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RNA Biol. 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.

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  • 1Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam CINIMA, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands.


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.


HIV; RNA structure; evolution; lentiviruses; mutational pattern; nucleotide composition

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