Same fold, different properties: polarizable molecular dynamics simulations of telomeric and TERRA G-quadruplexes

Abstract

DNA and RNA sequences rich in guanine can fold into noncanonical structures called G-quadruplexes (GQs), which exhibit a common stem structure of Hoogsteen hydrogen-bonded guanine tetrads and diverse loop structures. GQ sequence motifs are overrepresented in promoters, origins of replication, telomeres, and untranslated regions in mRNA, suggesting roles in modulating gene expression and preserving genomic integrity. Given these roles and unique aspects of different structures, GQs are attractive targets for drug design, but greater insight into GQ folding pathways and the interactions stabilizing them is required. Here, we performed molecular dynamics simulations to study two bimolecular GQs, a telomeric DNA GQ and the analogous telomeric repeat-containing RNA (TERRA) GQ. We applied the Drude polarizable force field, which we show outperforms the additive CHARMM36 force field in both ion retention and maintenance of the GQ folds. The polarizable simulations reveal that the GQs bind bulk K+ ions differently, and that the TERRA GQ accumulates more K+ ions, suggesting different ion interactions stabilize these structures. Nucleobase dipole moments vary as a function of position and also contribute to ion binding. Finally, we show that the TERRA GQ is more sensitive than the telomeric DNA GQ to water-mediated modulation of ion-induced dipole-dipole interactions.

Figure 1.

Rendering of the crystal structures of the (A) telomeric DNA GQ from PDB entry 1K8P (17) and (B) TERRA GQ from PDB entry 3IBK (29). Nucleobase atoms in guanine tetrads 1 (red, Gua3 and Gua9 in each oligonucleotide strand), 2 (green, Gua4 and Gua10), and 3 (blue, Gua5 and Gua11) are shown in ball-and-stick. The two K⁺ ions coordinated along the tetrad axis are shown as gold spheres. The 5′-3′ sense of the oligonucleotide strands is indicated by the labeling of Thy1/Ura1, Ade2 and Thy12/Ura12.

Figure 2.

2′-Hydroxyl sampling in the TERRA GQ for CHARMM36 and Drude-2017. Data from the simulations are the averages of the three pooled replicates. Error bars represent the root-mean-square fluctuation of the combined time series. Horizontal, dashed and dotted lines represent the boundaries of base (60–120°) and O3′ (190–270°) orientations of the 2′-hydroxyl group, respectively, as characterized by the C1′-C2′-O2′-H2′ dihedral.

Figure 3.

Sugar pucker in (A) the telomeric DNA GQ and (B) TERRA GQ. Data for CHARMM36 and Drude-2017 reflect the average values from the pooled trajectories, with error bars representing the root-mean-square fluctuation of the combined time series.

Figure 4.

K⁺ occupancy maps around the telomeric DNA GQ in the Drude-2017 simulations. (A) View along the GQ tetrad axis. (B) Side view. The crystal structure of the DNA GQ is shown as lines and colored by element, with a cartoon overlay of the backbone to illustrate the fold. Crystallographic K⁺ ions are shown as gold spheres.

Figure 5.

K⁺ occupancy maps around the TERRA GQ in the Drude-2017 simulations. (A) View along the GQ tetrad axis. (B) Side view. The crystal structure of the TERRA GQ is shown as lines and colored by element, with a cartoon overlay of the backbone to illustrate the fold. Crystallographic K⁺ ions are shown as gold spheres.

Figure 6.

Adenine, thymine, and uracil base dipole moments relative to duplex and single-stranded DNA and RNA. (A) Adenine in the telomeric DNA GQ, (B) thymine in the telomeric DNA GQ, (C) adenine in the TERRA GQ, and (D) uracil in the TERRA GQ. In panels (A) and (B), dsDNA dipole moments were computed from 1-μs MD simulations of the six duplex, B-DNA structures used in the validation of the Drude-2017 force field (45,46). In panels (C) and (D), the dsRNA dipole moments were calculated from 1-μs MD simulations of two duplex, A-RNA structures used in the validation of the Drude-2017 force field (47). Dipole moments in ssDNA and ssRNA were calculated from 1-μs trajectories of a single strand of the telomeric DNA and TERRA GQ, respectively (see Materials and Methods).

Figure 7.

Guanine base dipole moments in each of the three tetrads in (A) the telomeric DNA GQ and (B) the TERRA GQ relative to duplex and single-stranded DNA and RNA. Values of guanine base dipole moments in dsDNA and dsRNA in panels (A) and (B) were calculated from trajectories in the six B-DNA duplexes (45,46) and the two A-RNA duplexes (47) simulated in the validation of the Drude-2017 force field. Dipole moments in ssDNA and ssRNA were calculated from 1-μs trajectories of a single strand of the telomeric DNA and TERRA GQ, respectively (see Materials and Methods).