An A-DNA structure with two independent duplexes in the asymmetric unit

Abstract

The crystal and molecular structure of the self-complementary A-DNA decamer sequence d(G₄CGC₄) was solved at 1.9 Å resolution. The decamer crystallizes in space group P2₁ with two independent duplexes in the asymmetric unit. Duplex 1 has interactions which are distributed symmetrically about its length compared with duplex 2. The two end base pairs of duplex 1 have a similar NH...O hydrogen-bond pattern involving GGC segments of duplex 2 and a symmetry-related neighbour, while the end base pairs of duplex 2 interact with the GCC and GGG segments of its symmetry-related neighbours through NH...O and NH...N hydrogen bonds and a water-mediated hydrogen bond between the carboxyl groups of C40 and C8. In addition to the C4'-C5' torsion angle γ assuming the trans conformation in certain steps, this angle also adopts the gauche^- conformation at C37 as opposed to the preferred gauche⁺ conformation, with a concomitant change in phosphodiester P-O5' ([α]) in the opposite sense. This facilitates stacking between adjacent bases. The study suggests that the structural alterations in the two molecules in the asymmetric unit originate from an inherent propensity of the d(G₄CGC₄)base sequence for varied intermolecular interactions and malleability.