Analytical Sciences

The Effect of Local Structural Disruption on the Yield of Photochemical Ligation between Anthracene-Oligonucleotide Conjugates

Pelin ARSLAN,* Toshihiro IHARA,*^,** Motoko MUKAE,* and Akinori JYO*

*Department of Applied Chemistry and Biochemistry, Graduate School of Science and Technology, Kumamoto University, 2-39-1 Kurokami, Kumamoto 860-8555, Japan
**PRESTO, Japan Science and Technology Agency, San-bancho Building, 3-5 Sanbancho, Chiyoda, Tokyo 332-0012, Japan

The techniques of chemical ligation have attracted great attention as an alternative to enzymatic joining of DNA ends. Here we introduce the photoligation of anthracene-modified ODN conjugates through anthracene cyclodimer formation. The effect of the positions and the kinds of single base mismatch on the template was evaluated using eight templates with one-base displacements. We found out that the yield of the ligation was affected by mispairing in a position-dependent manner. Such results would be attributed to the disruption of the local structure at the ligation site.

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