A recombination hot spot in HIV-1 contains guanosine runs that can form G-quartet structure and promote strand transfer in vitro. - Related Articles
A recombination hot spot in HIV-1 contains guanosine runs that can form G-quartet structure and promote strand transfer in vitro.
J Biol Chem. 2009 Oct 12;
Authors: Shen W, Gao L, Balakrishnan M, Bambara RA
The co-packaged RNA genomes of HIV-1 recombine at a high rate. Recombination can mix mutations to generate viruses that escape immune response. A cell-culture based system was designed previously to map recombination events in a 459-bp region spanning the primer binding site (PBS) through a portion of gag protein coding region. Strikingly, a strong preferential site for recombination in vivo was identified within a 112-nt-long region near the beginning of gag. Strand transfer assays in vitro revealed that three pause bands in the gag hot spot each corresponded to a run of guanosine (G) residues. Pausing of reverse transcriptase (RT) is known to promote recombination by strand transfer both in vivo and in vitro. To assess the significance of the G runs we altered them by base substitutions. Disruption of the G runs eliminated both the associated pausing and strand transfer. Some G-rich sequences can develop G-quartet structures, which were first proposed to form in telomeric DNA. G-quartet structure formation is highly dependent on the presence of specific cations. Incubation in cations discouraging G-quartets altered gel mobility of the gag template consistent with breakdown of G-quartet structure. The same cations faded G-run pauses but did not affect pauses caused by hairpins, indicating that quartet structure causes pausing. Moreover, gel analysis with cations favoring G-quartet structure indicated no structure in mutated templates. Overall, results point to RT pausing at G runs that can form quartets as a unique feature of the gag recombination hot spot.
PMID: 19822521 [PubMed - as supplied by publisher] [PubMed-HIV]