Water structure around a left-handed Z-DNA fragment analyzed by cryo neutron crystallography
| Autor: | Leighton Coates, Brendan Sullivan, Martin Egli, Joel M. Harp |
|---|---|
| Jazyk: | angličtina |
| Rok vydání: | 2021 |
| Předmět: |
Models
Molecular Guanine AcademicSubjects/SCI00010 Metal ions in aqueous solution Crystal structure Biology 010402 general chemistry Crystallography X-Ray 01 natural sciences Nucleobase Phosphates Z-DNA 03 medical and health sciences chemistry.chemical_compound Cryoprotective Agents Structural Biology Genetics Molecule DNA Z-Form 030304 developmental biology Neutrons 0303 health sciences Crystallography Hydrogen bond Solvation Water Hydrogen Bonding 0104 chemical sciences Neutron Diffraction chemistry Nucleic Acid Conformation |
| Zdroj: | Nucleic Acids Research |
| ISSN: | 1362-4962 0305-1048 |
| Popis: | Even in high-quality X-ray crystal structures of oligonucleotides determined at a resolution of 1 Å 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 Å 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. |
| Databáze: | OpenAIRE |
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