Fig. 2
From: A potentially abundant junctional RNA motif stabilized by m6A and Mg2+
Structural requirements for m6A stabilization of junctional A–U base pairs. a Hairpin constructs that vary the secondary structural context of m6A. Secondary structures are predicted using MC-fold39 and supported by NMR data (see Supplementary Fig. 3c). The HCV sequence is derived from the base of stem loop 1 (SL1) in the 3ʹ end of HCV genome (nt 9633-9642 linked by UUCG to nt 9668-9678) from the genotype 2A JFH1 strain (GeneBank accession: AB047639 [https://www.ncbi.nlm.nih.gov/nuccore/AB047639]). b Comparison of 1H NMR spectra of unmodified and m6A6 substituted hairpin constructs recorded in 15 mM sodium phosphate, 25 mM NaCl, 0.1 mM EDTA and 3 mM Mg2+ at pH 6.4 and 10 °C. c Impact of methylation on the thermal stability of the hairpins with and without 3 mM Mg2+. Shown are the differences in the free energy of melting between methylated and unmodified RNA, i.e., ΔΔG = ΔG(methylated) − ΔG(unmodified). The uncertainty reflects the standard deviation from at least three measurements (see Supplementary Table 1)
