DNA i-motifs found in human cells

As if twisting itself into double helices isn’t hard enough, DNA also can fold into structures such as G-quadruplexes and i-motifs, which interrupt normal DNA base pairing. Researchers identified both forms of folded DNA in solution-based experiments and showed that they regulate gene transcription, making them potential cancer drug targets. But many questioned whether the folded structures actually existed in the human genome.

In 2013, a research group confirmed that G-quadruplexes were present in human cells (Nat. Chem. 2013, DOI: 10.1038/nchem.1548 and C&EN, Jan. 21, 2013, page 8). Now a separate group, led by Marcel E. Dinger and Daniel Christ of the Garvan Institute of Medical Research, has confirmed that i-motifs are also there (Nat. Chem. 2018, DOI: 10.1038/s41557-018-0046-3). The work helps pave the way for the search for i-motif-targeted drugs.

G-quadruplexes form when sets of guanine residues hydrogen bond to form flat structures called tetrads that stack into four-stranded DNA motifs. A molecule called quarfloxin (CX-3543) that targeted G-quadruplexes failed to show efficacy in clinical trials for different cancers. A related G-quadruplex-targeted agent, CX-5461, is now in trials for breast cancer.

I-motifs form when sets of cytosines pair with protonated cytosines, connecting U-shaped DNA strands. Because cytosines are normally protonated under acidic conditions that aren’t present in nuclei, researchers doubted that i-motifs existed in human cells. Previous studies included findings that small molecules targeting i-motifs could repress or activate gene expression in human cells (C&EN, March 24, 2014, page 7). But researchers didn’t believe these studies proved the presence of i-motifs in the human genome.

The Australian group used fluorescent-dye-labeled antibody fragments that bind i-motifs with high selectivity and affinity to detect the structures in human cells. The i-motifs were present in gene promoter regions and telomeres, suggesting that they regulate the genome.

“This is a very exciting discovery that will have an incredibly positive impact on the field,” says i-motif expert Zoë A. E. Waller of the University of East Anglia. “This work is the icing on what is now quite a large cake of evidence that these do exist in vivo. Hopefully, this will give people the evidence they need to believe these structures are worth working on.”