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Interactions between a symmetrical minor groove binding compound and DNA oligonucleotides: ^1H and ^(19)F NMR studies

Wang, Andrew H.-J. and Cottens, Sylvain and Dervan, Peter B. and Yesinowski, James P. and van der Marel, Gijs A. and van Boom, Jacques H. (1989) Interactions between a symmetrical minor groove binding compound and DNA oligonucleotides: ^1H and ^(19)F NMR studies. Journal of Biomolecular Structure and Dynamics , 7 (1). pp. 101-117. ISSN 0739-1102. https://resolver.caltech.edu/CaltechAUTHORS:20160510-155635020

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Abstract

High-resolution NMR techniques (proton and ^(19)F) have been used to study the interactions between several DNA oligonucleotides with varying length of AT base pairs and the synthetic pyrrole-containing compound (P1-F_4S-P1), which has properties similar to the DNA minor groove binding drug distamycin A. When this two-fold symmetrical DNA binding molecule is added to the self-complementary DNA oligomers, the resulting complex exhibits an NMR spectrum without any doubling of individual resonances, consistent with a two-fold symmetry of the complex. This is in contrast to all other complexes studied so far. The minimum length of an AT stretch for specific ligand binding is judged to be greater than 4 base pairs. Inter-molecular proton nuclear Overhauser effects between the ligand molecule and a DNA dodecamer d(CGCAAATTTGCG) provide evidence that P1-F_4S-P1 binds DNA in the minor groove and interacts with the middle AT base pairs. The presence of a specific interaction between P1-F_4S-P1 and DNA is conclusively demonstrated by ^(19)F NMR studies, in which four previously chemically equivalent fluorine nuclei in the free molecule become two non-equivalent pairs (yielding an AB quartet pattern) upon the binding of P1-F_4S-P1 to DNA duplex. A sequence-dependent binding behavior of P1-F_4S-P1 is evident by comparing the ^(19)F NMR spectra of the complexes between P1-F_4S-P1 and two different but related DNA dodecamers, d(CGCAAATTTGCG) and d(CGCTTTAAAGCG). P1-F_4S-P1 binds more strongly to the former dodecamer with an association constant of approximately 1 X 10^3 M^-1.


Item Type:Article
Related URLs:
URLURL TypeDescription
http://dx.doi.org/10.1080/07391102.1989.10507754DOIArticle
http://www.tandfonline.com/doi/abs/10.1080/07391102.1989.10507754PublisherArticle
Additional Information:© 1989 Taylor & Francis. Date received: May 18, 1989. Communicated by the Editor R.H. Sarma. This work was supported by a grant from the NSF (DMB 8612268) to AHJW. The Southern California Regional NMR Facility was supported by Grant No. CHE 8440137 from NSF.
Funders:
Funding AgencyGrant Number
NSFDMB 8612268
NSFCHE 8440137
Issue or Number:1
Record Number:CaltechAUTHORS:20160510-155635020
Persistent URL:https://resolver.caltech.edu/CaltechAUTHORS:20160510-155635020
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:66967
Collection:CaltechAUTHORS
Deposited By: Victoria Brennan
Deposited On:19 May 2016 22:27
Last Modified:03 Oct 2019 10:01

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