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Nucleic Acids Research 2005 33(9):2887-2900; doi:10.1093/nar/gki606
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Published online 20 May 2005

© The Author 2005. Published by Oxford University Press. All rights reserved
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Article

Formation and properties of hairpin and tetraplex structures of guanine-rich regulatory sequences of muscle-specific genes

Anat Yafe, Shulamit Etzioni, Pnina Weisman-Shomer and Michael Fry*

Department of Biochemistry, Rappaport Faculty of Medicine, Technion–Israel Institute of Technology PO Box 9649 Bat Galim, Haifa 31096, Israel

*To whom correspondence should be addressed. Tel: +972 4 829 5328; Fax: +972 4 851 0735; Email: mickey{at}tx.technion.ac.il

Received March 1, 2005. Revised April 4, 2005. Accepted May 2, 2005.

Clustered guanine residues in DNA readily generate hairpin or a variety of tetrahelical structures. The myogenic determination protein MyoD was reported to bind to a tetrahelical structure of guanine-rich enhancer sequence of muscle creatine kinase (MCK) more tightly than to its target E-box motif [K. Walsh and A. Gualberto (1992) J. Biol. Chem., 267, 13714–13718], suggesting that tetraplex structures of regulatory sequences of muscle-specific genes could contribute to transcriptional regulation. In the current study we show that promoter or enhancer sequences of various muscle-specific genes display a disproportionately high incidence of guanine clusters. The sequences derived from the guanine-rich promoter or enhancer regions of three muscle-specific genes, human sarcomeric mitochondrial creatine kinase (sMtCK), mouse MCK and {alpha}7 integrin formed diverse secondary structures. The sMtCK sequence folded into a hairpin structure; the {alpha}7 integrin oligonucleotide generated a unimolecular tetraplex; and sequences from all three genes associated to generate bimolecular tetraplexes. Furthermore, two neighboring non-contiguous guanine-rich tracts in the {alpha}7 integrin promoter region also paired to form a tetraplex structure. We also show that homodimeric MyoD bound bimolecular tetraplex structures of muscle-specific regulatory sequences more efficiently than its target E-box motif. These results are consistent with a role of tetrahelical structures of DNA in the regulation of muscle-specific gene expression.


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