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. 2009 Oct 7;37(22):7654–7664. doi: 10.1093/nar/gkp779

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© The Author(s) 2009. 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/2.5/uk/) 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. — Secondary structure of the mRNAs used in this study. The tow domains of the HIV-1 hairpin are labeled: lower stem (FSL) and upper stem (FSU). The slippery sequence is underlined and the Shine-Dalgarno sequence is boxed. The first nucleotide of codon 1 (position +1) is labeled. Toeprints that are observed when each codon is positioned in the ribosomal P-site are shown on the top. Nucleotides that were mutated are indicated in a box for the mSP-SL-CCC-HIV-1 RNA. The limit of accessibility (position +11) of a RNA double helix at ribosomal surface (15) is highlighted by a triangle. The spacer sequence that is expected to be single-stranded in the mRNA tunnel is indicated by a dashed line.