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

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

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,
,
 and
*
Department of Life Science, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Japan
* Author to whom correspondence should be addressed.
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 which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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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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