A new application for DNase I footprinting using capillary electrophoresis
(CE) has been developed in order to decrease analysis time and to eliminate
the use of radiochemicals. An additional advantage of the new method over
the traditional radioactive methods is that the DNA probe can be labeled on
both ends with different fluorescein dyes. This provides an internal check
of the identification of protein-binding sites on DNA, because the binding
region can be observed from both DNA strands. The initial parameters for t
he CE method were developed using the Promega Core Footprinting Kit for ana
lysis of AP-2 binding sites in the SV40 enhancer sequence. After optimizati
on of the method, the protocol was found to be effective for footprint anal
ysis of the immediate upstream region (bases -1 to -370) of the rat glutath
ione peroxidase (GPX) and it permitted identification of a previously unkno
wn binding site in the upstream sequence of the GPX gene.