Mg2+ in the major groove modulates B-DNA structure and dynamics

Abstract

This study investigates the effect of Mg(2+) bound to the DNA major groove on DNA structure and dynamics. The analysis of a comprehensive dataset of B-DNA crystallographic structures shows that divalent cations are preferentially located in the DNA major groove where they interact with successive bases of (A/G)pG and the phosphate group of 5'-CpA or TpG. Based on this knowledge, molecular dynamics simulations were carried out on a DNA oligomer without or with Mg(2+) close to an ApG step. These simulations showed that the hydrated Mg(2+) forms a stable intra-strand cross-link between the two purines in solution. ApG generates an electrostatic potential in the major groove that is particularly attractive for cations; its intrinsic conformation is well-adapted to the formation of water-mediated hydrogen bonds with Mg(2+). The binding of Mg(2+) modulates the behavior of the 5'-neighboring step by increasing the BII (ε-ζ>0°) population of its phosphate group. Additional electrostatic interactions between the 5'-phosphate group and Mg(2+) strengthen both the DNA-cation binding and the BII character of the 5'-step. Cation binding in the major groove may therefore locally influence the DNA conformational landscape, suggesting a possible avenue for better understanding how strong DNA distortions can be stabilized in protein-DNA complexes.

Figure 1. Interaction of Mg²⁺ in the DNA major groove.

The 5′-CpApG-3′ fragment binds Mg²⁺ in both crystallographic (left) and simulated (right) structures. Mg²⁺ (green) forms water-mediated hydrogen bonds (gray arrows) with the N7 of both purines and the O6 of the guanine via its first hydration shell (left: oxygen atoms in red; right: explicit water molecules). The phosphate groups of CpA and ApG are in BII and BI conformation, respectively. Owing to the orientation of the O2P-O1P vector in the BII-CpA linkage, an additional hydrogen bond occurs between Mg²⁺ and O2P (left) in several X-ray structures. For the same reason, Mg²⁺ remains close to O2P in the simulated structures (right, thin yellow arrow).

Figure 2. BI and BII phosphate groups

. The two panels represent two views of the same 5′-CpApG-3′ fragment and highlight the structural differences between BI (p in GpA, circled in blue in the left panel) and BII (p in CpA, circled in red in the right panel) phosphate groups. The orientation of the O1P-O2P vector is roughly perpendicular and parallel to the axis of the double helix in BI and BII, respectively. The O3′ atom points outside the helix in BI whereas it is turned towards the helix center in BII.

Figure 3. Distances characterizing the interaction between Mg²⁺ and DNA during the MD simulations.

The distances between Mg²⁺ and the electronegative atoms N7(A₂₂ and G₂₃), O6(G₂₃) and O2P(p₂₂) belonging to the p₂₂A₂₂p₂₃G₂₃ fragment were extracted from S1. Mg²⁺ interacts with A₂₂ and G₂₃ via its first hydration shell for roughly 20 ns, as shown by the values of the distances d(Mg²⁺ – N7(A₂₂)), d(Mg²⁺ – N7(G₂₃)), and d(Mg²⁺ – O6(G₂₃)). O2P(p₂₂) is transitorily close to Mg²⁺. Short Mg²⁺ – O2P(A₂₂) distances are associated with p₂₂ in BII (BI in blue, BII in red). Identical interaction patterns are observed in S2 and S3.

Figure 4. ApG step with and without Mg²⁺.

Superimposition of the average structures of A₂₂pG₂₃ either free of Mg²⁺ (blue) or binding Mg²⁺(red). In both cases, this step shows the same structural characteristics (low twist, positive roll and BI phosphate group). ApG is thus ideally adapted to the octahedral structure of hydrated Mg²⁺.

Figure 5. (ε-ζ) distribution without and with Mg²⁺ in the DNA major groove.

N is the percentage of snapshots within each (ε-ζ)_p22 interval. The distribution of (ε-ζ)_p22 values was calculated on two groups of structures extracted from S0–S3. The first group (blue) corresponds to snapshots in which Mg²⁺ does not interact with the DNA major groove. In the second group (red), Mg²⁺ binds to the N7 and O6 atoms of A₂₂/G₂₃ through three water-mediated hydrogen bonds. The BII population of the 5′ phosphate group, p₂₂, increases.

Figure 6. Effect of p₂₂ conformational state on Mg²⁺-p₂₂A₂₂ distances.

The distances between the OP2 and O3′ atoms of p₂₂ and A₂₂ (d(O2P(p₂₂)-N7(A₂₂)), indicated by a dashed red line; (d(O3′ (p₂₂)-N7(A₂₂) by a dashed blue line) depend on the conformational state of p₂₂, represented here by (ε-ζ) p₂₂ values. When Mg²⁺ interacts with A₂₂ and G₂₃, d(Mg²⁺-O2P(p₂₂)) (red) and d(Mg²⁺-O3′ (p₂₂)) (blue) are parallel to d(O2P(p₂₂)-N7(A₂₂)) and d(O3′ (p₂₂)-N7(A₂₂), respectively. The standard deviations for distances are 1.2 Å. The distances were examined on the two groups of structures defined in Figure 5 caption.

Figure 7. Changes in inter-base pair parameters as a function of (ε-ζ) values.

The C₂₁p₂₂A₂₂ average values of roll (°) and twist (°) and their standard deviations (bars) are plotted as a function of the (ε-ζ) values of p₂₂, considering S0–S3. Mg²⁺-mediated enhancement of the BII population of p₂₂ leads to an increase in the proportion of conformations characterized by negative rolls and high twists.