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. 2012 May 28;40(16):8011–8020. doi: 10.1093/nar/gks468

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© The Author(s) 2012. Published by Oxford University Press.

This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/3.0), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

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Figure 1. — Structures of the tP5abc RNA. (A) The secondary structures (top) and ribbon diagrams (bottom) of the extended tP5abc from NMR (6) are compared with (B) the folded P5abc structure from X-ray crystallography (22). Mg²⁺ ions visible in the X-ray structure are represented by spheres. Nucleotides are numbered discontinuously because 5 bp of the natural P5b are missing in tP5abc. Non-Watson–Crick base pairs are represented by Leontis/Westhof symbols (49). U185 was replaced with the fluorescent analog 2AP (cyan), which unstacks in the folded RNA. Base-pairing free energies are from mfold (35). (C) RNase T1 probing of tP5abc secondary structure at 25 and 50°C, with no Mg²⁺ (extended) or 2.5 mM Mg²⁺ (folded). Lane C, no digestion control; lane T, RNase T1 sequencing ladder.