A novel yeast gene product, G4p1, with a specific affinity for quadruplex nucleic acids

G4 nucleic acids are four-stranded helical structures that are formed in vitro by nucleic acids that contain guanine tracts. These structures anneal readily under physiological conditions and are unusually stable once formed. G4 nucleic acids are thought to participate in telomere function, retroviral genome dimerization, chromosome alignment during homologue pairing, and mitotic recombination, although the in vivo demonstration of these structures in any of these situations has not yet been achieved. Here we purify and characterize an activity from yeast, G4p1, which has a high and specific affinity for G4 nucleic acids. G4p1 prefers substrates containing multiple G4 domains, has an equal affinity for parallel and antiparallel G4 structures, and binds equivalently to RNA and DNA in G4 form. The Keq for G4p1 binding to a G4 DNA oligomer is 5.0 x 10(8) M-1, under near physiological conditions. G4p1 was purified and shown to derive from a 42-kDa protein (p42). We have cloned and sequenced the gene encoding p42 and show it to encode a novel protein with a region significantly homologous to bacterial methionyl-tRNA synthetase dimerization domains. We have reconstituted the G4p1 binding activity with recombinant p42 and present evidence that G4p1 is a homodimer of p42.