Figure 1. Protected imino protons indicate secondary structure formation. (a) Sequence and secondary structure of the apical R/G stem–loop RNA. (b) Imino proton region of the one‐dimensional spectra of the 27mer, apical R/G stem–loop RNA, recorded with a 600‐MHz spectrometer at 278 K. The assignments are annotated for the imino proton resonances [ 9].
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Figure 2. Assessment of resonance dispersion in natural abundance – HSQC spectrum. (a) A zoomed aromatic region of the natural abundance – HSQC spectrum of the apical R/G stem–loop RNA at 600 MHz, recorded at 303 K. The assignments of the C6/C8–H6/H8, C2–H2, and C5–H5 correlations are indicated. The C5–H5 peaks of pyrimidines are folded from their typical chemical shift range of 90–110 ppm. (b) Sequence and secondary structure of the apical R/G stem–loop RNA [ 9].
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Figure 3. NOE connectivities of imino, amino, and aromatic protons in the GC (A) and AU (b) base pairs.
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Figure 4. One‐bond (a), two‐bond (b), and long‐range (c) spin–spin scalar couplings in RNA bases.
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Figure 5. The coherence transfer pathways for the H8–C8–N9–C1′–H1′ (a) and H6–C6–N1–C1′–H1′ (b) correlations in purine and pyrimidine nucleotides, respectively.
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Figure 6. “Base–sugar sequential walk” in the two‐dimensional – NOESY spectra of an A‐form RNA double helix. A close‐up of the two‐dimensional NOE spectrum of the apical R/G stem–loop RNA, recorded with a 600‐MHz spectrometer (mixing time of 300 ms) at 303 K in D 2O. The assignments for the intra‐ and inter‐residue connectivities are shown.
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Figure 7. NOE sequential connectivities in an A‐RNA helix.
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Figure 8. Two‐bond and three‐bond spin–spin scalar couplings used in HCP experiments to establish the inter‐residual through‐bond connectivities.
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Figure 9. Flowchart of sample preparation.
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Figure 10. Flowchart of experimental data collection.
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Figure 11. Flowchart of structure calculation.
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Figure 12. T7 class III promoter region and the resulting transcript. (a) T7 class III promoter region with indicated binding and initiating regions. Position +1 indicates the first residue of the transcript. (b) The RNA transcript is generated from position +1 of the template strand. The recommended nucleotides for positions +1 and +2 are shown. These positions are strongly conserved within the initiating domain across various bacteriophage promoters (class III T7, T3 and SP6, and T7 f2.5 class II).
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