as downstream in the RNA are positively numbered according to their relative position to the plus one position. All positions designated as upstream of the start site are labeled with negative numbers according to their position relative to the start site. Sequences located just upstream of the start site, called the promoter region, contain the information that signals the RNA polymerase to start transcription.

The Structure of the Promoter Region

There are a number of key features to the promoter region that give it the ability to provide the signal initiating transcription. While nearly all promoters vary slightly, they all have general traits that can be identified. Located approximately 10 and 32 base pairs upstream of the start site are two such regions, called the -10 and -35 sequences. Each sequence consists of six base pairs. For an ideal promoter, the sequence is TTGACA for the -35 region and TATAAT for the -10 region.

Figure %: Traditional Promoter Region

In addition to the specificity of the bases in these sequences, the spacing between the two is also important. Ideally, this gap is 17 base pairs long. Deviations from this spacing have significant effects on the strength of the promoter region. The closer a promoter region is to matching this canonical promoter sequence, the greater its strength.

There is a third promoter element that is sometimes seen in very strong promoters which is called the UP element. It usually is composed of alternating stretches of 5 adenine and thymine bases. It is located upstream of the -35 region.

Recognition of the Promoter Region

RNA polymerase binds to the DNA helix at the start site. Bound to DNA, it covers a 60 base pair region within which it scans for the -35 and -10 promoters. Initially, the polymerase, and specifically the sigma subunit, binds in what is called a "closed complex" to the DNA. The RNA polymerase/promoter complex then undergoes a conformational change that breaks a number of base pairs extending from the -10 region to create a bubble in which the two DNA strands have separated. This bubble is usually approximately 17 base pairs in length. This new formation is called the "open complex". RNA synthesis is then initiated using one of the DNA strands as a template for adding complementary RNA base pairs. Transcription is usually initiated with a purine, rather than pyrimidine, base. Once initiated, the RNA polymerase moves down the DNA strand in the elongation process, which is covered in the next section.

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