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Shape selective recognition of T•A base pairs by hairpin polyamides containing N-terminal 3-methoxy (and 3-chloro) thiophene residues

Foister, Shane and Marques, Michael A. and Doss, Raymond M. and Dervan, Peter B. (2003) Shape selective recognition of T•A base pairs by hairpin polyamides containing N-terminal 3-methoxy (and 3-chloro) thiophene residues. Bioorganic and Medicinal Chemistry, 11 (20). pp. 4333-4340. ISSN 0968-0896. doi:10.1016/S0968-0896(03)00502-9.

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Hairpin polyamides selectively recognize predetermined DNA sequences with affinities comparable to naturally occurring proteins. Internal side-by-side pairs of unsymmetrical aromatic rings within the minor groove of DNA distinguish each of the four Watson-Crick base pairs. In contrast, N-terminal ring pairs exhibit less specificity, with the exception of Im/Py targeting G.C base pairs. In an effort to explore the sequence specificity of new ring pairs, a series of hairpin polyamides containing 3-substituted-thiophene-2-carboxamide residues at the N-terminus was synthesized. An N-terminal 3-methoxy (or 3-chloro) thiophene residue paired opposite Py displayed 6- (and 3-) fold selectivity for T.A relative to A.T base pair, while disfavoring G,C base pairs by >200-fold. Our data suggests shape selective recognition with projection of the 3-thiophene substituent (methoxy or chloro) to the floor of the minor groove.

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Dervan, Peter B.0000-0001-8852-7306
Additional Information:© 2003 Elsevier. Received 14 April 2003, Accepted 23 July 2003, Available online 3 September 2003. We are grateful to the National Institutes of Health for research support, the National Science Foundation for a predoctoral fellowship to S.F., the Parson's Foundation for a fellowship to M.A.M., and Caltech for a James Irvine Fellowship to R.M.D.
Funding AgencyGrant Number
NSF Predoctoral FellowshipUNSPECIFIED
Ralph M. Parsons FoundationUNSPECIFIED
James Irvine FoundationUNSPECIFIED
Issue or Number:20
Record Number:CaltechAUTHORS:20160510-080150107
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Official Citation:Shane Foister, Michael A Marques, Raymond M Doss, Peter B Dervan, Shape selective recognition of T·A base pairs by hairpin polyamides containing N-Terminal 3-Methoxy (and 3-Chloro) thiophene residues, Bioorganic & Medicinal Chemistry, Volume 11, Issue 20, October 2003, Pages 4333-4340, ISSN 0968-0896, (
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:66799
Deposited By: Victoria Brennan
Deposited On:18 May 2016 00:11
Last Modified:11 Nov 2021 00:03

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