Footprinting Procedures
· DNase I Footprinting (Mike A. Dyer)
· DNase I footprinting
Determining the site of binding for a protein on a DNA sequence
· DNase I Footprinting (Bowtell Lab)
· DNase I Footprinting (Crawford Lab)
Detailed protocol for footprinting, including strategy for probe labeling, recipes and more...
· Exonuclease III footprinting
· Hydroxyl radical footprinting (TTO)
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Hydroxyl radical footprinting is a powerful technique for investigating DNA-protein interactions. In contrast to DNase I footprinting, it allows the exact determination of contact sites in the DNA target sequence. This is a modification of this method in which the DNA fragments for the footprint assay are non-radioactively labeled and generated by PCR. The fragments are analyzed after incubation with the specific DNA-binding protein and subsequent treatment with hydroxyl radicals, on an ALFexpress DNA Sequencer
Other procedures
· DMS-treating DNA (Indiana U)
DMS treatment under controlled conditions, followed by piperidine cleavage, yeilds a ladder of fragments indicating the positions of all G residues in the DNA sequence. These ladders are useful MW standards for S1 experiments, footprinting, etc.
· Preparation of G+A Marker (Technical Tips Online)
A rapid one-step procedure for preparation of G plus A sequence markers by acid-induced apurinization and DNA cleavage
Preparation of G+A Marker
Simplified method for preparing G+A ladder run along with footprinting reaction. It's much simple than the original Maxima-Gilbert sequencing reaction and works fine.