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. Author manuscript; available in PMC: 2016 Jun 9.
Published in final edited form as: Biochemistry. 2015 May 27;54(22):3413–3415. doi: 10.1021/bi501564d

Figure 1.

Figure 1

Structural models of the influenza A segment 2 (PB1) 65–126 nucleotide region. To optimize SP6 polymerase efficiency the identities of nucleotides 63 and 64 (not shown) are both A’s, however in the wild-type sequence the nucleotides are A and U, respectively. The structure without Mg2+ is predicted with RNA structure15 where strongly reactive nucleotides were forced to be single-stranded. The structure shown in the presence of Mg2+ is the one most consistent with the model based on sequence comparison.16 This structure is also predicted by ShapeKnots.17 Predicted free energy at 37 °C for the structure without Mg2+ is reported at the bottom left.15 Predicted free energies at 37 °C from two pseudoknot prediction models are reported at the bottom right.18,19 Red boxes indicate the start codons for PB1-F2 and N40 ORFs, respectively. Colored dots represent strong chemical mapping hits for the reagent identified in the key. H1: Helix 1, H2: Helix 2.