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. 2013 Feb;10(2):211-5.
doi: 10.4161/rna.22896. Epub 2012 Dec 12.

The A-nucleotide preference of HIV-1 in the context of its structured RNA genome

Formijn J van Hemert  1 , Antoinette C van der Kuyl, Ben Berkhout
Affiliations

The A-nucleotide preference of HIV-1 in the context of its structured RNA genome

Formijn J van Hemert et al. RNA Biol. 2013 Feb.

Abstract

A bipartition of HIV-1 RNA genome sequences into single- and double-stranded nucleotides is possible based on the secondary structure model of a complete 9 kb genome. Subsequent analysis revealed that the well-known lentiviral property of A-accumulation is profoundly present in single-stranded domains, yet absent in double-stranded domains. Mutational rate analysis by means of an unrestricted model of nucleotide substitution suggests the presence of an evolutionary equilibrium to preserve this biased nucleotide distribution.

Keywords: HIV; RNA structure; evolution; lentiviruses; mutational pattern; nucleotide composition.

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Figures

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Figure 1. Base pair composition of the double-stranded portion of the HIV-1 NL4-3 RNA structure.
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Figure 2. SHAPE reactivity of each nucleotide (A, U, C and G) in HIV-1 NL4-3 RNA. The histograms show increasing SHAPE reactivity in windows of 0.2 (X-axis, relative units). Frequency refers to the number of nucleotides per SHAPE window. Note the deviant SHAPE reactivity of the A-nucleotide.
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