The High Resolution Crystal Structure of the DNA Decamer d(AGGCATGCCT)

The crystal structure of the DNA decamer d(AGGCATGCCT) has been determined to a resolution of 1.3 Å and Rfactor of 13.9%. The structure has a unique conformation with each of the decamer single strands forming base-pairing interactions with two symmetry-related strands. The central eight bases of the decamer form an A-DNA octamer duplex with one symmetry-related strand whilst the terminal 5′ -Aand T-3′ bases are flipped out and away from the octamer helix axis to form base-pairing interactions with a second symmetry-related strand. These A·T base-pairs lie perpendicular to the crystallographic caxis and pack within the unit cell in conjunction with a symmetry-related A·T base-pair displaced by 3.4 Å along the caxis. A novel base triplet interaction of the type A∗(G·C) is present in the structure with interaction from the major groove side of the terminal 5′-A base to the minor groove of the central A-DNA octamer. This structure reports the first example of cobalt hexammine binding to a right-handed DNA duplex. The crystallographic asymmetric unit contains two cobalt hexammine ligands with one site in the major groove coordinating viahydrogen bonds to the 5′-AGG bases, and the second site located between DNA molecules and interacting with the oxygen atoms of phosphate groups.