NMR Studies of G-Quadruplex Structures and G-Quadruplex-Interactive Compounds

Abstract

G-quadruplexes are noncanonical, four-stranded nucleic acid secondary structures formed in sequences containing consecutive runs of guanines. These G-quadruplex structures have been found to form in nucleic acid regions of biological significance, including human telomeres, gene promoters, and untranslated regions of mRNA. Thus, they are considered attractive therapeutic targets. Nuclear magnetic resonance (NMR) spectroscopy is a powerful method for understanding the structures of G-quadruplexes and their interactions with small molecules under physiologically relevant conditions. Here, we present the NMR methodology used in our research group for the study of DNA G-quadruplex structures in physiologically relevant solution and their ligand interactions.

DNA Binding Mode Analysis of a Core-Extended Naphthalene Diimide as a Conformation-Sensitive Fluorescent Probe of G-Quadruplex Structures

“…Under the specified conditions, all models gave high-quality NMR spectra, with the predominant G-quadruplex, for m-tel24 and M2, or duplex, in the case of ds12, with conformations accounting for >95% of the whole nucleotide material in the solution. More in detail, twelve narrow and well-resolved imino proton signals were observed in the range δ 10.5–12.2 ppm in the 1 H NMR spectra of both m-tel24 and M2 G-quadruplexes ( Figure 2 A,B, bottom), consistent with the formation of G-quadruplexes with three stacked G-quartets [ 36 , 37 , 39 , 40 ]. On the other hand, five narrow and well-resolved imino proton signals were observed in the range δ 12.5–13.8 ppm of the 1 H NMR spectrum of the ds12 duplex ( Figure 2 C, bottom), in accordance with previous reports for this self-complementary duplex consisting of twelve Watson-Crick base pairs [ 41 , 42 , 43 ].…”

“…Overall, the severe broadening of proton signals occurred at one molar ligand equivalent lower for M2 G-quadruplex (1:1 DNA/ligand ratio) than both m-tel24 G-quadruplex and ds12 duplex (1:2 DNA/ligand ratio). Moreover, even at high c ex -NDI concentration, no sharpening of 1 H NMR signals was observed, indicating that complex equilibria, intermediate-to-fast on the NMR time scale, occurred for c ex -NDI with all the investigated G-quadruplex and duplex models [ 39 , 40 ].…”

Controllable stereoinversion in DNA-catalyzed olefin cyclopropanation via cofactor modification

“…Moreover, the addition of FeTMPyP2 causes an obvious upeld peak-shi, which is attributed to the strong electronic shielding effect arising from the porphyrin ligand stacking upon the Gquartet. 50 Therefore, in combination with the CD and UV-vis results, we nd that FeTMPyP2 adjusts to an optimal conformation through bond rotation and distortion, thereby forming a tight p-p stacking mode with mA9A and creating a strong electronic shielding effect on the imino protons of the Gquartet.…”

Dual targeting of higher-order DNA structures by azacryptands induces DNA junction-mediated DNA damage in cancer cells

“…While structural data are now widely available for a number of small molecules interacting with G4s (notably via NMR and X-ray crystallography studies) ( 74–75 ), little is known about how ligands bind to TWJ, with the notable exception of the solid-state investigations performed by Hannon et al. ( vide supra ) ( 54 ).…”