Crystal chemistry of some DNA oligonucleotides and their complexes

This chapter begins with brief introductions to the fundamentals of oligonucleotide structure and to current aspects of crystal chemistry common to cyclodextrin complexes, tetraphenylporphyrin-metal complexes, and oligonucleotides and their complexes. This is followed by an outline of the special features of X-ray crystal structure analysis as applied to oligonucleotides, including the limitations on the resolution attainable. The implicit assumption usually made that native oligonucleotides are unary (single component) phases while their complexes (intercalation and minor groove binders are the two principal types) are binary can be a useful working hypothesis, but neglects the important effects of solvent and ion content. Here, the crystal chemical aspects of hexamer, octamer, decamer, and dodecamer oligonucleotide crystals are stressed, covering both native and complexed modifications. Many of the crystal structures are, group wise, isomorphous. Differences in base-pair sequence sometimes break the isomorphism, but usually do not. Other different crystal types are often found in addition to the major isomorphous families. An important problem is that the chemical compositions (solvent content, presence, and number of ions) are often not known, making it difficult to decide whether particular clusters of related crystals are polymorphs (different crystal structures, the same chemical compositions) or have different compositions. Comparison of unit cell volumes is a useful but limited tool in making such decisions. Attempts are made to classify particular crystalline complexes in phase rule terms as primary solid solutions or phase rule compounds. There are resemblances in behaviour and structural features to the cyclodextrins.