## 3 _E. coli_\(\sigma\)[70] Promoter Recognition
### Upstream Bending and Wrapping to Form More Advanced Closed Complexes  
The first conformational changes induced by RP\({}_{\rm C}\) formation may occur upstream of the \(-\)35 region. DNase footprinting of \(\lambda\)P\({}_{\rm R}\) closed complexes reveals enhanced reactivity at \(-\)38 on the template strand and within the UP element region (\(-\)48 on the template strand, \(-\)45 on the nontemplate strand), indicating DNA bending or other distortions at these positions [75]. Periodic protection of the upstream DNA from OH attack is observed upstream to approximately base \(-\)80 [27], and downstream to base \(+\)20. This indicates that the far upstream promoter duplex is lying on the \"back\" surface of RNAP (see Figure 3 and [27]).  
The mechanism of forming this bent, wrapped interface is unclear. Since the \(\alpha\)CTD are on flexible tethers, extension of the tethers allows them to bind specifically to the UP element or nonspecifically to DNA upstream of the \(-\)35 element in RP\({}_{\rm C}\) (see Figure 3). Specific binding to the proximal UP element brings one \(\alpha\)CTD (binding site centered at \(-\)42) into contact with region 4 of \(\sigma^{70}\); mutation of \(\sigma\) region 4 residues within this \(\sigma\)-\(\alpha\)CTD interface reduces transcription from some, but not all, UP element-containing promoters [81, 83]. A second \(\alpha\)CTD binds to the distal site, centered at base \(-\)52 [72]. There is no evidence that the two \(\alpha\)CTD interact in open complex formation [68], but efficient transcription from promoters having only a distal UP element requires both \(\alpha\)CTDs, suggesting that the second \(\alpha\)CTD must somehow affect the overall stability of the complex [68, 72]. In the model of [PERSON] _et al._[27], formation of these interfaces bends the DNA between \(-\)35 and \(-\)60 nearly 100\({}^{\circ}\), driving presumably nonspecific interactions between RNAP and DNA upstream of base \(-\)60.  
Interactions of the upstream promoter DNA with the \(\alpha\)CTD are observed to be very important for efficient open complex formation at \(\lambda\)P\({}_{\rm R}\), which appears to have a distal UP element [75], and for efficient initiation at _lac_UV5, which has no UP element [78]. Truncation of \(\lambda\)P\({}_{\rm R}\) at base \(-\)47 (removing the specific distal UP element sequence and upstream DNA and, thus, probably most of the effect of the UP element [72]), or of _lac_UV5 at base \(-\)45 reduces the rate of the isomerization/DNA opening step (see Section 5) by 1.5-2 orders of magnitude; deletion of the \(\alpha\)CTD and mutation of a single residue which eliminates \(\alpha\)CTD-DNA binding have similar effects [78, 128]. Smaller but significant effects of truncations upstream of \(-60\) on the isomerization/DNA opening step are also observed [78, 128]. Because the strong dependences of the kinetics on upstream DNA length are similar for both promoters, only nonspecific interactions with the \(\alpha\)CTD appear necessary to generate these effects.  
Far upstream interactions persist in the open complex at some (perhaps many) promoters. For _lac_UV5 open complexes, crosslinks between the \(\alpha\)CTDs and nonspecific upstream DNA are observed even to base \(-90\)[129]. Atomic force microscopy demonstrates that at \(\lambda\)Pr, DNA is extensively wrapped around RNAP in the open complex [76].