Solvent-Induced DNA Conformational Transition

Modified water models with scaled charges are used to investigate solvent polarity effects on DNA structure. Several intensive molecular dynamics simulations of the DNA EcoRI dodecamer d(CGCGAATTCGCG) in different model solvents are performed. When the polarity of the solvent molecule decreases, from overpolarized to less polarized, DNA experiences the conformational transitions of $\mathrm{\text{constrained}}\to B\mathrm{\text{form}}\to (A\mathrm{\text{−}}B)\mathrm{\text{mix}}\to A\mathrm{\text{form}}$. We demonstrate that one important cause of these structure changes is the competition between hydration and direct cation coupling to the free oxygen atoms in the phosphate groups on DNA backbones.

Figure 1

Stereo views of the initial 171dPDB and the averaged resulting structures in the last 2 ns simulations. We present here three typical views from major, minor groove and top.

Figure 2

RMSD of the DNA trajectories with respect to the canonical $B$ (red or gray), $A$ (black) forms, and the starting PDB structure (blue or dark gray).

Figure 3

Averaged DNA structure parameters during the last 2 ns simulations. They are the x-displacement (Xdp) and inclination angle (Inc) of a base pair from the helical axis, sugar pucker angle (Phi), end-to-end length (Len), width (MW and mW), and depth (MD and mD) of minor and major grooves. The horizontal dashed lines indicate the reference values of typical $A$ (orange or light gray) and $B$ (cyan or dark gray) forms and the short red or gray line shows the parameters of the starting PDB structure.

Figure 4

RDF [part (a)] and the corresponding coordination numbers [parts (b),(c)] of ${\mathrm{Na}}^{+}$ ions (the $S=1.2$ case is shown in the inset for a longer scale) and solvent molecules around the free oxygen atoms of the phosphate groups on DNA backbones. The blue (or dark gray) dashed lines show the radii in which the coordinate number is 1 for ${\mathrm{Na}}^{+}$ ions and 5 for solvent molecules.