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Assessment of Immunologically Relevant Dynamic Tertiary Structural Features of the HIV-1 V3 Loop Crown R2 Sequence by ab initio Folding
Published on: September 15, 2010
The A-nucleotide preference of HIV-1 in the context of its structured RNA genome
Formijn J van Hemert1, Antoinette C van der Kuyl, Ben Berkhout
1Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam CINIMA, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands. f.j.vanhemert@amc.uva.nl
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.
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