Sticky DNA, a self-associated complex formed at long GAA*TTC repeats in intron 1 of the frataxin gene, inhibits transcription.

Friedreich's ataxia (FRDA) is an autosomal recessive neurodegenerative disease caused by the expansion of GAA.TTC repeats in the first intron of the frataxin (X25) gene. FRDA patients carrying two expanded GAA.TTC repeats show very low levels of mature frataxin mRNA and protein. A novel type of unusual DNA structure, sticky DNA, was previously found in the expanded GAA.TTC repeats from FRDA patients. To evaluate the effect of sticky DNA on transcription, in vitro transcription studies of (GAA.TTC)(n) repeats (where n = 9-150) were carried out using T7 or SP6 RNA polymerase. When a gel-isolated sticky DNA template was transcribed, the amount of full-length RNA synthesized was significantly reduced compared with the transcription of the linear template. Surprisingly, transcriptional inhibition was observed not only for the sticky DNA template but also another DNA molecule used as an internal control in an orientation-independent manner. The molecular mechanism of transcriptional inhibition by sticky DNA was a sequestration of the RNA polymerases by direct binding to the complex DNA structure. Moreover, plasmids containing the (GAAGGA.TCCTTC)(65) repeat, which does not form sticky DNA, did not inhibit in vitro transcription, as expected. These results suggest that the role of sticky DNA in FRDA may be the sequestration of transcription factors.