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J. Biol. Chem., Vol. 280, Issue 32, 29340-29345, August 12, 2005

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The AUUCU Repeats Responsible for Spinocerebellar Ataxia Type 10 Form Unusual RNA Hairpins^*

Vaishali Handa, Herman J. C. Yeh¶, Peter McPhie||, and Karen Usdin**

From the Laboratory of Molecular and Cellular Biology, the ^||Laboratory of Biochemistry and Genetics, and the ^¶Laboratory of Bioorganic Chemistry, NIDDK, National Institutes of Health, Bethesda, Maryland 20892-0830

Spinocerebellar ataxia type 10 is an autosomal dominant disorder caused by expansion of a pentameric repeat tract (ATTCT·AGAAT)_n in intron 9 of the gene that encodes ataxin-10. We have analyzed duplex DNA containing the repeat, the individual DNA strands, and the RNA that would be generated by transcription of the repeat. Circular dichroism and UV absorbance measurements suggest that the previously reported tendency of the repeat to unpair when supercoiled is probably related simply to GC content rather than reflecting any unusual property of the duplex. DNA containing d(ATTCT)₉ forms a folded structure at relatively low temperatures, whereas the antisense strand, d(AGAAT)₉, does not form a structure even at 0 °C. In contrast r(AUUCU)₉ forms a folded structure under physiologically reasonable conditions. S1 nuclease analysis reveals a single region of hypersensitivity in the middle of the repeat tract, whereas V1 digestion is consistent with a hydrogen bonded or well stacked structure. CD spectroscopy shows that the structure is unimolecular and hydrogen bonded and has a significant amount of A-form helix. NMR spectroscopy demonstrates that these hydrogen bonds comprise an equal number of A·U and U·U base pairs. Our data thus suggest that the repeat forms an unusual RNA hairpin. Thus the ability to form an RNA hairpin seems to be a common property of those Repeat Expansion Diseases that are not recessively inherited and are caused by repeats that are transcribed but not translated.

Received for publication, March 30, 2005 , and in revised form, May 31, 2005.

^* The costs of publication of this article were defrayed in part by the payment of page charges. This article must therefore be hereby marked "advertisement" in accordance with 18 U.S.C. Section 1734 solely to indicate this fact.

Both authors contributed equally to this work and should be considered joint first authors.

^** To whom correspondence should be addressed: Bldg. 8, Rm. 202, National Institutes of Health, 8 Center Dr. MSC 0830, Bethesda, MD 20892-0830. Tel.: 301-496-2189; Fax: 301-402-0053; E-mail: ku{at}helix.nih.gov.

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