Major groove contacts drive binding. These interactions have been shown to arise via direct contacts ("direct read-out") of bases in the major groove. This recognition extends from position -12 through to position -5.
The TATA sequence immediately downstream of the tight binding region serves to facilitate melting of the promoter at the start site. The sequence TATA has been shown to have the lowest energetic barrier to melting.
The template strand in the TATA region serves to tether positions +1 and +2 near the active site. The template strand in the TATA region tethers the initial templating bases to the tight binding region, localizing them near the start site. We have recently shown that the exact nature of this linkage is not essential to overall initiation of transcription.
The precise nature of the linkage is essential to the fidelity with which the polymerase initiates. Looser linkages allow misinitiation at sites other than +1.
Evidence for a bend centered at position +1 suggests that bending at the start site might further facilitate the melting necessary to initiate transcription.
Substantial melting of the base pair at position +3 is not required for efficient formation of the first phosphodiester bond between bound nucleotides at positions +1 and +2. This surprising result limits the extent of the transcription "bubble," which we now envision at initiation, to extend from position -4 to +2.