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(Fig. 6.43). DNase I is added and conditions favouring a partial digestion are then carried

out. This limited digestion ensures that a number of fragments are produced where the

DNA is not protected by the DNA-binding protein. The region protected by the DNA-

binding protein will remain undigested. All the fragments are then separated on a high-

resolution polyacrylamide gel alongside a control digestion where no DNA-binding

Restriction fragment/oligonucleotide

e.g. promoter region

DNA-binding proteins

e.g. transcription factors

Protein-binding domain

End-label^32 P

DNase I DNase I

Protein protects DNA

from digestion

No protein protection

Footprint

Gel electrophoresis and

autoradiography

Fig. 6.43Steps involved in DNA footprinting.

246 Recombinant DNA and genetic analysis