title: The A-nucleotide preference of HIV-1 in the context of its structured RNA genome.
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.
authors.affiliation: Laboratory 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
authors.forename: Formijn J
authors.initials: FJ
authors.lastname: van Hemert
authors.forename: Antoinette C
authors.initials: AC
authors.lastname: van der Kuyl
authors.forename: Ben
authors.initials: B
authors.lastname: Berkhout
mesh_terms: D000227:Adenine Nucleotides / Q000235:genetics*; D020029:Base Pairing; D001483:Base Sequence; D019143:Evolution, Molecular; D016679:Genome, Viral; D015497:HIV-1 / Q000235:genetics*; D009154:Mutation; D059645:Mutation Rate; D009690:Nucleic Acid Conformation; D012330:RNA, Double-Stranded / Q000235:genetics; D012367:RNA, Viral / Q000235:genetics*; D012641:Selection, Genetic
chemical_list: D000227:Adenine Nucleotides; D012330:RNA, Double-Stranded; D012367:RNA, Viral