Biophysical studies of the nucleic acid chaperone properties of the HIV-1 nucleocapsid protein

Insights into the mechanisms of RNA secondary structure destabilization by the HIV-1 nucleocapsid protein

“…Other factors may also contribute to NMR line broadening: (i) the higher correlation time associated with complex formation; (ii) fast-to intermediateregime exchange associated with free and bound forms of the oligonucleotide, as previously described (Barraud et al 2008). Many biophysical studies on DNA and RNA oligonucleotides have demonstrated destabilization of the nucleic acid secondary structure by NC (Beltz et al 2005;Levin et al 2005;Godet and Mély 2010;Godet et al 2013) and some NMR studies described the direct impact on base pair dynamics (Johnson et al 2000;Tisné et al 2001). Line broadening preferentially affected the short stem surrounded by two single-stranded regions (apical loop and bulge U23C24U25).…”

“…During reverse transcription, the nucleic acid chaperone activity of NC facilitates the rearrangement of nucleic acids into their most thermodynamically stable structures. This activity results from three different properties of NC: (i) nucleic acid aggregation; (ii) duplex destabilization; (iii) rapid on-off kinetics (Cruceanu et al 2006a,b;StewartMaynard et al 2008;Godet and Mély 2010;Levin et al 2010). Nucleic acid aggregation is thought to be dependent on the N-terminal basic part of NC, whereas duplex destabilization is associated with the zinc fingers (Beltz et al 2005;Levin et al 2005Levin et al , 2010Vo et al 2009a,b;Godet and Mély 2010).…”

“…NC promotes the annealing of the TAR RNA hairpin with the cTAR DNA hairpin. This is an essential step in the first strand transfer process and has thus been the subject of many studies (Godet et al 2006;Liu et al 2007;Vo et al 2009a,b;Godet and Mély 2010). The NC-mediated destabilization of the secondary structures of TAR and cTAR stem-loops is one of the initial steps in the annealing process.…”

“…This activity results from three different properties of NC: (i) nucleic acid aggregation; (ii) duplex destabilization; (iii) rapid on-off kinetics (Cruceanu et al 2006a,b;StewartMaynard et al 2008;Godet and Mély 2010;Levin et al 2010). Nucleic acid aggregation is thought to be dependent on the N-terminal basic part of NC, whereas duplex destabilization is associated with the zinc fingers (Beltz et al 2005;Levin et al 2005Levin et al , 2010Vo et al 2009a,b;Godet and Mély 2010). However, some studies have suggested a role of zinc fingers in nucleic acid aggregation (Krishnamoorthy et al 2003;Levin et al 2005;Mirambeau et al 2006;Mitra et al 2013) and others have implicated basic residues in nucleic acid destabilization .…”

“…The first-strand transfer occurring during reverse transcription of the HIV-1 genome has been widely studied (Basu et al 2008;Godet and Mély 2010;Levin et al 2010). After the initiation of reverse transcription at the PBS (primer binding site) with tRNA lys Sleiman et al 2012Sleiman et al , 2013, the minus-strand strong-stop DNA [(−)ssDNA] is synthesized from the 5 ′ terminal part of the RNA genome.…”