title: G-quartets direct assembly of HIV-1 nucleocapsid protein along single-stranded DNA.
abstract: The d(TTGGGGGGTACAGTGCA) sequence, derived from the human immunodeficiency virus type 1 (HIV-1) central DNA flap, can form in vitro an intermolecular parallel DNA quadruplex. This work demonstrates that the HIV-1 nucleocapsid protein (NCp) exhibits a high affinity (10(8) M(-1)) for this quadruplex. This interaction is predominantly hydrophobic, maintained by a stabilization between G-quartet planes and the C-terminal zinc finger of the protein. It also requires 5 nt long tails flanking the quartets plus both the second zinc-finger 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 finger, and was found to occur for DNA site sizes shorter than usual in a sequence-dependent manner. Concurrently, NCp binding is efficient on a G'2 quadruplex also derived from the HIV-1 central DNA flap. Apart from their implication within the DNA flap, these data lead to a model for the nucleic acid architecture within the viral nucleocapsid, where adjacent single-stranded tails and NCp promote a compact assembly of NCp and nucleic acid growing from stably and primary bound NCp.
mesh_terms: D001483:Base Sequence; D001665:Binding Sites; D036022:Capsid Proteins / Q000737:chemistry / Q000378:metabolism*; D004247:DNA / Q000737:chemistry* / Q000378:metabolism*; D004277:DNA, Single-Stranded / Q000737:chemistry / Q000378:metabolism*; D054856:G-Quadruplexes; D015683:Gene Products, gag / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D006147:Guanine / Q000737:chemistry*; D015497:HIV-1; D046911:Macromolecular Substances; D008954:Models, Biological; D009690:Nucleic Acid Conformation; D011485:Protein Binding; D011498:Protein Precursors / Q000235:genetics / Q000378:metabolism; D017434:Protein Structure, Tertiary; D011994:Recombinant Proteins / Q000032:analysis
chemical_list: D036022:Capsid Proteins; D004277:DNA, Single-Stranded; D015683:Gene Products, gag; D046911:Macromolecular Substances; D011498:Protein Precursors; D011994:Recombinant Proteins; C059767:p55 gag precursor protein, Human immunodeficiency virus 1; D006147:Guanine; D004247:DNA