Quantitative footprinting analysis of the netropsin-dna interaction

Brian Ward, Robert Rehfuss, Janies C. Dabrowiak

Research output: Contribution to journalArticlepeer-review

27 Scopus citations


The results of a series of quantitative footprinting experiments of the netropsin-DNA interaction as studied using two different DNA cleaving probes, the enzyme DNase I and a cationic manganese porphyrin complex, are described. Plots of the relative change in oligonucleotide concentration as a function of drug concentration, covering -110 base pairs of a DNA restriction fragment, revealed netropsin induced changes in the cleavage rates of both probes. These appeared as inhibitions for the binding sites, enhancements where no binding took place, and enhancement/inhibitions for the weak binding sites. Determination of the concentration of drug necessary to reduce the amount of a particular oligomer to half of its initial value allowed a ranking of the affinities of the various binding sites on the fragment. In addition to uncovering the location of a number of overlapping netropsin binding sites, the data allowed additional insight on the manner in which both probes alter their DNA cleavage rates in the drug-footprinting experiment.

Original languageEnglish (US)
Pages (from-to)685-695
Number of pages11
JournalJournal of Biomolecular Structure and Dynamics
Issue number5
StatePublished - Apr 1987

ASJC Scopus subject areas

  • Structural Biology
  • Molecular Biology


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