NUCLEIC ACID-BINDING PROPERTIES OF THE XENOPUS OOCYTE Y-BOX PROTEIN MRNP(3+4)

Y box proteins contain the conserved cold shock domain (CSD) and sever al basic/aromatic (B/A) islands; that are rich in arginine and aromati c residues. The binding of purified Xenopus oocyte 6S Y box protein, m RNP(3+4), to Y box RNA, single-stranded (ss) DNA, and double-stranded (ds) DNA was studied by gel mobility shift and nitrocellulose filter b inding assays. mRNP(3+4) specifically bound Y box ssDNA or RNA, while binding of dsDNA was not detected. Y box ssDNA and RNA did not efficie ntly cross-compete for mRNP(3+4) binding, and no evidence for;ternary complex formation was detected. However, Y box ssDNA binding was compe ted by high concentrations of Y box RNA or nonspecific RNA competitors , indicating that the ssDNA-binding site; has a lower affinity for RNA . mRNP(3+4) demonstrated similar affinity for either Y box RNA or ssDN A. However, at elevated ionic strength RNA binding was markedly greate r than ssDNA binding, indicating that RNA binding involves nonionic in teractions that are not utilized for ssDNA binding. Recombinant polype ptides containing B/A islands bound Y box RNA exclusively, but inclusi on of the CSD led to preferential ssDNA binding. The results demonstra te that the B/A. islands are exclusively RNA-binding, while the CSD ex hibits preferential binding of ssDNA. The inability of Y box RNA and s sDNA to efficiently cross-compete for mRNP(3+4) binding suggests that isoforms exhibit preferential ssDNA or RNA binding.