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. 2010 Oct 8;39(3):902–912. doi: 10.1093/nar/gkq885

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© The Author(s) 2010. 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), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

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Figure 5. — The structure of IRENE influences the activity of HIV-1 5′UTR IRES. (A) The secondary structure (boxed) of WT IRENE. The presence of the 3A bulge causes a bend between the upper and the lower parts of this stem-loop. (B) In the absence of IRENE (M2.ΔSL134–178), the IRES activity is increased 1.5-fold. (C) With the M3.stem134, M6.stem143bot, M7.Δloop151 and M8.loop151 mutants, the IRES activity is unchanged and the secondary structure of IRENE (boxed) is very similar to that of WT. (D) In the M4.stem143 mutant, the structure of IRENE is drastically changed and the IRES activity is increased 2-fold. (E) The M5.stem143up mutation moderately changes the structure of IRENE (boxed), and the IRES activity is increased 1.5-fold. The secondary structure of WT or mutant IRENE was predicted by the mfold algorithm (version 3.2; http://frontend.bioinfo.rpi.edu/applications/mfold/cgi-bin/rna-form1.cgi) (60,61).