Interactions between HIV-1 nucleocapsid protein and viral DNA may have important functions in the viral life cycle

In the virion core of retroviruses, the genomic RNA is tightly associated with nucleocapsid (NC) protein molecules, forming the nucleocapsid structure. NC protein, a highly basic protein with two zinc fingers, is indispensable for RNA dimerization, encapsidation and the initiation of reverse transcription in avian, murine and human retroviruses. Here we show that NC protein of HIV-1 (NCp7) and NCp7 mutants bind to DNA fragments representing proviral DNA sequences, forming stable complexes. NCp7 and NCp7 mutants form high molecular weight complexes with large DNA fragments and show cooperativity in binding to the DNAs. It appears that the conserved basic residues, and not the zinc fingers, are important for complex formation. In addition, NCp7 and several NCp7 mutants protect DNAs from nuclease digestion while the DNA ends appear to be poorly protected. NCp7 has been found to bind to strong stop cDNA, the initial product of reverse transcription, and to promote the annealing of this cDNA to HIV-1 RNA corresponding to the 3' end of the genome. In addition, NCp7 slightly stimulates an in vitro IN cleavage assay. These results indicate that the interactions between NCp7 and proviral DNA may be important during provirus synthesis and/or prior to integration.