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Molecules 2015, 20(11), 20832-20840; doi:10.3390/molecules201119733

Identification of RNA Oligonucleotides Binding to Several Proteins from Potential G-Quadruplex Forming Regions in Transcribed Pre-mRNA

1
Department of Biotechnology and Life Science, Graduate School of Engineering, Tokyo University of Agriculture & Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
2
School of Biotechnology and Bioscience Tokyo University of Technology, 1404-1 Katakura-cho, Hachioji, Tokyo 192-0982, Japan
These authors contributed equally to this work.
*
Author to whom correspondence should be addressed.
Academic Editors: Alain O.A. Miller and Jean Jacques Vanden Eynde
Received: 15 September 2015 / Revised: 6 November 2015 / Accepted: 12 November 2015 / Published: 23 November 2015
(This article belongs to the Special Issue Aptamers: Past, Present, and Future)
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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. View Full-Text
Keywords: RNA aptamer; G-quadruplex; first intron; 5′ UTR; heparin-binding proteins RNA aptamer; G-quadruplex; first intron; 5′ UTR; heparin-binding proteins
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This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. (CC BY 4.0).

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Saito, T.; Yoshida, W.; Yokoyama, T.; Abe, K.; Ikebukuro, K. Identification of RNA Oligonucleotides Binding to Several Proteins from Potential G-Quadruplex Forming Regions in Transcribed Pre-mRNA. Molecules 2015, 20, 20832-20840.

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