The nucleocapsid protein (NC) of all animal retroviruses is the major structural protein of the core ribonucleoprotein complex, bound to genomic RNA in mature virions. In a previous report, we showed that recombinant NC protein from HIV-1, a 71-amino-acid protein (NC71), is apparently able to form two types of protein-nucleic acid complexes under low [NaCl], pH 8.3 and 25 degrees C. These appeared to differ in occluded apparent site size, napp, forming n = 8 and n = 14 complexes on poly(A) (Dib-Hajj, F., Khan, R., and Giedroc, D. P. (1993) Protein Sci. 2, 331-243) under conditions of high and low protein-nucleotide ratios, respectively. Here we show that both NC71-poly(A) complexes strongly scatter light under these solution conditions. Examination of the wavelength dependence of the light scattering at lambda < or = 320 nm indicates that each complex is characterized by a different scattering coefficient. Optical density measurements suggest that upon formation of the saturated n = 8 complex, additional polynucleotide is not incorporated into the complex over a period of hours, i.e. the n = 14 complex is not formed via redistribution of the n = 8 complex under low salt conditions, 25 degrees C. In contrast, the n = 14 complex readily incorporates additional protein until that sufficient to form the n = 8 complex is present. The n = 14 complex efficiently precipitates poly(A) and shows spectral characteristics expected for an extensively charge-neutralized nucleic acid complex. At [NC71] in excess of that required to form the n = 8 complex, this n = 14 complex is best described as a kinetic intermediate on the pathway to the n = 8 complex, which forms over a period of hours under low salt conditions, 25 degrees C. This slow kinetics of binding provides a possible explanation for the finding that the previously observed moderate cooperativity of Zn2 NC71 binding to poly(A) (omega = 200) at pH 8.3 and 0.29 M NaCl (Khan, R., and Giedroc, D. P. (1992) J. Biol. Chem. 267, 6689-6695) is shown here to represent a nonequilibrium phenomenon, apparently converting to a low or no cooperativity complex over a period of hours. Proteolytic removal of the COOH-terminal 14 amino acids from NC71, forming a 57-amino-acid protein (denoted NC57), removes this apparent binding site size heterogeneity of NC71 on poly(A). At 20 mM NaCl, NC57 binds with n = 6-7 nucleotides, in a manner which is independent of the protein-poly(A) nucleotide ratio. The implications of these findings on processing of the gag precursor which leads to mature NC in HIV-1 virions is discussed.