Crystal structure of d(GCGAAAGCT) containing a parallel‐stranded duplex with homo base pairs and an anti‐parallel duplex with Watson–Crick base pairs

摘要

A DNA fragment d(GCGAAAGCT), known to adopt a stable mini‐hairpin structure in solution, has been crystallized in the space group I4₁22 with the unit‐cell dimensions a = b = 53.4 ? and c = 54.0 ?, and the crystal structure has been determined at 2.5 ? 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, C₂:C₂+ (singly‐protonated between the Watson– Crick sites), G₃:G₃ (between the minor groove sites), A₄:A₄ (between the major groove sites) and A₅:A₅ (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.