Crystallization of DNA binding proteins with oligodeoxynucleotides

In contrast to oligodeoxynucleotides, protein:DNA complexes crystallize from a broad range of precipitants and conditions, much as proteins by themselves. There are, however, a number of factors that should be considered, at least in the early stages of cocrystallization attempts. These include the length and construction of the oligodeoxynucleotide itself, a pH near or below neutrality, a stoichiometric excess of DNA, and di- and polyvalent cations. By far the more important of these factors are the length of the DNA fragment and the nature of the terminal nucleotides. Unfortunately, experience suggests that, in general, the length and construction of the DNA fragment for optimal crystal growth cannot be predicted in advance. A systematic search of cocrystallization conditions with different DNA fragments will normally be required. It is important to avoid sequences that provide possible subsites within the fragment or at junctions between fragments related by translations. Sample purity, especially that of the DNA, can also have important effects. Detailed protocols for the purification of chemically synthesized fragments are suggested. Finally, a set of conditions for initial cocrystallization trials with a new DNA binding protein is suggested.