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

Andrea Galli, Alessia Lai, Stefano Corvasce, Francesco Saladini, Chiara Riva, Lorenzo Dehò, Ilaria Caramma, Marco Franzetti, Laura Romano, Massimo Galli, Maurizio Zazzi, Claudia Balotta

14 Citationer (Scopus)

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.
OriginalsprogEngelsk
TidsskriftJournal of General Virology
Vol/bind89
Udgave nummerPt 12
Sider (fra-til)3119-25
Antal sider7
ISSN0022-1317
DOI
StatusUdgivet - 2008

Fingeraftryk

Dyk ned i forskningsemnerne om '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'. Sammen danner de et unikt fingeraftryk.

Citationsformater