Water structure around a left-handed Z-DNA fragment analyzed by cryo neutron crystallography

Even in high-quality X-ray crystal structures of oligonucleotides determined at a resolution of 1 angstrom or higher, the orientations of first-shell water molecules remain unclear. We used cryo neutron crystallography to gain insight into the H-bonding patterns of water molecules around the left-handed Z-DNA duplex [d(CGCGCG)](2). The neutron density visualized at 1.5 angstrom resolution for the first time allows us to pinpoint the orientations of most of the water molecules directly contacting the DNA and of many second-shell waters. In particular, H-bond acceptor and donor patterns for water participating in prominent hydration motifs inside the minor groove, on the convex surface or bridging nucleobase and phosphate oxygen atoms are finally revealed. Several water molecules display entirely unexpected orientations. For example, a water molecule located at H-bonding distance from O6 keto oxygen atoms of two adjacent guanines directs both its deuterium atoms away from the keto groups. Exocyclic amino groups of guanine (N2) and cytosine (N4) unexpectedly stabilize waters H-bonded to O2 keto oxygens from adjacent cytosines and O6 keto oxygens from adjacent guanines, respectively. Our structure offers the most detailed view to date of DNA solvation in the solid-state undistorted by metal ions or polyamines.

Automated summary

Cryo neutron crystallography was used to investigate the hydrogen bonding patterns of water molecules around a left-handed Z-DNA duplex, revealing orientations of first-shell and second-shell water molecules and uncovering hydration motifs within the minor groove, on the convex surface, and bridging nucleobase and phosphate oxygen atoms. The high-resolution neutron density visualized for the first time pinpointed the orientations of water molecules in contact with the DNA, highlighting unexpected orientations and surprising stabilization effects of exocyclic amino groups of guanine and cytosine. This structure provides the most detailed view to date of DNA solvation in the solid-state unaffected by metal ions or polyamines.