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

Van Dyke, Michael W. and Dervan, Peter B. (1983) Methidiumpropyl-EDTA•Fe(II) and DNase I footprinting report different small molecule binding site sizes on DNA. Nucleic Acids Research, 11 (16). pp. 5555-5567. ISSN 0305-1048. PMCID PMC326297. http://resolver.caltech.edu/CaltechAUTHORS:VANnar83

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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.


Item Type:Article
Related URLs:
URLURL TypeDescription
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC326297/PubMed CentralArticle
http://dx.doi.org/10.1093/nar/11.16.5555DOIArticle
http://nar.oxfordjournals.org/content/11/16/5555.abstractPublisherArticle
Additional Information:© 1983 IRL Press Limited, Oxford, England. Received 4 April 1983; Revised 5 July 1983; Accepted 21 July 1983. We are grateful to the National Institutes of Health for grant support (GM-27681) and a National Research Service Award (GM-07616) to MWV. Division of Chemistry and Chemical Engineering, Contribution Number 6797, California Institute of Technology, Pasadena, CA, 91125, USA
Funders:
Funding AgencyGrant Number
NIHGM-27681
NIH Predoctoral FellowshipGM-07616
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Caltech Division of Chemistry and Chemical Engineering6797
PubMed Central ID:PMC326297
Record Number:CaltechAUTHORS:VANnar83
Persistent URL:http://resolver.caltech.edu/CaltechAUTHORS:VANnar83
Alternative URL:http://www.pubmedcentral.gov/articlerender.fcgi?artid=326297
Official Citation:Michael W.Van Dyke and Peter B. Dervan Methidiumpropyl-EDTA-Fe(II) and DNase I footprinting report different small molecule binding site sizes on DNA Nucl. Acids Res. (1983) 11 (16): 5555-5567 doi:10.1093/nar/11.16.5555
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:4142
Collection:CaltechAUTHORS
Deposited By: Tony Diaz
Deposited On:07 Aug 2006
Last Modified:09 May 2016 18:15

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