Direct Observation of Azimuthal Correlations between DNA in Hydrated Aggregates

This study revisits the classical x-ray diffraction patterns from hydrated, noncrystalline fibers originally used to establish the helical structure of DNA. We argue that changes in these diffraction patterns with DNA packing density reveal strong azimuthally dependent interactions between adjacent molecules up to $\sim 40\AA$ interaxial or $\sim 20\AA$ surface-to-surface separations. These interactions appear to force significant torsional “straightening” of DNA and strong azimuthal alignment of nearest neighbor molecules. The results are in good agreement with the predictions of recent theoretical models relating DNA-DNA interactions to the helical symmetry of their surface charge patterns.

Figure 1

Azimuthal alignment of adjacent DNA in aggregates. Each base pair is represented by a disk with two negatively charged phosphate groups (spheres) attached to it. The phosphates are connected into the sugar-phosphate backbone. Bold vectors depict altitude-dependent azimuthal orientations $\varphi (z)$ of the middle of the minor groove.

Figure 2

Dependence of x-ray diffraction patterns from oriented DNA fibers on the interaxial distance $d_{\mathrm{int}}$. The Bragg peaks at the equator (two dark spots at $k_z=0$, $K=k_{\mathrm{Bragg}}$) originate from the positional order of the molecules ($k_{\mathrm{Bragg}}=4\pi /\sqrt{3}{d}_{\mathrm{int}}$ in a hexagonal lattice). Other diffraction maxima along the dotted layer lines ($n=1,2,3$) originate from the helical structure of DNA. Their meridional coordinates ($k_z$) are determined by the helical pitch of DNA, and $K$ are determined by Eqs. (4, 7). The white arrows depict the varying locations of the diffraction maxima at the first helical layer line indicating strong azimuthal correlations between adjacent molecules.

Figure 3

Variation in the locations $K_n$ of the diffraction maxima on the first ($n=1$), second ($n=2$), and third ($n=3$) layer lines with separation between DNA. The bold lines show expected locations of the intramolecular maxima [Eq. (4)]. Thin solid lines show the locations of the diffraction peaks in hexagonal crystals with the same azimuthal orientation of all molecules; dashed lines, in crystals with alternating orientations of molecules in consecutive rows; dotted lines, in crystals with different azimuthal orientations of all three molecules in the unit cell. The corresponding Miller indices are shown near each line. Intermolecular scattering appears to determine $K_1$ at all separations. $K_2$ are dominated by intramolecular scattering at $d_{\mathrm{int}}>35\AA$, resulting in flattening of the observed dependence. $K_3$ are consistent with intramolecular scattering at all $d_{\mathrm{int}}$.