NMR analysis of the 5BSL3.2 apical stem–loop. (A) Predicted secondary structure of the 5BSL3.2 apical stem–loop, highlighting residues for which imino proton resonances were assigned. (B) Imino proton region of the NOESY spectrum (mixing time: 250 msec) recorded in H2O at 303 K. The corresponding one-dimensional spectrum is displayed above. Sequential imino–imino cross-peaks are labeled with residue numbers. (C) Predicted secondary structure of the 5BSL3.2 apical stem–loop, color-coded based on NMR assignments: left stem region in green, right stem region in red, and apical loop in purple. (D) NOESY spectra recorded in D2O at 303 K (sample was prepared using rNTPs in which the ribose H3′–H5′′ positions and the H5 position of pyrimidines were selectively deuterated). The upper panel shows intranucleotide H2′–H6/H8 and internucleotide H2′–H6/H8 cross-peaks; the lower panel presents intranucleotide H1′–H6/H8 and internucleotide H1′–H6/H8/H2 correlations. Assigned cross-peaks are annotated with residue numbers; adenosine H2 protons are marked in red.
