FIGURE 2.

Identification of peptides associated with the nascent RNA by the RCAP assay. (A) Peptides identified in the RCAP assay performed with nascent RNAs synthesized in the presence of different nucleotides. Peptides were resolved by a Bruker Autoflex III MALDI-TOF mass spectrometer set in reflectron mode. The reactions were performed as described in Materials and Methods. Peak assignments to peptides within NS5B were based on theoretical digests that match calculated masses within 0.5 Da. (Red) Peptides within a region only identified during RNA synthesis; (*) peptides from the primer grip region that were not identified in any of the experimental setups. (B,C) Molecular model of the peptides within NS5B found to contact RNA (PDB: 1QUV). (Gray) Peptides found to contact 5P or 5P/12T; (red) peptides present only with the ternary complex generated in the presence of UTP or UTP and ATP; (green) the active site of NS5B; (blue in the ribbon structure) the Δ1 loop.