A nonradioactive functional assay was developed to quantitate DNA bind
ing proteins. The assay was designed to allow the use of 96-well micro
plates for high sample throughput. We show that the assay can measure
sequence-specific DNA binding of purified proteins as well as DNA bind
ing activity present in whole cell extracts. By using a temperature-se
nsitive DNA binding protein, we demonstrate that DNA binding as measur
ed by this novel assay correlates with the biological function of the
protein.