Analysis of DNA Binding Proteins by Mobility Shift Assay

DNA binding proteins are involved in replication, repair, recombination, and transcription. In recent years, the heightened interest in transcriptional regulation has led to the development of several distinct techniques for the study of DNA binding proteins. These include the gel mobility shift assay (1 ,2 ), DNase I footprinting analyses (3 ), and the methylation-interference assay (4 ,5 ). Although each technique can be used to obtain valuable information regarding DNA/protein interactions, each method has its limitations and technical difficulties. Taken together, these methods can be used to identify important regulatory elements in mammalian and viral gene promoters, to characterize the DNA binding activity of the proteins that bind to these elements and to identify protein(s) that bind to these sites.