DNase I footprinting.
Footprinting is a method for determining the sequence selectivity of DNA-binding compounds in which ligands protect DNA from cleavage at their binding sites. Footprinting templates are typically 50-200 base pairs long, and DNase I is the most commonly used nuclease for these experiments. This chapter describes the preparation and labelling of suitable DNA footprinting substrates, the footprinting experiment itself, and the way in which these data can be used to estimate the dissociation constant of the interaction.
Cardew
Antonia S
AS
School of Biological Sciences, University of Southampton, Southampton, UK.
Fox
Keith R
KR
D000818:Animals; D001345:Autoradiography; D001483:Base Sequence; D002417:Cattle; D004247:DNA / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D018983:DNA Footprinting / Q000379:methods*; D003850:Deoxyribonuclease I / Q000378:metabolism*; D004586:Electrophoresis; D007553:Isotope Labeling; D008969:Molecular Sequence Data; D010957:Plasmids / Q000235:genetics; D011116:Polynucleotide 5'-Hydroxyl-Kinase / Q000378:metabolism; D012194:RNA-Directed DNA Polymerase / Q000378:metabolism
D004247:DNA; D011116:Polynucleotide 5'-Hydroxyl-Kinase; D012194:RNA-Directed DNA Polymerase; D003850:Deoxyribonuclease I