Purification of a yeast centromere-binding protein that is able to distinguish single base-pair mutations in its recognition site.

A centromere-specific DNA-binding protein has been purified to homogeneity by a combination of conventional and sequence-affinity chromatography from the yeast Saccharomyces cerevisiae. This protein (designated CBP-I) has an apparent molecular weight of 16,000. It binds specifically to the CDEI (centromere DNA element I) region of yeast centromere DNA, as shown by the electrophoretic mobility retardation assay and DNase I protection analysis, but does not bind specifically to other regions of yeast centromere DNA such as CDEII and CDEIII. The relative binding affinity of purified CBP-I to five different point mutations of CDEI correlates directly with the previously determined ability of each point mutation to convey centromere function in a mitotic chromosome segregation assay (J. H. Hegemann, J. H. Shero, G. Cottarel, P. Philippsen, and P. Hieter, Mol. Cell. Biol. 8:2523-2535, 1988). This supports the authenticity of CBP-I as a functional component of the yeast kinetochore.