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PMID: 6225070 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, P.H.S.

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

Nucleic acids research ·Vol. 11 ·No. 16 ·1983-08-25 ·Pages 5555-67

Van Dyke MW, Dervan PB

Abstract

DNase I and MPE.Fe (II) footprinting both employ partial cleavage of ligand-protected DNA restriction fragments and Maxam-Gilbert sequencing gel methods of analysis. One method utilizes the enzyme, DNase I, as the DNA cleaving agent while the other employs the synthetic molecule, methidium-propyl-EDTA (MPE). For actinomycin D, chromomycin A3 and distamycin A, DNase I footprinting reports larger binding site sizes than MPE.Fe (II). DNase 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. MPE.Fe (II) and DNase I report the same sequence and binding site size for lac repressor protein on operator DNA.

MeSH Terms
Base Composition Base Sequence Chemical Phenomena Chemistry Chromomycin A3 DNA Dactinomycin Deoxyribonuclease I Distamycins Edetic Acid/analogs & derivatives Endodeoxyribonucleases/metabolism Plasmids Repressor Proteins/genetics Substrate Specificity
Chemicals
Distamycins Repressor Proteins methidiumpropyl-EDTA-iron(II) Dactinomycin stallimycin DNA Edetic Acid Chromomycin A3 Endodeoxyribonucleases Deoxyribonuclease I
Authors & Affiliations
2 authors, click to expand affiliations / ORCID
Van Dyke M W
Dervan P B
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19 references, click to expand
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Article Info
Journal
Nucleic acids research
Abbr.
Nucleic Acids Res
ISSN
0305-1048
DOI
10.1093/nar/11.16.5555
Published
1983-08-25
Pages
5555-67
Language
English
Region
England
NLM ID
0411011
PMCID
PMC326297
Subset
IM
Grants
NIGMS NIH HHS · GM-07616 · United States
NIGMS NIH HHS · GM-27681 · United States
External Links
PubMed source DOI: 10.1093/nar/11.16.5555 PMC Full Text View journal details
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