Common G-Quadruplex Binding Agents Found to Interact With i-Motif-Forming DNA: Unexpected Multi-Target-Directed Compounds

Abstract

G-quadruplex (G4) and i-motif (iM) are four-stranded non-canonical nucleic acid structural arrangements. Recent evidences suggest that these DNA structures exist in living cells and could be involved in several cancer-related processes, thus representing an attractive target for anticancer drug discovery. Efforts toward the development of G4 targeting compounds have led to a number of effective bioactive ligands. Herein, employing several biophysical methodologies, we studied the ability of some well-known G4 ligands to interact with iM-forming DNA. The data showed that the investigated compounds are actually able to interact with both DNA in vitro, thus acting de facto as multi-target-directed agents. Interestingly, while all the compounds stabilize the G4, some of them significantly reduce the stability of the iM. The present study highlights the importance, when studying G4-targeting compounds, of evaluating also their behavior toward the i-motif counterpart.

Toward G-Quadruplex-Based Anticancer Agents: Biophysical and Biological Studies of Novel AS1411 Derivatives

“…These oligonucleotides are characterized by the presence of the donor fluorophore FAM (6-carboxyfluorescein) and the acceptor fluorophore TAMRA (6-carboxytetramethylrhodamine) that are covalently bound at 5′- and 3′-ends, respectively. Typically, when a G4 is folded, the two dyes are in close proximity so FAM fluorescence peak at 522 nm (upon excitation at 492 nm) is quenched by TAMRA [ 44 , 45 ]. On the other hand, if a G4 is unfolded or the oligonucleotide is degraded by nucleases, the distance-dependent interaction between the two dyes is disrupted, and an increase of the FAM fluorescence signal at 522 nm is observed [ 45 ].…”

“…Typically, when a G4 is folded, the two dyes are in close proximity so FAM fluorescence peak at 522 nm (upon excitation at 492 nm) is quenched by TAMRA [ 44 , 45 ]. On the other hand, if a G4 is unfolded or the oligonucleotide is degraded by nucleases, the distance-dependent interaction between the two dyes is disrupted, and an increase of the FAM fluorescence signal at 522 nm is observed [ 45 ]. Figure 5 shows the fluorescence spectra of the five FAM/TAMRA-labeled GROs in the presence of 10% FBS recorded at different times of incubation at 37 °C.…”

Recent Progress in Fluorescence Signal Design for DNA‐Based Logic Circuits

“…As mentioned, i‐motifs have similar spatial property as G‐quadruplexes and have been involved in some logic systems. However, few multi‐output circuits designed provide signals that are directly based on the structural conversion of i‐motif till now, owing to the lack of highly specific i‐motif probes . Therefore, designing probes targeting the i‐motif specifically can make the most of C‐rich and G‐rich DNA and might be a possible solution for constructing label‐free multi‐output circuits.…”

“…A G‐quadruplex can only provide one label‐free channel. Although the i‐motif can also provide a label‐free signal by itself, most of its probes lack specificity and cannot tell the i‐motif from a G‐quadruplex or duplex; hence although the i‐motif structure was indeed involved in some advanced circuits, it usually did not produce output signal directly. To achieve a totally label‐free system, fluorescence nanoparticles, like AgNCs and CuNPs, have been introduced in some investigations.…”

Native Ion Mobility Mass Spectrometry: When Gas-Phase Ion Structures Depend on the Electrospray Charging Process

“…NMR spectroscopy was further employed to investigate the i-motif formation in solutions with ammonium concentrations ranging from 15 to 150 mM. The sequence d(CCCTAA)3CCCT (named 22CT), containing one additional thymine at 3'-end, was used for these experiments because it has been well characterized by NMR [10,41]. The imino and aromatic proton regions of 22CT and 21CTC are shown in Figure 2G-I.…”