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Nucleic Acids Symposium Series 2007 51(1):25-26; doi:10.1093/nass/nrm013
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© 2007 Oxford University Press

Recognition of triplex forming oligodeoxynucleotides incorporating abasic sites by 5-arylcytosine residues in duplex DNAs

Masahiro Mizuta, Jun-ichi Banba, Takashi Kanamori, Akihiro Ohkubo, Mitsuo Sekine* and Kohji Seio

Department of life science, Tokyo Institute of Tecnology and CREST, JST, Nagatsuta, Midoriku, Yokohama, 226-8501, Japan

*Corresponding Author. E-mail: msekine{at}bio.titech.ac.jp

Abstract

In this paper, we reported our attempt to use a 5arylcytosine (dCar) and the abasic site ({phi}) as an artificial base pair for DNA triplex. The idea was confirmed by the molecular modeling studied in which the aromatic group of ph which protrudes in the major groove was buried into the cleft formed by the {phi} residue in the TFO. We synthesized three kinds of dCar and the oligonucleotides incorporating them. Our UV-melting experiments revealed that the DNA triplex containing the dCph{blacksquare}{phi} was more stable than that containing dC{blacksquare}{phi} pair. Moreover, the dCph{blacksquare}{phi} pair was more stable than any other dCph{blacksquare}Y pairs such as dCph{blacksquare}G, dCph{blacksquare}C, dCph{blacksquare}T and dCph{blacksquare}A. These results indicated the possibility that the appropriate pair of dCAr and {phi} could be the new sequence code of DNA triplex. We also carried out the Tm analyses of other TFOs incorporating dCAr and {phi}, and clarified the stability of these triplexes.


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