Structural changes and enhancements in DNase I footprinting experiments.
In footprinting experiments, an increase in DNA cleavage with addition of ligand to a system may be due to a ligand-induced structural change. Ligand binding also enhances cleavage by displacing the cleavage agent from ligand-binding sites, thus increasing its concentration elsewhere. The theory and characteristics of this mass-action enhancement are given, and it is shown how it may be recognized. Results of DNase I footprinting of small oligomers, with actinomycin D as ligand, are analyzed to reveal which enhancements are due to mass action, and which can reasonably be ascribed to structural changes. Patterns in the footprinting plots from our experiments on actinomycin D binding to a 139-base-pair DNA fragment (with DNase I as a probe) are studied in the same way. The likely origins of these patterns are discussed, as are enhancements occurring with other probes commonly used in footprinting experiments.
Goodisman
J
J
Department of Chemistry, Syracuse University, New York 13244-4100.
Dabrowiak
J C
JC
D001483:Base Sequence; D001665:Binding Sites; D004247:DNA / Q000737:chemistry* / Q000187:drug effects; D015342:DNA Probes; D003609:Dactinomycin / Q000494:pharmacology; D003850:Deoxyribonuclease I; D006868:Hydrolysis; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation / Q000187:drug effects; D009710:Nucleotide Mapping; D013816:Thermodynamics
D015342:DNA Probes; D003609:Dactinomycin; D004247:DNA; D003850:Deoxyribonuclease I