Molecules 2010, 15, 7509-7531; doi:10.3390/molecules15117509 OPEN ACCESS molecules ISSN 1420-3049 www.mdpi.com/journal/molecules Article Synthesis of Oligodeoxynucleotides Using Fully Protected Deoxynucleoside 3′-Phosphoramidite Building Blocks and Base Recognition of Oligodeoxynucleotides Incorporating N3-Cyano-Ethylthymine Hirosuke Tsunoda, Tomomi Kudo, Akihiro Ohkubo, Kohji Seio and Mitsuo Sekine * Department of Life Science, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Japan; E-Mails:
[email protected] (H.T.);
[email protected] (T.K.);
[email protected] (A.O.);
[email protected] (K.S.) * Author to whom correspondence should be addressed; E-Mail:
[email protected]; Tel.: +81-45-924-5706; Fax: +81-45-924-5772. Received: 27 August 2010; in revised form: 8 October 2010 / Accepted: 14 October 2010 / Published: 27 October 2010 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.