Destabilization of i-Motif DNA at Neutral pH by G-Quadruplex Ligands

Abstract

Numerous studies have been published stressing the importance of finding ligands that can bind specifically to DNA secondary structures. Several have identified ligands that are presented as having specific binding to the G-quadruplex; however, these were not originally tested on the complementary i-motif structure. The i-motif was overlooked and presumed to be irrelevant due to the belief that the hemiprotonated (cytosine + − cytosine) base pair at the core of the structure required acidic pH. The pathophysiological relevance of i-motifs has since been documented, as well as the discovery of several genomic sequences, which can form i-motif at neutral pH. Using different biophysical methodologies, we provide experimental evidence to show that widely used G-quadruplex ligands interact with i-motif structures at neutral pH, generally leading to their destabilization. Crucially, this has implications both for the search for quadruplex binding compounds as well as for the effects of compounds reported to have G-quadruplex specificity without examining their effects on i-motif.

Scaffold stabilization of a G-triplex and study of its interactions with G-quadruplex targeting ligands

“…In the past years, G4 ligands have also been shown to interact with i-motif DNA structures. 27 Our study, along with those previous reports, suggest that G4 targeting ligands may also regulate gene expression via alternative molecular mechanisms. Putative G3 forming sequences soundly outnumber putative G4 forming sequences and their dynamic regulation by endogenous proteins could be significant for genome stability.…”

DNA Nanotechnology for Multimodal Synergistic Theranostics

“…The fundamental sequence of DNA determines the structure and reaction characteristics of the biopolymer. For example, G-rich DNA sequences can self-assemble into G-quadruplex structures in the presence of potassium ions [65], and C-rich DNA sequences can transform into i-motif under pH stimulation [66,67]. The functional DNA nanostructures can load different types of organic molecules to construct therapeutic nanoplatforms.…”

The i-Motif as a Molecular Target: More Than a Complementary DNA Secondary Structure

“…Although FID assays showed that the other compounds bound to the i-motif, subsequent experiments showed that these interactions had no effect on structure stability. In the 2019 paper, the same compounds along with TmPyP4 were tested on i-motif sequences from promoter regions that form structures at neutral pH, death-associated protein (DAP) and ataxin type 2-related protein (ATXN2L) [72]. Again, all compounds were shown to interact with these two promoter i-motif structures.…”