Combination of native and denaturing PAGE for the detection of protein binding regions in long fragments of genomic DNA.

Kristel Kaer, Mart Speek

Department of Gene Technology, Tallinn University of Technology, Tallinn, Estonia.

Methods in molecular biology (Clifton, N.J.) 2013

filter terms:

In traditional electrophoresis mobility shift assay (EMSA) a single (32)P-labeled double-stranded DNA oligonucleotide or a restriction fragment bound to a protein is separated from the unbound DNA by polyacrylamide gel electrophoresis (PAGE) under nondenaturing conditions. An extension of this method uses a population of DNA restriction fragments derived from long genomic regions for the identification of fragments containing protein binding regions. Although the method allows simultaneous analysis of large fragments, it is relatively laborious and can be used to detect only fragments containing high affinity protein binding sites. Here we describe an alternative and straightforward strategy which is based on a combination of native and denaturing PAGE. With this strategy restriction fragments, derived from genomic DNA (<10 kb), containing high as well as low affinity protein binding regions may be easily identified.

Citation

Kristel Kaer, Mart Speek. Combination of native and denaturing PAGE for the detection of protein binding regions in long fragments of genomic DNA. Methods in molecular biology (Clifton, N.J.). 2013;977:169-81