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Nucleic Acids Symposium Series 2004 48(1):15-16; doi:10.1093/nass/48.1.15
© 2004 by Oxford University Press
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Synthesis and properties of 5-pyrrolyl-cytidine and uridine derivatives

Kenichi Miyata1,3, Ryouta Mineo1, Ryuji Tamamushi1, Haruhiko Taguchi1,3, Kohji Seio2,3 and Mitsuo Sekine1,3

1 Department of Life Science, Faculty of Bioscience and Biotechnology, Tokyo Institute of Technology, Japan, 2 Frontier Collaborative Research, Tokyo Institute of Technology, Japan, 3 CREST, JST (Japan Science and Technology Agency), Nagatsuda, Midoriku, Yokohama 226-8501, Japan

New 5-modified pyrimidine derivatives that were expected to form Hoogsteen-type triplexes have been synthesized, 5-Pyrrolyl-2'-O-methylcytosine was designed as a protonated cytosine mimic to realize pH-independent triplex formation with the complementary G-C Watson-Crick base pair by inducing the imino tautomer of cytosine. 5-Pyrrolyl-2'-O-methyluridine was also synthesized to enhance the stacking effect for stabilization of triplexes. For the deprotection of the DMTr group in the phosphoramidite method, EtSi3H was added as the scavenger of the dimethoxytrityl-cation to avoid side-reactions on the pyrrolyl group. The triplex forming ability of TFOs containing modified nucleosides was evaluated by Tm experiments under various conditions.


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