SEQUENCE-SPECIFIC BINDING OF HUMAN-IMMUNODEFICIENCY-VIRUS TYPE-1 NUCLEOCAPSID PROTEIN TO SHORT OLIGONUCLEOTIDES

We have analyzed the binding of recombinant human immunodeficiency vir us type 1 nucleocapsid protein (NC) to very short oligonucleotides by using surface plasmon resonance (SPR) technology. Our experiments, whi ch were conducted at a moderate salt concentration (0.15 M NaCl), show ed that NC binds more stably to runs of d(G) than to other DNA homopol ymers. However, it exhibits far more stable binding with the alternati ng base sequence d(TG)(n) than with any homopolymeric oligodeoxyribonu cleotide; thus, it shows a strong sequence preference under our experi mental conditions, We found that the minimum length of an alternating d(TG) sequence required for stable binding was five nucleotides, Stabl e binding to the tetranucleotide d(TG)(2) was observed only under cond itions where two tetranucleotide molecules were held in close spatial proximity. The stable, sequence-specific binding to d(TG)(n) required that both zinc fingers be present, each in its proper position in the NC protein, and was quite salt resistant, indicating a large hydrophob ic contribution to the binding, Limited tests with RNA oligonucleotide s indicated that the preferential sequence specific binding observed w ith DNA also occurs with RNA, Evidence was also obtained that NC can b ind to nucleic acid molecules in at least two distinct modes, The biol ogical significance of the specific binding we have detected is not kn own; it may reflect the specificity with which the parent Gag polyprot ein packages genomic RNA or may relate to the functions of NC after cl eavage of the polyprotein, including its role as a nucleic acid chaper one.