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with the DNA template in the active site available for pairing with the substrate. DNA strand separation occurs one position downstream of the active site, implying that only one substrate at a time can bind to the EC. At the upstream edge of the RNA/DNA hybrid, the first displaced RNA base is trapped within a protein pocket, suggesting a mechanism for RNA displacement. The displaced RNA resides in the RNA exit channel and adopts a conformation mimicking that of a double helix, providing insight into a mechanism for hairpin-dependent pausing and termination. The mechanism of substrate loading in multi-subunit RNA polymerases is crucial for understanding the general principles of transcription. We have determined the EC structures (3Å) with a non-hydrolysable substrate analogue (AMPcPP), and with AMPcPP plus the antibiotic streptolydigin (Stl). In the EC/AMPcPP structure, the substrate binds to the active (‘insertion’) site closed through refolding of the trigger loop (TL). In contrast, the EC/AMPcPP/Stl structure reveals an inactive (‘preinsertion’) open substrate intermediate stabilized by Stl-induced displacement of the TL. Our data suggest three main implications. First, the two-step preinsertion/insertion mechanism of substrate loading may be universal for all RNA polymerases. Second, freezing of the preinsertion state is an attractive target for the drug design. Last, the TL emerges as a regulatory target whose refolding can be modulated by transcription factors. 1. Vassylyev et al. (2007a) Nature, 448, 157-162. 2. Vassylyev et al. (2007b) Nature, 448, 163-168.

Recent developments in GISAXS and GISANS – nanobeams andin situkinetic investigations