DNA binding properties of the zinc-bound and zinc-free HIV nucleocapsid protein: supercoiled DNA unwinding and DNA-protein cleavable complex formation

The HIV nucleocapsid (NC) protein contains, as those of other retroviruses, two Cys-His arrays which function as zinc finger binding domains. The nucleic acid binding properties of retroviral NC have been previously demonstrated. In this study, we characterized the DNA binding ability of the zinc-bound and zinc-free forms of HIV NC. We found that in addition to binding single-stranded DNA, both forms bind and unwind supercoiled plasmid DNA. The binding ability of the zinc-bound form was higher than the zinc-free form. In addition we showed the formation of NC protein-DNA cleavable complex which is the result of a presumably covalent bond formed between the protein and the phosphate moiety of the DNA backbone. The NC unwinding activity and the protein-DNA cleavable complex formation resembles the first step of the relaxing mechanism of DNA topoisomerase. Our results shed light on the possibility of a novel physiological function for the HIV NC protein in the viral life cycle.