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Nucleic Acids Symposium Series 2006 50(1):61-62; doi:10.1093/nass/nrl030
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© 2006 Oxford University Press

Synthesis of oligonucleotides containing the Dewar valence isomer of the (6–4) photoproduct and their application to (6–4) photolyase studies

Junpei Yamamoto1, Kenichi Hitomi1,2, Takeshi Todo3 and Shigenori Iwai1

1 Division of Chemistry, Graduate School of Engineering Science, Osaka University, 1-3 Machikaneyama, Toyonaka, Osaka 560-8531, Japan, 2 Department of Molecular Biology and the Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA, 3 Radiation Biology Center, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan

The (6–4) photoproduct, which is a major UV light-induced lesion formed between adjacent pyrimidine bases, is isomerized to its Dewar valence isomer by exposure to longer wavelengths. We have synthesized a phosphoramidite building block of the Dewar photoproduct formed at the thymidylyl(3'–5')thymidine site, and incorporated it into oligonucleotides on a DNA synthesizer, aiming to use them for biological studies. An alternative activator, benzimidazolium triflate, gave better results, while by-products were detected at longer retention time in the ordinary synthesis. We characterized the synthetic oligonucleotides by UV conversion, nuclease digestion and mass spectrometry. Their use in the study of the (6–4) photolyase, a DNA repair enzyme, revealed its different recognition modes between the (6–4) photoproduct and the Dewar isomer.


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