FIGURE 1.
5′-Adenylated RNA. (A) The structure of 5′-AppRNA. X is the 5′-terminal nucleotide of the RNA substrate before adenylation. (B) The T4 RNA ligase mechanism, showing the 5′-AppRNA intermediate 2. X and X′ may be any nucleotides. (C) Nucleophilic displacement reaction on 5′-triphosphorylated RNA (5′-pppRNA). Nu, nucleophile. The 5′-terminal nucleotide of the RNA is shown as guanosine G because 5′-triphosphorylated RNAs are most typically prepared by in vitro transcription, which introduces G at this position. The nucleophilic substitution reaction on 5′-AppRNA is analogous, except with displacement of AMP instead of PPi (cf. 2 → 3 in B).