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DNA Research 1998 5(6):349-354; doi:10.1093/dnares/5.6.349
© 1998 by Kazusa DNA Research Institute
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Localization and Characterization of Curved DNA in the Human Erythropoietin Receptor Gene by Experimental and Theoretical Approaches

Philip Rodley1, Naoko S. Nishikawa2, Maiko Hirota3, Yuko Wada-kiyama4, Constance T. Noguchi5, Michio Oishi6 and Ryoiti Kiyama1,*

1Department of Molecular Biology, National Institute of Bioscience and Human-Technology, Ministry of International Trade and Industry Tsukuba, Ibaraki 305, Japan
2Cell. Physiol. Lab., The Institute of Physical and Chemical Research (RIKEN) Wako, Saitama 351-0198, Japan
3Kyowa Hakko Kogyo Co., LTD. Machida, Tokyo 194, Japan
4Department of Physiology, Nippon Medical School Sendagi, Bunkyo-ku, Tokyo 113, Japan
5LCB, NIDDK, National Institutes of Health Bethesda, Maryland 20892-1822, USA
6Kazusa DNA Research Institute 1532-3 Yana, Kisarazu, Chiba 292, Japan

* To whom correspondence should be addressed. Tel. +81-298-54-6189, Fax. +81-298-54-6190, E-mail: kiyamar{at}nibh.go.jp

We report here the locations of curved DNA in the human erythropoietin receptor gene. A total of 13 DNA bend sites were mapped by circular permutation assays, appearing at an average interval of 651.2 ± 214.6 (S.D.) in the 8-kb region. The bend centers in these 13 bend sites were confirmed by oligonucleotide-based assays where most of these centers had bend angles higher than that shown by (AAACCGGGCC)·(A)20 and lower than that shown by (AAACCGGGCC)2·(A)10. DNA curvature mapping by TRIF software, which is based on the distribution of dinucleotides, primarily AA and TT, provided a highly accurate prediction for the locations of the bend sites. They showed approximately 20° to 40° of bend angles demonstrated by the oligonucleotide assays and by computer analysis.

Key words: DNA bendsite; periodicity; bend angle


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