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Molecules 2010, 15(11), 7509-7531; doi:10.3390/molecules15117509

Synthesis of Oligodeoxynucleotides Using Fully Protected Deoxynucleoside 3′-Phosphoramidite Building Blocks and Base Recognition of Oligodeoxynucleotides Incorporating N3-Cyano-Ethylthymine

Department of Life Science, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Japan
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Received: 27 August 2010 / Revised: 8 October 2010 / Accepted: 14 October 2010 / Published: 27 October 2010
(This article belongs to the Special Issue Protecting Group in Organic Synthesis)
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Abstract

Oligodeoxynucleotide (ODN) synthesis, which avoids the formation of side products, is of great importance to biochemistry-based technology development. One side reaction of ODN synthesis is the cyanoethylation of the nucleobases. We suppressed this reaction by synthesizing ODNs using fully protected deoxynucleoside 3′-phosphoramidite building blocks, where the remaining reactive nucleobase residues were completely protected with acyl-, diacyl-, and acyl-oxyethylene-type groups. The detailed analysis of cyanoethylation at the nucleobase site showed that N3-protection of the thymine base efficiently suppressed the Michael addition of acrylonitrile. An ODN incorporating N3-cyanoethylthymine was synthesized using the phosphoramidite method, and primer extension reactions involving this ODN template were examined. As a result, the modified thymine produced has been proven to serve as a chain terminator.
Keywords: protecting group; oligodeoxynucleotide synthesis; cyanoethylation protecting group; oligodeoxynucleotide synthesis; cyanoethylation
This is an open access article distributed under the Creative Commons Attribution License (CC BY 3.0).

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Tsunoda, H.; Kudo, T.; Ohkubo, A.; Seio, K.; Sekine, M. Synthesis of Oligodeoxynucleotides Using Fully Protected Deoxynucleoside 3′-Phosphoramidite Building Blocks and Base Recognition of Oligodeoxynucleotides Incorporating N3-Cyano-Ethylthymine. Molecules 2010, 15, 7509-7531.

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