title: 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 P4(3)2(1)2 and hexagonal P6(1)22. 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.
authors.affiliation: Department of Biochemistry, College of Agricultural and Life Sciences, University of Wisconsin, Madison 53706.
authors.forename: S
authors.initials: S
authors.lastname: Jain
authors.forename: M
authors.initials: M
authors.lastname: Sundaralingam
mesh_terms: D001482:Base Composition; D003460:Crystallization; D004247:DNA; D015394:Molecular Structure; D009690:Nucleic Acid Conformation; D009692:Nucleic Acid Heteroduplexes; D011110:Polymorphism, Genetic; D013096:Spermine
chemical_list: D009692:Nucleic Acid Heteroduplexes; D013096:Spermine; D004247:DNA