title: Identification of RNA Oligonucleotides Binding to Several Proteins from Potential G-Quadruplex Forming Regions in Transcribed Pre-mRNA.
abstract: G-quadruplexes (G4s) are noncanonical DNA/RNA structures formed by guanine-rich sequences. Recently, G4s have been found not only in aptamers but also in the genomic DNA and transcribed RNA. In this study, we identified new RNA oligonucleotides working as aptamers by focusing on G4-forming RNAs located within the pre-mRNA. We showed that the G4 in the 5' UTR and first intron of VEGFA bound to the protein encoded in VEGFA gene, VEGF165, with high affinity. Moreover, G4-forming RNAs located within the PDGFA and the PDGFB introns bound to PDGF-AA and PDGF-BB, respectively, indicating that G4 in the pre-mRNA could be an aptamer. It had been reported that the putative G4-forming RNA sequences are located in some parts of most genes, thus our strategy for aptamer identification could be applicable to other proteins. It has been reported that some G4-forming RNAs in 5' UTRs are involved in translation control; however, G4-forming excised intronic RNA function has not been revealed previously. Therefore, these findings could not only contribute to the identification of RNA aptamers but also provide new insights into the biological functioning of G4-forming RNAs located within intronic RNA sequences.
authors.affiliation: Department of Biotechnology and Life Science, Graduate School of Engineering, Tokyo University of Agriculture &amp; Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan. 50013831103@st.tuat.ac.jp.
authors.forename: Taiki
authors.initials: T
authors.lastname: Saito
authors.affiliation: School of Biotechnology and Bioscience Tokyo University of Technology, 1404-1 Katakura-cho, Hachioji, Tokyo 192-0982, Japan. yoshidawtr@stf.teu.ac.jp.
authors.forename: Wataru
authors.initials: W
authors.lastname: Yoshida
authors.affiliation: Department of Biotechnology and Life Science, Graduate School of Engineering, Tokyo University of Agriculture &amp; Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan. tyokoyama472@gmail.com.
authors.forename: Tomomi
authors.initials: T
authors.lastname: Yokoyama
authors.affiliation: Department of Biotechnology and Life Science, Graduate School of Engineering, Tokyo University of Agriculture &amp; Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan. abe79kou@gmail.com.
authors.forename: Koichi
authors.initials: K
authors.lastname: Abe
authors.affiliation: Department of Biotechnology and Life Science, Graduate School of Engineering, Tokyo University of Agriculture &amp; Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan. ikebu@cc.tuat.ac.jp.
authors.forename: Kazunori
authors.initials: K
authors.lastname: Ikebukuro
mesh_terms: D002942:Circular Dichroism; D054856:G-Quadruplexes; D006801:Humans; D009690:Nucleic Acid Conformation; D009843:Oligoribonucleotides / Q000737:chemistry* / Q000378:metabolism*; D010982:Platelet-Derived Growth Factor / Q000737:chemistry / Q000235:genetics; D011485:Protein Binding; D020574:Proto-Oncogene Proteins c-sis / Q000737:chemistry / Q000235:genetics; D012322:RNA Precursors / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D016601:RNA-Binding Proteins / Q000378:metabolism*; D020349:Surface Plasmon Resonance; D014158:Transcription, Genetic; D042461:Vascular Endothelial Growth Factor A / Q000737:chemistry / Q000235:genetics
chemical_list: D009843:Oligoribonucleotides; D010982:Platelet-Derived Growth Factor; D020574:Proto-Oncogene Proteins c-sis; D012322:RNA Precursors; D016601:RNA-Binding Proteins; D042461:Vascular Endothelial Growth Factor A; C075278:platelet-derived growth factor A
keywords: 5′ UTR; G-quadruplex; RNA aptamer; first intron; heparin-binding proteins