Water mediated Dickerson-Drew-type crystal of DNA dodecamer containing 2′-deoxy-5-formyluridine

To investigate the role of divalent cations in crystal packing, a Dickerson-Drew-type dodecamer with the sequence d(CGCGAATXCGCG), containing 2′-deoxy-5-formyluridine at X, was crystallized under several conditions with Ba 2+ ion instead of Mg 2+ ion. The crystal structure is isomorphous with the original Dickerson-type crystal containing Mg 2+ ion. In the Mg 2+-free crystals, however, a five-membered ring of water molecules occupies the same position as the magnesium site found in the Mg 2+-containing crystals, and connects the two duplexes similarly to the hydrated Mg 2+ ion. It has been concluded that the five-membered water molecules can take the place of the hydrated magnesium cation in crystallization. The 5-formyluracil residues form the canonical Watson–Crick pair with the opposite adenine residues.