ABSTRACT
For DNA footprinting, Maxam-Gilbert sequencing reactions are often used. Denaturing Polyacrylamide gel electrophoresis is essential to a DNA footprinting study to separate the end-labeled fragments according to length, and thus map out positions occupied by the nucleic acid-binding proteins. RNase protection assays are also more tolerant of degradation in the RNA sample. RNase protection assays are therefore the method of choice for quantitation of an mRNA species but a Northern blot must be used when the full length of the mRNA species needs to be determined. Although many of these tasks could be accomplished by the newer technique of RNase protection, the nuclease technique will be described here since it appears frequently in the literature and it covers the analysis of transcriptional start sites, for which RNase protection could also be used.
