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Originally published In Press as doi:10.1074/jbc.M205209200 on August 2, 2002

J. Biol. Chem., Vol. 277, Issue 42, 39217-39227, October 18, 2002
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Sticky DNA, a Long GAA·GAA·TTC Triplex That Is Formed Intramolecularly, in the Sequence of Intron 1 of the Frataxin Gene*

Alexandre A. VetcherDagger , Marek NapieralaDagger , Ravi R. IyerDagger §, Paul D. Chastain, Jack D. Griffith, and Robert D. WellsDagger ||

From the Dagger  Center for Genome Research, Institute of Biosciences and Technology, Texas A&M University, Texas Medical Center, Houston, Texas 77030-3303 and the  Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina 27599

Friedreich's ataxia is caused by the massive expansion of GAA·TTC repeats in intron 1 of the frataxin (X25) gene. Our prior investigations showed that long GAA·TTC repeats formed very stable triplex structures which caused two repeat tracts to adhere to each other (sticky DNA). This process was dependent on negative supercoiling and the presence of divalent metal ions. Herein, we have investigated the formation of sticky DNA from plasmid monomers and dimers; sticky DNA is formed only when two tracts of sufficiently long (GAA·TTC)n (n = 59-270) are present in a single plasmid DNA and are in the direct repeat orientation. If the inserts are in the indirect (inverted) repeat orientation, no sticky DNA was observed. Furthermore, kinetic studies support the intramolecular nature of sticky DNA formation. Electron microscopy investigations also provide strong data for sticky DNA as a single long triplex. Hence, these results give new insights into our understanding of the capacity of sticky DNA to inhibit transcription and thereby reduce the level of frataxin protein as related to the etiology of Friedreich's ataxia.

* This work was supported by Grants GM52982, NS37554, and ES11347 from the National Institutes of Health, the Robert A. Welch Foundation, and the Friedreich's Ataxia Research Alliance (to R. D. W.) and National Institutes of Health Grant GM31819 (to J. D. G.).The costs of publication of this article were defrayed in part by the payment of page charges. The article must therefore be hereby marked "advertisement" in accordance with 18 U.S.C. Section 1734 solely to indicate this fact.

§ Present address: Dept. of Biochemistry, Duke University Medical Center, 150 Nanaline H. Duke Bldg., Research Drive, Durham, NC 27710.

|| To whom correspondence should be addressed: Center for Genome Research, Institute of Biosciences and Technology, Texas A&M University, Texas Medical Center, 2121 W. Holcombe Blvd., Houston, TX 77030-3303. Tel.: 713-677-7651; Fax: 713-677-7689; E-mail: rwells@ibt.tamu.edu.

Copyright © 2002 by The American Society for Biochemistry and Molecular Biology, Inc.
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