PMID: 9159124May 27, 1997Paper

Estimation of the DNA sequence discriminatory ability of hairpin-linked lexitropsins

Proceedings of the National Academy of Sciences of the United States of America
W L WalkerD S Goodsell

Abstract

Three- and four-ring polyamides containing N-methylimidazole and N-methylpyrrole, and their hairpin-linked derivatives, bind side-by-side in the minor groove of DNA in a sequence-specific manner. The sequences recognized by side-by-side molecules are dependent on the pairings of the polyamide rings to the bases. In this study we report a mathematical model for estimating the free energies of binding for gamma-aminobutyric acid-linked polyamides to 5- and 6-bp DNA sequences. The model parameters are calibrated by a least-squares fit to 35 experimental binding constants. The model performs well in cross-validation experiments and the parameters are consistent with previously proposed empirical rules of polyamide-DNA binding. We apply the model to the design of targeted polyamides, evaluating the ability of the proposed polyamides to bind to a DNA sequence of interest while minimizing binding to the remaining DNA sequences.

References

May 1, 1986·Journal of Medicinal Chemistry·D Goodsell, R E Dickerson
Aug 1, 1989·Proceedings of the National Academy of Sciences of the United States of America·J G Pelton, D E Wemmer
Oct 24, 1995·Proceedings of the National Academy of Sciences of the United States of America·J ChoP B Dervan
Sep 1, 1995·Nature Structural Biology·X ChenM Sundaralingam
Mar 1, 1994·Nature Structural Biology·X ChenM Sundaralingam
Oct 28, 1994·Science·B H GeierstangerD E Wemmer

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Citations

Jan 1, 1997·Biopolymers·W L WalkerD S Goodsell
Feb 15, 2002·Journal of Biomolecular Structure & Dynamics·Sylvia Mansilla, José Portugal
May 16, 1998·Proceedings of the National Academy of Sciences of the United States of America·W L WalkerD S Goodsell
Nov 22, 2005·Bioorganic & Medicinal Chemistry·Jaipal HoodaSteven M Firestine
Oct 17, 1998·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·W L WalkerE M Landaw
Oct 12, 2012·Organic & Biomolecular Chemistry·Robin C K YangLeung Sheh

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