title: An RNA aptamer with high affinity and high specificity for the 5S RNA binding zinc finger proteins TFIIIA and p43.
abstract: The Xenopus zinc finger proteins TFIIIA and p43 bind to 5S RNA in immature oocytes to form 7S and 42S ribonucleoprotein storage particles. To probe the similarities and differences in the RNA binding domains of these two proteins, a library of random RNA molecules was enriched using TFIIIA as the bait protein. One of the abundant aptamers isolated, RNA22, bound to both TFIIIA and p43 derived zinc finger peptides with high affinity and specificity even though the predicted secondary structure of the RNA was unrelated to that of 5S RNA. The interactions of TFIIIA and p43 peptides with RNA22 were compared to their interactions with 5S RNA by characterizing the effects of assay conditions, mutations in RNA22, and mutations in the zinc finger proteins. The similarities and differences in the mechanisms by which these two zinc finger proteins interact with 5S RNA compared to RNA22 suggest they share a common platform for RNA binding with enough flexibility to form specific interactions with both RNAs.
authors.affiliation: Department of Biochemistry and Microbiology, University of Victoria, P.O. Box 3055, Victoria, British Columbia V8W 3P6, Canada.
authors.forename: Tristen C
authors.initials: TC
authors.lastname: Weiss
authors.forename: Gary G
authors.initials: GG
authors.lastname: Zhai
authors.forename: Paul J
authors.initials: PJ
authors.lastname: Romaniuk
mesh_terms: D000818:Animals; D052157:Aptamers, Nucleotide / Q000737:chemistry* / Q000378:metabolism*; D001483:Base Sequence; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D011485:Protein Binding; D016601:RNA-Binding Proteins / Q000235:genetics / Q000378:metabolism*; D012269:Ribosomal Proteins / Q000235:genetics / Q000378:metabolism*; D035582:Transcription Factor TFIIIA / Q000235:genetics / Q000378:metabolism*; D029867:Xenopus Proteins / Q000235:genetics / Q000378:metabolism*; D014982:Xenopus laevis
chemical_list: D052157:Aptamers, Nucleotide; C489267:LOC397745 protein, Xenopus; D016601:RNA-Binding Proteins; D012269:Ribosomal Proteins; D035582:Transcription Factor TFIIIA; D029867:Xenopus Proteins