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Nucleic Acids Research, 1983, Vol. 11, No. 16 5555-5567
© 1983

MOLECULAR BIOLOGY

Methidiumpropyl-EDTA-Fe(II) and DNase I footprinting report different small molecule binding site sizes on DNA

Michael W.Van Dyke and Peter B. Dervan*

Division of Chemistry and Chemical Engineering, Contribution Number 6797, California Institute of Technology Pasadena, CA 91125, USA

*To whom correspondence should be addressed

Received April 4, 1983. Revised July 5, 1983. Accepted July 21, 1983.

DNase I and MPE-Fe(II) footprinting both employ partial cleavage of ligand-protected ENA restriction fragments and Haxam-Gilbert sequencing gel methods of analysis. One method utilizes the enzyme, DNase I, as the ENA cleaving agent while the other employs the synthetic molecule, methidiura-propyl-EDEA (MPE). For actinoraycin D, chromomycin A3 and distamycin A, ENase I footprinting reports larger binding site sizes than MPE'Fe(II). ENase I footprinting appears more sensitive for weakly bound sites. MPE'Fe(II) footprinting appears more accurate in determining the actual size and location of the binding sites for small molecules on DNA, especially in cases where several small molecules are closely spaced on the DNA. HPE-Fe(II) and ENase I report the same sequence and binding site size for lac repressor protein on operator DNA.


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