Crystal Packing Effects on A-DNA Helix Parameters: A Comparative Study of the Isoforms of the Tetragonal & Hexagonal Family of Octamers with Differing Base Sequences

Abstract

The helix and base pair parameters of A-DNA octamers have been compared having different base sequences both in the tetragonal and hexagonal crystal systems. For the eight structures in the tetragonal family, the twist, rise, slide, inclination and tilt are essentially the same, influenced by the similarity in crystal packing. The propeller twist and the base pair buckle display small sequence dependent variations. But the base pair roll appears to be changed by the specific intermolecular hydrogen bonding interactions. For four of the five octamer structures in the hexagonal family, the base pair rise, slide, inclination, tilt, as well as the propeller twist and buckle are all very similar, while the twist angle and the base pair roll are not. The intermolecular hydrogen bonding interactions seem to be primarily responsible for the differences in the roll angle in the tetragonal structures but for both the roll and twist angles in the hexagonal structures. These results demonstrate that the majority of the observed helix base pair parameters for A-DNA octamers in crystals are affected by the crystal packing environment, while a few parameters, like propeller twist and base pair buckle display some base sequence dependence.

Structure of d(CCCCGGTACCGGGG)2at 1.65 Å resolution

“…A common packing pattern in crystals of A-DNA helices is that the terminal base pairs of one helix stack on the nearly flat minor groove of a neighbouring molecule (Rabinovich et al, 1988;Shakked et al, 1990;Ramakrishnan & Sundaralingam, 1993). Such an interaction is observed in the present structure.…”

Crystal structure and conformation of a DNA–RNA hybrid duplex with a polypurine RNA strand: d(TTCTTBr5CTTC)–r(GAAGAAGAA)

“…All the unliganded single crystal structures of hybrid duplexes, however, are essentially in the A-form. As indicated in a comparative study of the crystalpacking effects on A-DNA helix parameters [32], the conformation of short oligonucleotides was found to depend on both their interactions with the environment (i.e. crystal packing) and base sequence.…”

“…crystal packing) and base sequence. Linear oligonucleotides are prone to packing deformations in the solid state [32], therefore caution should be exercized when relating the observed crystal structure to base sequence. Nevertheless, the comparisons presented here suggest the influence of RNA PPT on the hybrid structure and, more specifically, on the conformation of the DNA backbone.…”

Molecular Dynamics Simulations of the d(CCAACGTTGG)2 Decamer: Influence of the Crystal Environment

“…X-ray crystallography has proved to be particularly valuable in the examination of DNA structure, but the principal limitation of this technique is the need to obtain high-quality crystals for every sequence of interest. Another criticism that is sometimes invoked is that crystal packing effects may constrain the DNA structure, thereby confounding an analysis of the relationship of sequence to structure (Ramakrishnan and Sundaralingam, 1993;Tippin and Sundaralingam, 1997). NMR has also proved valuable in the structural analysis of DNA, but a problem associated with NMR is that the data are relatively short-ranged, and consequently fewer data can be collected when an extended structure like DNA is studied, as compared to more globular structures like proteins (Hartmann and Lavery, 1996).…”