Octaplex formation of d(GCGAAAGC) with the double A-quartet.

We reported that the sequence gcGA[X]1Agc adopts a specific structure to form several multiplexes. In the case of X=G, an octaplex formation occurs, in which the stacked double G-quartet stabilizes the architecture through potassium cation mediations. In the case of a mutant X=A, too, it has been found that the oligomers form an octaplex. The eight central A residues form a stacked double A-quartet, which is a first example of adenine associations. Several water molecules occupy the centre to stabilize the quartets, so that the octaplex seems to be swollen as compared with that of X=G. In any multiplex formations, the building block is a base-intercalated duplexes.

Crystal structures of a DNA octaplex with I-motif of G-quartets and its splitting into two quadruplexes suggest a folding mechanism of eight tandem repeats.

Recent genomic analyses revealed many kinds of tandem repeats of specific sequences. Some of them are related to genetic diseases, but their biological functions and structures are still unknown. Two X-ray structures of a short DNA fragment d(gcGA[G]1Agc) show that four base-intercalated duplexes are assembled to form an octaplex at a low K+ concentration, in which the eight G5 residues form a stacked double G-quartet in the central part. At a higher K+ concentration, however, the octaplex is split into just two halves. These structural features suggest a folding process of eight tandem repeats of d(ccGA[G]4Agg), according to a double Greek-key motif. Such a packaging of the repeats could facilitate slippage of a certain sequence during DNA replication, to induce increase or decrease of the repeats.

X-ray analyses of d(GCGAXAGC) containing G and T at X: the base-intercalated duplex is still stable even in point mutants at the fifth residue.

DNA fragments containing the sequence d(GCGAAAGC) prefer to adopt a base-intercalated (zipper-like) duplex in the crystalline state. To investigate effects of point mutation at the 5th residue on the structure, two crystal structures of d(GCGAGAGC) and d(GCGATAGC) have been determined by X-ray crystallography. In the respective crystals, the two octamers related by a crystallographic two-fold symmetry are aligned in an anti-parallel fashion and associated to each other to form a duplex, suggesting that the base-intercalated duplex is stable even when the 5th residue is mutated with other bases. The sheared G3:A6 pair formation makes the two phosphate backbones closer and facilitates formation of the A-X*-X-A* base-intercalated motif. The three duplexes are assembled around the three-fold axis, and their 3rd and 4th residues are bound to the hexamine cobalt chloride. The central 5th residues are bound to another cation.

The base-intercalated duplexes of d(GCGAXAGC) with mutation at X (X=G, T or C).

DNA fragments containing the sequence d(GCGAAAGC) adopt a base-intercalated (zipper-like) duplex in crystalline state at high ionic strength. To investigate effects of point mutation at the 5th residue on the structure, two crystal structures of d(GCGAGAGC) and d(GCGATAGC) have been determined by X-ray crystallography. In both crystals, the two octamers related by a crystallographic two-fold symmetry are aligned in an anti-parallel fashion and associated to each other to form a duplex, suggesting that the base-intercalated duplex is stable even when the 5th residue is mutated with other bases. The sheared G3:A6 pair formation makes the two phosphate backbones closer and facilitates formation of the A-X*-X-A* base-intercalated motif. The three duplexes are assembled around the two hexamine cobalt chlorides. The central X and X* residues are bound to a different cation depending on the kinds of bases.

The octaplex structure of d(GCGAGAGC) with I-motif of guanine quartet, controlled by potassium concentration.

Crystal structures of DNA octamer with the sequence d(GCGAGAGC) have been determined by X-ray analyses to investigate the specific DNA structural motifs that are useful for designing various functional DNA molecules. The octamers are assembled to form an octaplex with G-quartets and water-mediated A-quartets. At relatively high potassium concentration, however, the octaplex is split into two quadruplexes, each of which contains two G-duets. The two crystal forms suggest a dynamic formation of an octaplex from two quadruplexes in solution.