Effect of Crystal Packing Environment on Conformation of the DNA Duplex: Molecular Structure of the A-DNA Octamer d(G-T-G-T-A-C-A-C) in Two Crystal Forms

Abstract

The structure of the octamer d(G-T-G-T-A-C-A-C) was determined in two different crystal forms, tetragonal P43212 and hexagonal P6122. Although in both forms the octamer adopts an A-DNA structure, there are significant conformational differences between them. In particular, the P-05′ and the C5′-C4′ bonds of the middle adenine (A5) residue exhibit a distorted trans-trans conformation in the tetragonal form, while they adopt the standard gauche-, gauche+ conformation in the hexagonal form. These differences can be correlated with certain features of the crystal packing interactions in the two forms. Furthermore, a comparison of the structures of various A-DNA octamers reveals that the A-form can be divided into two subclasses such that the hexagonal structures have helical and base pair parameters that fall closer to fiber A-DNA values, while in the tetragonal structures these parameters deviate more from fiber A-DNA. These results indicate that environment plays a major role in determining DNA conformation.