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Distamycin and penta-N-methylpyrrolecarboxamide binding sites on native DNA. A comparison of methidiumpropyl-EDTA-Fe(II) footprinting and DNA affinity cleaving

Schultz, Peter G. and Dervan, Peter B. (1984) Distamycin and penta-N-methylpyrrolecarboxamide binding sites on native DNA. A comparison of methidiumpropyl-EDTA-Fe(II) footprinting and DNA affinity cleaving. Journal of Biomolecular Structure and Dynamics, 1 (5). pp. 1133-1147. ISSN 0739-1102. https://resolver.caltech.edu/CaltechAUTHORS:20160511-153003259

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Abstract

Using two direct methods we have studied the binding locations and site sizes of distamycin and penta-N-methylpyrrolecarboxamide on three DNA restriction fragments from pBR322 plasmid. We find that methidiumpropyl-EDTA·Fe(II) footprinting and DNA affinity cleaving methods report common binding locations and site sizes for the tri- and pentapeptides bound to heterogeneous DNA. The tripeptide distamycin binds 5-base-pair sites with a preference for poly(dA)·poly(dT) regions. The pentapeptide binds 6–7-base-pair sites with a preference for poly(dA)·poly(dT) regions. These results are consistent with distamycin binding as an isogeometric helix to the minor groove of DNA with the four carboxamide N-H's hydrogen bonding five A+T base pairs. The data supports a model where each of the carboxamide N-H's can hydrogen bond to two bases, either O(2) of thymine or N(3) of adenine, located on adjacent base pairs on opposite strands of the helix. In most (but not all) cases the tri- and pentapeptide can adopt two orientations at each A+T rich binding site.


Item Type:Article
Related URLs:
URLURL TypeDescription
http://dx.doi.org/10.1080/07391102.1984.10507508DOIArticle
http://www.tandfonline.com/doi/abs/10.1080/07391102.1984.10507508PublisherArticle
ORCID:
AuthorORCID
Dervan, Peter B.0000-0001-8852-7306
Additional Information:© 1984 Adenine Press. Date Received: October 13, 1983. We are grateful to the National Institutes of Health for grant support (GM-27681) and to the John Simon Guggenheim Memorial Foundation for a Fellowship to P.B.D. Contribution No. 6921 from the Laboratories of Chemistry, California Institute of Technology, Pasadena, California, 91125.
Funders:
Funding AgencyGrant Number
NIHGM-27681
John Simon Guggenheim Memorial FoundationUNSPECIFIED
Other Numbering System:
Other Numbering System NameOther Numbering System ID
Caltech Laboratories of Chemistry6921
Issue or Number:5
Record Number:CaltechAUTHORS:20160511-153003259
Persistent URL:https://resolver.caltech.edu/CaltechAUTHORS:20160511-153003259
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:67027
Collection:CaltechAUTHORS
Deposited By: Victoria Brennan
Deposited On:19 May 2016 22:28
Last Modified:26 Nov 2019 11:15

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