The main focus of this research is to continue the single crystal X-ray diffraction studies of DNA oligomers of defined sequence. The work is aimed at providing a better understanding of the global/local conformations of DNA as regulated by base sequence. Studies of DNA octamers will be continued to look for other examples of DNA sequences the bind spermine, an ubiquitous oligocation in cells. The determination of the structure of the first A-DNA dodecamer in this laboratory provided precise values for the geometry of A-DNA, particularly the major groove dimension, which was found to be markedly narrower than in the shorter A-DNA oligomers. More dodecamers will be studied to provide better estimates of the major groove width and explore the influence of sequence changes on the A-DNA conformational parameters. Besides the A-DNA oligomers, B-DNA dodecamers, which have an inverted sequence at the core, viz with the T's preceding the A's, will be studied. These are of interest because, unlike the AxTx sequences, the TxAx sequences do not display anomalous gel migration properties. Crystals and data on at least one structure in each class (A-octamer, A-dodecamer, B-dodecamer) are already available. Whenever possible, complexes of drugs, such as netropsin, with the B-DNA will be investigated. Different crystal forms of the same sequence will be studied whenever available to compare sequence effects and crystal environmental effects on DNA conformation. The role of solvents in nucleic acids will be investigated by carefully examining the interaction of the waters of hydration with individual bases, sugars and phosphates, as well as its distribution in the grooves, along the sugar-phosphate backbone and its participation in intermolecular interactions. These X-ray crystallographic studies will be carried out using the highest resolution data. The long term goals of this project are to determine the molecular structures of DNAs with longer sequences (more than 12 nucleotides), oligomers with adjacent stretches having the potential for forming A- and B-DNA and B- and Z-DNA, to study the geometries of the geometries of the A-B and B-Z junctions. Longer DNA oligomers having sequential A-tracts will also be studied to obtain a better picture of DNA bending. This investigation will provide important details on the molecular geometries and conformations of DNAs which will be of fundamental importance in the understanding of the molecular basis of gene regulation and expression.
