Crystal structure of d(CGAAGC); association of two parallel-stranded duplexes through anti-parallel-stranded duplex formation.

We reported that d(CGAA) prefers to form a parallel duplex with homo base pair formations. To survey a possibility of longer parallel duplex, crystal structure of d(CGAAGC) has been determined. As expected, the CGAA part of the hexamer forms a parallel duplex with the corresponding part of another hexamer. The remaining G and C residues of one strand are stacked on the end of the parallel duplex, while those of the other strand are flip out and extended to the outside. The stacked residues form an anti-parallel duplex with the extended residues of the adjacent parallel duplex to form a dimer between the two parallel duplexes.