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Nucleic Acids Symposium Series 2006 50(1):259-260; doi:10.1093/nass/nrl129
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© 2006 Oxford University Press

Studies of DNA recognition mechanism of transcription factor IRF-4

Kyoko Furuita1, Itsuko Ishizaki1, Harumi Fukada2, Kazuo Yamamoto3, Toshifumi Matsuyama3, Makoto Nomura1, Masaki Mishima1 and Chojiro Kojima1

1 Laboratory of Biophysics, Graduate School of Biological Sciences, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan, 2 Laboratory of Biophysical Chemistry, Graduate School of Life and Environmental Sciences, Osaka Prefecture University, 1-1 Gakuen-cho, Nakaku, Sakai, Osaka 599-8531, Japan, 3 Division of Cytokine Signaling, Department of Molecular Microbiology and Immunology, Nagasaki University Graduate School of Biomedical Sciences, 1-12-4 Sakamoto, Nagasaki 852-8523, Japan

Transcription factor IFN regulatory factor-4 (IRF-4) prefers a DNA sequence including CCGAAA, though the consensus DNA-binding sequence of the IRF family proteins is NNGAAA, and the crystal structure of PU.1/IRF-4/DNA (GTGAAA) ternary complex indicates the NN region of DNA does not interact with IRF-4 directly. This suggests that there is an indirect DNA recognition mechanism in IRF-4. In order to account for the sequence preference of IRF-4, we focused on structural properties of DNA duplexes recognized by IRF-4. Here, we performed solution NMR studies on DNA duplexes containing GGGAAA and CCGAAA sequences, and assigned most of proton resonances of DNA 17 mer with GGGAAA. 1H-1H NOESY spectra indicated B-form like structure for GGGAAA. We also assigned imino proton resonances of DNA 17 mer with CCGAAA. For the imino proton region, the 1H-1H NOESY spectra of these two DNA duplexes were similar.


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