Abstract
DNA crystallography provides essential structural information to understand the biochemical and biological functions of oligonucleotides. Therefore, it is necessary to understand the factors affecting crystallization of DNA to develop a strategy for production of diffraction-quality DNA crystals. We analyzed key factors affecting intermolecular interactions in 509 DNA crystals from the Nucleic Acid Database and Protein Databank. Packing interactions in DNA crystals were classified into four categories based on the intermolecular hydrogen bonds in base or backbone, and their correlations with other factors were analyzed. From this analysis, we confirmed that hydrogen bonding between terminal end and mid-region is most common in crystal packing and in high-resolution crystal structures. Interestingly, P212121 is highly preferred in DNA crystals in general, but the P61 space group is relatively abundant in A-DNA crystals. Accordingly, P212121 contains more terminal end-mid-region interactions than other space groups, confirming the significance of this interaction. While metals play a role in the production of a good crystal in B-DNA conformation, their effect is not significant in other conformations. From these analyses, we found that packing interaction and other factors have a strong influence on the quality of DNA crystals and provide key information to predict crystal growth of candidate oligonucleotides.
Highlights
Biomacromolecules and their interactions are essential for biochemical reactions and maintenance of cellular homeostasis
Structures were visualized and rendered in CCP4mg suite [18], and interactions within packed crystals were analyzed in Visual Molecular Dynamics tool (VMD) (Version 1.9.4) [19]
We looked at bases involved in the inter-strand interaction (Table S6), and learned that only Type 1 packing structures have base-base intermolecular packing interactions and that guanine bases are predominantly present in the terminal end (75.8%)
Summary
Biomacromolecules and their interactions are essential for biochemical reactions and maintenance of cellular homeostasis. A vast number of oligdeoxyonucleotides (ODNs) have been successfully crystallized, and the structures are determined by X-ray diffraction analyses [12] This structural information enables understanding of fine details of the conformation of DNA molecules and their interactions with other ligands such as small molecules and metals. Correlations between DXPI and other factors that affect crystal formation and diffraction quality such as conformation, sequence length, resolution, symmetry, and metal/ligands are analyzed. Based on this analysis, we propose key factors and packing interactions in the achievement of diffraction-quality DNA crystal
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