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DNA minor-groove recognition by 3-methylthiophene/pyrrole pair

Doss, Raymond M. and Marques, Michael A. and Foister, Shane and Dervan, Peter B. (2004) DNA minor-groove recognition by 3-methylthiophene/pyrrole pair. Chemistry and Biodiversity, 1 (6). pp. 886-899. ISSN 1612-1880. doi:10.1002/cbdv.200490071.

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Hairpin polyamides are synthetic oligomers, which fold and bind to specific DNA sequences in a programmable manner. Internal side-by-side pairings of the aromatic amino acid residues 1-methyl-1H-pyrrole (Py), 1-methyl-1H-imidazole (Im), and 3-hydroxy-1-methyl-1H-pyrrole (Hp) confer the ability to distinguish between all four Watson-Crick base pairs in the minor groove of B-form DNA. In a broad search to expand the heterocycle repertoire, we found that when 3-methylthiophene (Tn), which presents a S-atom to the minor groove, is paired with Py, it exhibits a modest threefold specificity for TA>AT presumably by shape-selective recognition. In this study, we explore the scope and limitations of this lead by incorporating multiple Tn residues within a single hairpin polyamide. It was found that hairpin polyamides containing more that one Tn/Py pair exhibit lowered affinities and specificities for their match sites. It appears that little deviation is permissible from the parent five-membered ring 1-methyl-1H-pyrrole-2-carboxamide scaffold for DNA recognition.

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Dervan, Peter B.0000-0001-8852-7306
Additional Information:© 2004 Verlag Helvetica Chimica Acta AG, Zürich. Manuscript Received: 12 MAR 2004. Version of Record online: 24 JUN 2004.
Issue or Number:6
Record Number:CaltechAUTHORS:20160509-114913928
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Official Citation:Doss, Raymond M., Marques, Michael A., Foister, S. and Dervan, Peter B. (2004), DNA Minor-Groove Recognition by 3-Methylthiophene/Pyrrole Pair. Chemistry & Biodiversity, 1: 886–899. doi: 10.1002/cbdv.200490071
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:66772
Deposited By: Victoria Brennan
Deposited On:17 May 2016 22:23
Last Modified:11 Nov 2021 00:02

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