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Completion of a Programmable DNA-Binding Small Molecule Library

Hsu, Carey F. and Phillips, John W. and Trauger, John W. and Farkas, Michelle E. and Belitsky, Jason M. and Heckel, Alexander and Olenyuk, Bogdan Z. and Puckett, James W. and Wang, Clay C. C. and Dervan, Peter B. (2007) Completion of a Programmable DNA-Binding Small Molecule Library. Tetrahedron, 63 (27). pp. 6146-6151. ISSN 0040-4020. PMCID PMC2151752. doi:10.1016/j.tet.2007.03.041.

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Hairpin pyrrole-imidazole (Py-Im) polyamides are programmable oligomers that bind the DNA minor groove in a sequence-specific manner with affinities comparable to those of natural DNA-binding proteins. These cell-permeable small molecules have been shown to enter the nuclei of live cells and downregulate endogenous gene expression. We complete here a library of 27 hairpin Py-Im polyamides, which bind seven-base-pair sequences of the general form 5′-WWGNNNW-3′ (where W=A or T, N=W, G, or C). Their equilibrium association constants (K_a) range from K_a=1×10^8 to 4×10^(10) M^(−1) with good sequence specificity. A table of binding affinities and sequence contexts for this completed 27-member library has been assembled for the benefit of the chemical biology community interested in molecular control of transcription.

Item Type:Article
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URLURL TypeDescription CentralArticle
Dervan, Peter B.0000-0001-8852-7306
Additional Information:© 2007 Elsevier Ltd. Received 27 January 2007; revised 2 March 2007; accepted 6 March 2007; Available online 12 March 2007. We are grateful to the National Institutes of Health for research support.
Funding AgencyGrant Number
Subject Keywords:Molecular recognition; Gene regulation; Polyamide; Small molecule–nucleic acid interaction
Issue or Number:27
PubMed Central ID:PMC2151752
Record Number:CaltechAUTHORS:20160509-110446789
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Official Citation:Carey F. Hsu, John W. Phillips, John W. Trauger, Michelle E. Farkas, Jason M. Belitsky, Alexander Heckel, Bogdan Z. Olenyuk, James W. Puckett, Clay C.C. Wang, Peter B. Dervan, Completion of a programmable DNA-binding small molecule library, Tetrahedron, Volume 63, Issue 27, 2 July 2007, Pages 6146-6151, ISSN 0040-4020, (
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:66750
Deposited By: Victoria Brennan
Deposited On:17 May 2016 20:07
Last Modified:11 Nov 2021 00:02

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