Ion-Dependent Conformational Plasticity of Telomeric G-Hairpins and G-Quadruplexes

Abstract

Telomeric DNA is guanine-rich and can adopt structures such as G-quadruplexes (GQs) and G-hairpins. Telomeric GQs influence genome stability and telomerase activity, making understanding of enzyme-GQ interactions and dynamics important for potential drug design. GQs have a characteristic tetrad core, which is connected by loop regions. Within this architecture are G-hairpins, fold-back motifs that are thought to represent the first intermediate in GQ folding. To better understand the relationship between G-hairpin motifs and GQs, we performed polarizable simulations of a two-tetrad telomeric GQ and an isolated SC11 telomeric G-hairpin. The telomeric GQ contains a G-triad, which functions as part of the tetrad core or linker regions, depending on local conformational change. This triad and another motif below the tetrad core frequently bound ions and may represent druggable sites. Further, we observed the unbiased formation of a G-triad and a G-tetrad in simulations of the SC11 G-hairpin and found that cations can be partially hydrated while facilitating the formation of these motifs. Finally, we demonstrated that K⁺ ions form specific interactions with guanine bases, while Na⁺ ions interact nonspecifically with bases in the structure. Together, these simulations provide new insights into the influence of ions on GQs, G-hairpins, and G-triad motifs.

Figure 1

Structure of the two-tetrad telomeric GQ. (A) Schematic of all residues in the GQ. The guanine bases of the core are colored by triad (yellow) and tetrad (1—red and 2—blue), while loop and linker residues are gray. (B) Full structure taken from model 1 of the NMR ensemble deposited in PDB entry 2KF8. Important noncanonical base pairs (Gua3•Ade18 and Thy11•Thy22) are highlighted within the structure.

Figure 2

Structure of the telomeric SC11 G-hairpin. (A) Schematic and (B) structure showing the folded topology and the glycosidic bond classification of the nuclear magnetic resonance (NMR) model 1 deposited in PDB entry 5M1W. (C) Noncanonical base pairs (Gua1•Gua5, Gua6•Gua9, and Gua7•Gua11) stabilizing the G-hairpin. Atoms are labeled exactly as they are assigned in the deposited NMR structure, and we note the assignment of “H21” and “H22” to denote equivalent atoms in different bases. Throughout our discussion, we retain the nomenclature assigned in the PDB structure to avoid confusion despite this discrepancy.

Figure 3

Ion–DNA interactions in the two-tetrad GQ. (A) K⁺ and (B) Na⁺ occupancy maps show ion sampling around the GQ at an occupancy threshold of ≥1%. The percentages shown indicate the persistence of each ion at that location throughout the three replicate simulations. (C) Heat map that shows the average number of ions within 3.5 Å of nonhydrogen atoms in GQ bases (left) and the sugar-phosphate backbone (right) in KCl and NaCl.

Figure 4

Images of water–triad and ion–triad interactions overlaid on a heatmap of water within 3.5 Å (inner circle) and 7 Å (outer circle) from the ion binding site. Structures are representative examples of water–ion–triad interactions during (A) bipyramidal K⁺ coordination, (B) nonlinear K⁺ coordination, (C) coplanar Na⁺ coordination, and (D) nonlinear Na⁺ coordination.

Figure 5

Ion–DNA interactions in g-DNA simulations. The heat maps show the average number of ions within 3.5 Å of nonhydrogen atoms of the bases and sugar-phosphate backbone in (A) telomeric two-tetrad GQ, (B) isolated G-hairpin simulations, (C) simulations starting in the triad/tetrad state, (D) simulations starting in G-hairpin state 2, and (E) simulations starting in unfolded states.

Figure 6

Comparison of the triad motif within (A and B) two-tetrad telomeric GQ and (C) SC11 G-hairpin. Structure, Hoogsteen hydrogen bonding interactions, and average RMSF values for each guanine base are highlighted. The average guanine–ion interaction energy in each system is listed below the representative structure.