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Low-energy conformers of AB-dUMP and AB-(Gly)2-dUMP in the DNA major groove. Molecular simulation was used to predict the various possible conformers in each case. The photoreactive nitrene is shown in blue.
Topological model of the RNAP II preinitiation complex. (A and B) Top (A) and side (B) of the proposed trajectory of the promoter DNA around the mobile clamp of RNAP II. The path of promoter DNA has been drawn to account for our in-gel photo-cross-linking results (see the text). (C and D) Locations of TFIIF (C) and TFIIE (D) subunits according to our photo-cross-linking results. For each subunit, we obtained cross-linking to two distinct promoter regions (dashed circles). Although our results suggest that two copies each of TFIIE and TFIIF subunits are present within the complex, we cannot rule out the possibility that these factors have two (or more) distinct domains held together by an unfolded linker.
A model representing the relocalization of XPC in the presence of TFIIH and the various steps driving to the removal of the damaged oligonucleotide. Each step is characterized by an increase in the remodeling of damaged DNA that is progressively opened by the repair machinery. In the absence of TFIIH, XPC approaches the damaged DNA from nucleotides -20 to +20, the contact at positions -8/-7 being the strongest. In the presence of TFIIH, XPC crosslink strongly to positions -23/-20 and weakly to positions -8/-7 but does not crosslink to positions on the 3’ end of the cisplatin adduct. The fully open complex (-19 to +8) is used as a template for incision by XPF/ERCC1 and XPG as indicated by arrows.
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