Kondo Jiro

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 Ba2+ ion instead of Mg2+ ion. The crystal structure is isomorphous with the original Dickerson-type crystal containing Mg2+ ion. In the Mg2+-free crystals, however, a five-membered ring of water molecules occupies the same position as the magnesium site found in the Mg2+-containing crystals, and connects the two duplexes similarly to the hydrated Mg2+ 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. (C) 2002 Elsevier Science B.V. All rights reserved.

In a series of structural studies on damaged DNA. a modified Dickerson-Drew dodecamer with the sequence d(CGCGAATTmo(4)CGCG), where mo(4)C is 2'-deoxy-N-4-methoxycytidine, was synthesized and its structure in a new crystal form has been determined by the X-ray diffraction method. The two dodecamers form a B-form duplex, in which the two mo(4)C residues, respectively, form a wobble pair and a Watson-Crick type pair with the guanine residues of the opposite strand. A comparison of the sugar conformations with those of the other related DickersonDrew dodecamers indicates a common feature of their puckering patterns. The sugar pucker of the third residue always adopts an intermediate state (C4'-exo similar to O4'-endo) between the A-form and B-form. This deviation is ascribed to the stacking interaction of the ribose ring at the third residue with the guanine base at the 12th residue, which is brought about by an extra G12:G2 interaction between two duplexes related by a crystallographic 2, symmetry. (C) 2002 Elsevier Science B.V. All rights reserved.