title: Recombination analysis and structure prediction show correlation between breakpoint clusters and RNA hairpins in the pol gene of human immunodeficiency virus type 1 unique recombinant forms.
abstract: Recombination is recognized as a primary force in human immunodeficiency virus type 1 (HIV-1) evolution, increasing viral diversity through reshuffling of genomic portions. The strand-switching activity of reverse transcriptase is required to complete HIV-1 replication and can occur randomly throughout the genome, leading to viral recombination. Some recombination hotspots have been identified and found to correlate with RNA structure or sequence features. The aim of this study was to evaluate the presence of recombination hotspots in the pol gene of HIV-1 and to assess their correlation with the underlying RNA structure. Analysis of the recombination pattern and breakpoint distribution in a group of unique recombinant forms (URFs) detected two recombination hotspots in the pol region. Two stable and conserved hairpins were consistently predicted corresponding to the identified hotspots using six different RNA-folding algorithms on the URF parental strains. These findings suggest that such hairpins may play a role in the higher recombination rates detected at these positions.
authors.affiliation: Department of Clinical Sciences 'L. Sacco', University of Milan, Milan, Italy.
authors.forename: Andrea
authors.initials: A
authors.lastname: Galli
authors.affiliation: Department of Clinical Sciences 'L. Sacco', University of Milan, Milan, Italy.
authors.forename: Alessia
authors.initials: A
authors.lastname: Lai
authors.affiliation: Department of Clinical Sciences 'L. Sacco', University of Milan, Milan, Italy.
authors.forename: Stefano
authors.initials: S
authors.lastname: Corvasce
authors.affiliation: Department of Molecular Biology, University of Siena, Siena, Italy.
authors.forename: Francesco
authors.initials: F
authors.lastname: Saladini
authors.affiliation: Department of Clinical Sciences 'L. Sacco', University of Milan, Milan, Italy.
authors.forename: Chiara
authors.initials: C
authors.lastname: Riva
authors.affiliation: Department of Clinical Sciences 'L. Sacco', University of Milan, Milan, Italy.
authors.forename: Lorenzo
authors.initials: L
authors.lastname: Dehò
authors.affiliation: Department of Clinical Sciences 'L. Sacco', University of Milan, Milan, Italy.
authors.forename: Ilaria
authors.initials: I
authors.lastname: Caramma
authors.affiliation: Department of Clinical Sciences 'L. Sacco', University of Milan, Milan, Italy.
authors.forename: Marco
authors.initials: M
authors.lastname: Franzetti
authors.affiliation: Department of Molecular Biology, University of Siena, Siena, Italy.
authors.forename: Laura
authors.initials: L
authors.lastname: Romano
authors.affiliation: Department of Clinical Sciences 'L. Sacco', University of Milan, Milan, Italy.
authors.forename: Massimo
authors.initials: M
authors.lastname: Galli
authors.affiliation: Department of Molecular Biology, University of Siena, Siena, Italy.
authors.forename: Maurizio
authors.initials: M
authors.lastname: Zazzi
authors.affiliation: Department of Clinical Sciences 'L. Sacco', University of Milan, Milan, Italy.
authors.forename: Claudia
authors.initials: C
authors.lastname: Balotta
mesh_terms: D015684:Gene Products, pol / Q000737:chemistry / Q000235:genetics*; D015751:Genes, pol; D016333:HIV Protease / Q000235:genetics; D054303:HIV Reverse Transcriptase / Q000235:genetics; D015497:HIV-1 / Q000235:genetics*; D006801:Humans; D008969:Molecular Sequence Data; D012367:RNA, Viral / Q000737:chemistry / Q000235:genetics; D011995:Recombination, Genetic; D017422:Sequence Analysis, DNA
chemical_list: D015684:Gene Products, pol; D012367:RNA, Viral; C514824:reverse transcriptase, Human immunodeficiency virus 1; D054303:HIV Reverse Transcriptase; D016333:HIV Protease