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. 2015 Jun 3:61:4.62.1-4.62.22.
doi: 10.1002/0471142700.nc0462s61.

Synthesis of Nonnatural Oligonucleotides Made Exclusively of Alkynyl C-Nucleosides with Nonnatural Bases

Junya Chiba  1 , Masahiko Inouye  1
Affiliations

Synthesis of Nonnatural Oligonucleotides Made Exclusively of Alkynyl C-Nucleosides with Nonnatural Bases

Junya Chiba et al. Curr Protoc Nucleic Acid Chem. .

Abstract

This unit describes detailed procedures for the preparation of nonnatural C-nucleosides comprising seven types of nonnatural nucleobases attached to 1'-position of 2'-deoxyribose through an acetylene bond with the β-configuration. In addition, derivatization of these alkynyl C-nucleosides into the corresponding phosphoramidites and the subsequent oligonucleotide synthesis are also presented. The processes are depicted in three parts. The first basic protocol deals with the synthesis of a key intermediate, 5-O-DMTr-protected 1-ethynyl-2-deoxy-β-D-ribofuranoside. The second basic protocol mentions the procedures of the preparation of nonnatural C-nucleosides by a palladium-catalyzed coupling reaction of the ethynyl intermediate and halogen-attached nonnatural nucleobases. The synthetic procedures of the corresponding nonnatural phosporamidites are also described. The third basic protocol presents the solid-phase, automated synthesis of nonnatural oligonucleotides composed exclusively of the nonnatural C-nucleotides.

Keywords: alkynyl C-nucleosides; nonnatural nucleobases; oligonucleotides.

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References

Literature Cited

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    1. Chiba, J. and Inouye, M. 2010. Exotic DNA made of nonnatural bases and natural phosphodiester bonds. Chem. Biodivers. 7:259-282.
    1. Chiba, J. , Shirato, W. , Yamade, Y. , Kim, B.S. , Matsumoto, S. , and Inouye, M. 2012. Furanose ring conformations in a 1′-alkynyl C -nucleoside and the dinucleotide. Tetrahedron 68:9045-9049.
    1. Chiba, J. , Takeshima, S. , Mishima, K. , Maeda, H. , Nanai, Y. , Mizuno, K. , and Inouye, M. 2007. Artificial DNAs based on alkynyl C -nucleosides as a superior scaffold for homo- and heteroexcimer emissions. Chem. Eur. J. 13:8124-8130.

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