近藤 次郎

A DNA fragment d(GCGAAAGCT), known to adopt a stable mini-hairpin structure in solution, has been crystallized in the space group I4(1)22 with the unit-cell dimensions a = b = 53.4 Angstrom and c = 54.0 Angstrom, and the crystal structure has been determined at 2.5 Angstrom resolution. The four nucleotide residues CGAA of the first half of the oligomer form a parallel duplex with another half through the homo base pairs, C-2:C-2(+) (singly-protonated between the Watson- Crick sites), G(3):G(3) (between the minor groove sites), A(4):A(4) (between the major groove sites) and A(5):A(5) (between the Watson-Crick sites). The two strands remaining in the half of the parallel duplex are split away in different directions, and they pair in an anti-parallel B-form duplex with the second half extending from a neighboring parallel duplex, so that an infinite column is formed in a head-to-tail fashion along the c-axis. It seems that a hexa-ammine cobalt cation supports such a branched and bent conformation of the oligomer. One end of the parallel duplex is stacked on the corresponding end of the adjacent parallel duplex; between them, the guanine base of the first residue is stacked on the fourth ribose of another duplex.

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.