Stress-induced acidification may contribute to formation of unusual structures in C9orf72-repeats

Abstract Background Expansion of the C9orf72 hexanucleotide repeat (GGGGCC) n ·(GGCCCC) n is the most common cause of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). Both strands of the C9orf72 repeat have been shown to form unusual DNA and RNA structures that are thought to be involved in mutagenesis and/or pathogenesis. We previously showed that the C-rich DNA strands from the C9orf72 repeat can form four-stranded quadruplexes at neutral pH. The cytosine residues become protonated under slightly acidic pH (pH 4.5–6.2), facilitating the formation of intercalated i-motif structures. Methods Using CD spectroscopy, UV melting, and gel electrophoresis, we demonstrate a pH-induced structural transition of the C-rich DNA strand of the C9orf72 repeat at pHs reported to exist in living cells under stress, including during neurodegeneration and cancer. Results We show that the repeats with lengths of 4, 6, and 8 units, form intercalated quadruplex i -motifs at low pH (pH  i -motif structures. Conclusions In the proper sequence context, i -motif structures can form at pH values found in some cells in vivo. General significance DNA conformational plasticity exists over broad range of solution conditions.