Mechanism for nucleic acid chaperone activity of HIV-1 nucleocapsid protein revealed by single molecule stretching

The nucleocapsid protein (NC) of HIV type 1 is a nucleic acid chaperone tha t facilitates the rearrangement of nucleic acids into conformations contain ing the maximum number of complementary base pairs. We use an optical tweez ers instrument to stretch single DNA molecules from the helix to coil state at room temperature in the presence of NC and a mutant form (SSHS NC) that lacks the two zinc finger structures present in NC. Although both NC and S SHS NC facilitate annealing of complementary strands through electrostatic attraction, only NC destabilizes the helical form of DNA and reduces the co operativity of the helix-coil transition. In particular, we find that the h elix-coil transition free energy at room temperature is significantly reduc ed in the presence of NC. Thus, upon NC binding, it is likely that thermody namic fluctuations cause continuous melting and reannealing of base pairs s o that DNA strands are able to rapidly sample configurations to find the lo west energy state. The reduced cooperativity allows these fluctuations to o ccur in the middle of complex double-stranded structures. The reduced stabi lity and cooperativity, coupled with the electrostatic attraction generated by the high charge density of NC, is responsible for the nucleic acid chap erone activity of this protein.