Quantitative footprinting analysis

Michael Shubsda, Hiroko Kishikawa, Jerry Goodisman, James Dabrowiak

Research output: Contribution to journalReview articlepeer-review

7 Scopus citations


This review outlines the steps for obtaining relative constants for drugs from footprinting data. After correcting the autoradiographic spot intensities for differing amounts of radioactive DNA loaded into the lanes of a sequencing gel, footprinting plots, showing individual spot intensities as a function of drug concentration, are constructed. The initial relative slopes of footprinting plots are proportional to the binding constant of the drug for its DNA sites. Slopes of plots outside the drug binding sites can be used to identify locations of altered DNA structure. It illustrates the power of quantitative footprinting analysis by analyzing the binding of the antiviral agent netrospin to a 139‐base pair restriction fragment in the presence of the antitumor agent actinomycin D. While two netrospin binding regions are unaffected by actinomycin D a third region experiences enhanced binding in the presence of the antitumor agent.

Original languageEnglish (US)
Pages (from-to)133-139
Number of pages7
JournalJournal of Molecular Recognition
Issue number2
StatePublished - Jun 1994

ASJC Scopus subject areas

  • Structural Biology
  • Molecular Biology


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