Although the core polymerase crystal structure provides considerable information about RNA polymerase structure, it provides no direct information about interactions that exist among core polymerase, σ factor, and DNA. Darst and coworkers addressed these and related structural issues by preparing crystals that contained the Trq holoenzyme bound ta a synthetic DNA with a fork-junction sequence (the junction between double-stranded DNA and single-stranded DNA in the transcription bubble).

    The DNA molecule they synthesized for this purpose has a double-stranded -35 box, a mostly open -10 box, and an extended -10 element. The crystal structure of the RNA polymerase holoenzyme· fork-junction DNA complex, which appears to resemble the open complex. The σ⁷⁰ factor assumes a different conformation when bound to core polymerase. One notable change is the disruption of an interaction between subdomain 1. 1 and domain 4. This interaction prevents the free σ⁷⁰ factor from binding DNA. In essence, negatively charged subdomain 1.1 acts as a DNA mimic, which competes with promoter DNA for the binding site on domain 4.

    Darst and coworkers have also determined the crystal structure for the Taq RNA polymerase holoenzyme without bound DNA and Shigeyuki Yokoyama and coworkers have done the same for the Thermus thermopbilus RNA polymerase holoenzyme. Thus, a considerable amount of structural information is now available for the core enzyme, the holoenzyme, and the holoenzyme · fork-junction DNA complex. Based on comparisons of these structures, it appears that the bulk of the enzyme consisting of the N-terminal domains of the α subunits, the ω subunit, and regions of β and β'subunits near the active site form a stationary core module.

    Four other modules move with respect to this core module. The β' clamp domain forms the β' pincer, which can close down around the main channel, helping to hold the DNA and RNA: DNA hybrid in the active center. The β pincer is made of two mobile domains (β1 and β2), which also help to open and close the main channel. The fourth mobile domain, the β flap, covers the RNA exit channel. The pincers must be in an open position during the transcription initiation stage so that DNA can enter the active-site channel.