Crystallization and crystal packing analysis of DNA oligonucleotides

There are now over 30 DNA oligonucleotides that have been crystallized and their structure determined by X-ray diffraction analysis. From these studies there is a new wealth of information available to us concerning the fine details of the conformation of DNA molecules and their interactions with other ligands such as antitumor drugs and ions. In addition, the intensive efforts in attempting to crystallize many DNA fragments from several laboratories have resulted in a considerable amount of data related to the crystallization conditions for DNA molecules. Various factors such as the types of metal ion, precipitant, buffer and pH all play important roles in obtaining suitable crystals. We have also analyzed the packings of DNA molecules in the crystal lattice and found that they can be arranged into four different general categories. Those four types of packing interactions are: (1) base-base stacking plus intermolecular hydrogen bonds such as in the crystals of Z-DNA, daunomycin/DNA complex, triostin A/DNA complex, etc.; (2) base pair/A-DNA minor groove stacking, as in several DNA oligomer crystals in the A-DNA conformation; (3) guanine-guanine pairing in the minor groove of B-DNA dodecamers; (4) miscellaneous hydrogen bonding and stacking interactions. Many of those intermolecular interactions are examined in details and their possible biological relevance is discussed.