Abstract
Regulation of gene expression by short oligonucleotides (antisense oligonucleotides), which can modulate RNA structures and inhibit subsequent associations with the translation machinery, is a potential approach for gene therapy. This chapter describes an alternative antisense strategy using guanine-tethered antisense oligonucleotides (G-ASs) to introduce a DNA–RNA heteroquadruplex structure at a designated sequence on RNA targets. The feasibility of using G-ASs to modulate RNA conformation may allow control of RNA function by inducing biologically important quadruplex structures. This approach to manipulate quadruplex structures using G-ASs may expand the strategies for regulating RNA structures and the functions of short oligonucleotide riboregulators.
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References
Roth A, Breaker RR (2009) The structural and functional diversity of metabolite-binding riboswitches. Annu Rev Biochem 78:305–334
Serganov A, Patel DJ (2007) Ribozymes, riboswitches and beyond: regulation of gene expression without proteins. Nat Rev Genet 8:776–790
Mandal M, Breaker RR (2004) Gene regulation by riboswitches. Nat Rev Mol Cell Biol 5:451–463
Link KH, Breaker RR (2009) Engineering ligand-responsive gene-control elements: lessons learned from natural riboswitches. Gene Ther 16:1189–1201
Burge S, Parkinson GN, Hazel P et al (2006) Quadruplex DNA: sequence, topology and structure. Nucleic Acids Res 34:5402–5415
Lane AN, Chaires JB, Gray RD et al (2008) Stability and kinetics of G-quadruplex structures. Nucleic Acids Res 36:5482–5515
Kumari S, Bugaut A, Huppert JL et al (2007) An RNA G-quadruplex in the 5′ UTR of the NRAS proto-oncogene modulates translation. Nat Chem Biol 3:218–221
Arora A, Dutkiewicz M, Scaria V et al (2008) Inhibition of translation in living eukaryotic cells by an RNA G-quadruplex motif. RNA 14:1–7
Stein CA, Cheng YC (1993) Antisense oligonucleotides as therapeutic agents—is the bullet really magical? Science 261:1004–1012
Eckstein F (2007) The versatility of oligonucleotides as potential therapeutics. Expert Opin Biol Ther 7:1021–1034
Hagihara M, Yamauchi L, Seo A et al (2010) Antisense-induced Guanine Quadruplexes inhibit reverse transcription by HIV-1 reverse transcriptase. J Am Chem Soc 132:11171–11178
Hagihara M, Yoneda K, Yabuuchi H et al (2010) A reverse transcriptase stop assay revealed diverse quadruplex formations in UTRs in mRNA. Bioorg Med Chem Lett 20:2350–2353
Maurizot JC (2000) Circular dichroism of nucleic acids: nonclassical conformations and modified oligonucleotides. In: Berova N, Nakanishi K, Woody RW (eds) Circular dichroism: principles and applications, 2nd edn. Wiley-VCH, New York, pp 719–739
Porumb H, Monnot M, Fermandjian S (2002) Circular dichroism signatures of features simultaneously present in structured guanine-rich oligonucleotides: a combined spectroscopic and electrophoretic approach. Electrophoresis 23:1013–1020
Sun XG, Cao EH, He YJ et al (1999) Spectroscopic comparison of different DNA structures formed by oligonucleotides. J Biomol Struct Dyn 16:863–872
Mergny JL, Phan AT, Lacroix L (1998) Following G-quartet formation by UV-spectroscopy. FEBS Lett 435:74–78
Mergny JL, Lacroix L (2009) UV melting of G-Quadruplexes. In: Egli M, Herdewijn P, Matusda A, Yogesh S (eds) Curr Protoc Nucleic Acid Chem, Wiley-VCH, New York, Chapter 17: Unit 17.1
Xiao Y, Pavlov V, Niazov T et al (2004) Catalytic beacons for the detection of DNA and telomerase activity. J Am Chem Soc 126:7430–7431
Deng M, Zhang D, Zhou Y et al (2008) Highly effective colorimetric and visual detection of nucleic acids using an asymmetrically split peroxidase DNAzyme. J Am Chem Soc 130:13095–13102
De Cian A, Guittat L, Kaiser M et al (2007) Fluorescence-based melting assays for studying quadruplex ligands. Methods 42:183–195
Fukada H, Takahashi K (1998) Enthalpy and heat capacity changes for the proton dissociation of various buffer components in 0.1 M potassium chloride. Proteins 33:159–166
Steely HT Jr, Gray DM, Ratliff RL (1986) CD of homopolymer DNA-RNA hybrid duplexes and triplexes containing A-T or A-U base pairs. Nucleic Acids Res 14:10071–10090
Jin R, Gaffney BL, Wang C et al (1992) Thermodynamics and structure of a DNA tetraplex: a spectroscopic and calorimetric study of the tetramolecular complexes of d(TG3T) and d(TG3T2G3T). Proc Natl Acad Sci U S A 89:8832–8836
Benz A, Hartig JS (2008) Redesigned tetrads with altered hydrogen bonding patterns enable programming of quadruplex topologies. Chem Commun (Camb) 34:4010–4012
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This work was supported by a grant from the Ichiro Kanehara Foundation.
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Hagihara, M. (2014). Guanine-Tethered Antisense Oligonucleotides as Synthetic Riboregulators. In: Ogawa, A. (eds) Artificial Riboswitches. Methods in Molecular Biology, vol 1111. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-62703-755-6_14
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DOI: https://doi.org/10.1007/978-1-62703-755-6_14
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