Influence of pH and Mg(ii) on the catalytic core domain 5 of a bacterial group II intronElectronic supplementary information (ESI) available: Overlay of [1H,1H]-NOESY spectra of AvD5 in the presence of increasing amounts of MnCl2 (Fig. S1) and MgCl2 (Fig. S2) are provided. In addition, KDs for single protons calculated by ISTAR are detailed in Table S1. Fluorescence emission of AvD5-AP3 dependent on pH is provided in Fig. S3. See DOI: 10.1039/c6dt04784j

RNA molecules fold into complex structures that allow them to perform specific functions. To compensate the relative lack of diversity of functional groups within nucleotides, metal ions work as crucial co-factors. In addition, shifted p K a s are observed in RNA, enabling acid-base reactions at ambient pH. The central catalytic domain 5 (D5) hairpin of the Azotobacter vinelandii group II intron undergoes both metal ion binding and pH dependence, presumably playing an important functional role in the ribozyme's reaction. By NMR spectroscopy we have here characterized the metal ion binding sites and affinities for the hairpin's internal G-A mismatch, bulge, and pentaloop. The influence of Mg( ii ) and pH on the local conformation of the catalytically crucial region is also explored by fluorescence spectroscopy. The combination of NMR and fluorescence spectroscopy was used to elucidate how Mg( ii ) and pH influence the local conformation and metal ion binding in domain 5 of Azotobacter vinelandii group II intron.