G-quartets direct assembly of HIV-1 nucleocapsid protein along single-stranded DNA. Nucleic Acids Res

The d(TTGGGGGGTACAGTGCA) sequence, derived from the human immunode®ciency virus type 1 (HIV-1) central DNA ¯ap, can form in vitro an inter-molecular parallel DNA quadruplex. This work dem-onstrates that the HIV-1 nucleocapsid protein (NCp) exhibits a high af®nity (108 M±1) for this quadruplex. This interaction is predominantly hydrophobic, maintained by a stabilization between G-quartet planes and the C-terminal zinc ®nger of the protein. It also requires 5 nt long tails ¯anking the quartets plus both the second zinc-®nger and the N-terminal domain of NCp. The initial binding nucleates an ordered arrangement of consecutive NCp along the four single-stranded tails. Such a process requires the N-terminal zinc ®nger, and was found to occur for DNA site sizes shorter than usual in a sequence-dependent manner. Concurrently, NCp binding is ef®cient on a G¢2 quadruplex also derived from the HIV-1 central DNA ¯ap. Apart from their implication within the DNA ¯ap, these data lead to a model for the nucleic acid architecture within the viral nucleo-capsid, where adjacent single-stranded tails and NCp promote a compact assembly of NCp and nucleic acid growing from stably and primary bound NCp