Closed promoter complexes

Various types of RNA polymerase-DNA binding complexes. A nonspecific complex is formed at any point along the DNA. The closed promoter complex is formed at a polymerase-binding site. Following the formation of the closed promoter complex, an open promoter complex is formed at the same site. 

The transition from the closed promoter complex (in which DNA is double helical) to the open promoter complex (in which a DNA segment is unwound) is an essential event in transcription. The stage is now set for the formation of the first phosphodiester bond of the new RNA chain. 

The answer is h. (Murray, pp 435-451. Scriver, pp 3-45. Sack, pp 1-40. Wilson, pp 101—120.) Promoter sites are initiation sites for transcription. Transcription starts when RNA polymerase binds to the promoter. It then unwinds the closed promoter complex, where DNA is in the form of a double helix, to form the open promoter complex in which about 17 base pairs of template DNA are unwound. RNA synthesis then begins with either a pppA or a pppG inserted at the beginning 5 -terminus of the new RNA chain, which is synthesized in the 5 to 3 direction. 

The initial encounter between RNA polymerase holoenzyme and a promoter generates a closed-promoter complex. Whereas DNA strands unwind later in transcription, no unwinding is detectable in a closed-promoter complex. This complex forms with a Ka between 10 and 10 M l at 0.1 MNaCl. Binding is primarily electrostatic, for Ka depends on ionic strength. The complex is relatively labile, dissociating with a half-life of about 10 seconds. 

Open-promoter complex A complex between RNA polymerase holoenzyme and a promoter that has undergone initial unwinding (has opened ) preparatory to the start of transcription. It is preceded by a much less stable closed-promoter complex, in which the promoter has not unwound, that may either fall apart or proceed to an open-promoter complex. 

Another whole set of bacterial promoters utilize an alternative sigma factor (o ) which together with RNAP form a stable closed promoter complex that, unlike its a counterpart, is unable to initiate transcription by itself (Amit et al. 2011 Buck... 

Fig. 1.27. Two-step mechanism of transcription initiation. The binding of a procaryotic RNA polymerase to its promoter can be subdivided into two steps. In the first step the RNA polymerase binds to the closed promoter with low affinity. The closed complex isomerizes in a second step to an open complex in which the promoter is partially unwound. Detailed consideration reveals that further steps can be distinguished. These are not shown here for simplicity reasons.

A satisfactory mathematical model for initiation of transcription supposes that the polymerase and DNA bind reversibly to form a complex with formation constant Kf. This initial specific polymerase-promoter complex is referred to as a closed complex because it is thought that the bases in the DNA chain are all still paired. It is postulated that in a rate-determining step the closed complex is converted into an open complex, which is ready to initiate mRNA synthesis (Eq. 28-1).26 67 In the open complex the hydrogen bonds... 

A set of photochemically promoted elimination reactions has been described for the d6 dithiolene complex CpCo(PBu3)(mnt) (47) and several closely related complexes 48-50 (152). Complexes 48 and 49 form by the reaction of the... 

Describe how topoisomerase I was used to determine the number of promoter DNA base pairs that are unwound upon the binding of RNA polymerase. Relate negative supercoiling to promoter efficiency. Distinguish between closed promoter and open promoter complexes. 

It is believed that when the initial specific polymerase-promoter complex forms, the bases in the DNA chains are still paired. This is termed the "closed complex" and is believed to be in equilibrium through a conformational change with an open complex. The latter serves as the template to initiate mRNA synthesis, since interbase hydrogen bonds have been broken, thus uncovering the bases of the template chain so that they can pair with ribonucleoside triphosphates. 

The promoter proximal elements are usually 100 to 200 base pairs long and relatively close to the site of initiation of transcription. Within each of these elements there are DNA sequences specifically recognized by several different transcription factors which either interact directly with the preinitiation complex or indirectly through other proteins. 

The interfacial transfer kinetics were then investigated by perturbing the equilibrium, through the depletion of Cu + in the aqueous phase, by reduction to Cu at an UME located in close proximity to the aqueous-organic interface. This process promoted the transfer of Cu into the aqueous phase, via the transport and decomplexation of the cupric ion-oxime complex, resulting in an enhanced steady-state current at the UME. Approach curve measurements of i/i oo) vs. d allowed the kinetics of the transfer process to be determined unambiguously [9,18]. 

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