The hydration and unusual hydrogen bonding in the crystal structure of an RNA duplex containing alternating CG base pairs

Abstract

The X-ray structures of two crystal forms of the RNA duplex [CGCG(5-FC)G]2 are the first crystal structures for an RNA duplex containing alternating CG base pairs with unmodified 2′-hydroxyl groups. The triclinic and the rhombohedral crystal forms (PDB ids 3jxq, 3jxr) differ in the molecular packing, the amount of ordered structure and in molecular details, especially the hydration. The P1 data extend to 1.45 Å resolution, while the R32 data reach 1.25 Å. In both structures the RNA oligomers take the form of a right-handed half-turn with conformational parameters close to the canonical A-RNA. The duplexes stack coaxially in the crystal lattice. The geometry of C:G vs. 5-FC:G pairing is similar in terms of H-bond geometry. In CG steps, inter-strand guanines are parallel while cytosines are not parallel. In steps GC this motif is reversed. Both structures contain ordered water molecules, forming characteristic hydration network in the major and the minor grooves. In addition to water, the triclinic structure contains four magnesium cations, one of them forming an inner complex with a phosphate. Two types of unusual interactions are observed. In the major groove, the 5-fluorocytidine residues form C–F⋯H–O–H hydrogen bonds with water molecules. In the minor groove, intermolecular contacts include C–H hydrogen bonds (C1′–H1⋯O2′ and C4′–H4′⋯O4′) between two ribose rings.