Extended Data Fig. 9: Comparison of WC and rWC base pairing, and NAD binding to RNAP AS.
From: Molecular insight into 5′ RNA capping with NpnNs by bacterial RNA polymerase
a, In TC-Ap3G, the glycosidic bond of the distal Ap3G adenosine and the glycosidic bond of the template −1 T are in mutual trans orientation, which results in their reverse WC base pairing. b, In a regular RNA/DNA duplex, here represented by a 5′-end hydroxyl dinucleotide primer/DNA complex (PDB 7EH1), the glycosidic bond of the distal adenosine in ApG (featuring regular 5′ to 3′ monophosphate linker) and the glycosidic bond of the template −1 T are in mutual cis orientation, which favors canonical WC base pairing. The original CC template and GpG dinucleotide in PDB ID 7EH1 were mutated to TC and ApG for the sake of direct comparison of A-T base pairing in the i − 1 site. c, In TC-Ap4A, the distal Ap4A adenosine flanks due to purine-purine base-pairing incompatibility at the i − 1 site. d, NAD as NCIN visualized after incorporation into nascent product and translocation (PDB 5D4D). The proximal adenosine of NAD base pairs in the i − 1 site, while the distal nicotinamide moiety does not base pair with the template strand adenine purine base in line with the i − 2 site. A direct comparation of NAD and Np4N binding at the i and i − 1 site of the AS during the very initial step of transcription awaits the determination of a structure with NAD bound in the respective sites.
