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Fluorescence Assay of polyamide-DNA Interactions

Fluorescence Assay of polyamide-DNA Interactions

Cynthia M Dupureur, James K Bashkin, Karl Aston, Kevin J Koeller, Kimberly R Gaston, Gaofei He

Anal Biochem. 2012 Apr 1;423(1):178-83.

PMID: 22342620

Abstract:

Polyamides (PAs) are distamycin-type ligands of DNA that bind the minor groove and are capable of sequence selective recognition. This capability provides a viable route to their development as therapeutics. Presented here is a simple and convenient fluorescence assay for PA-DNA binding. PAs are titrated into a sample of a hairpin DNA featuring a TAMRA dye attached to an internal dU near the PA binding site. In a study of 6 PAs, PA binding leads to a steady reproducible decrease in fluorescence intensity that can be used to generate binding isotherms. The assay works equally well with both short (6- to 8-ring) and long (14-ring) PAs, and K(d) values ranging from approximately 1 nM to at least 140 nM were readily obtained using a simple monochromator or filter configuration. Competition assays provide a means to assessing possible dye interference, which can be negligible. The assay can also be used to determine PA extinction coefficients and to measure binding kinetics; thus, it is an accessible and versatile tool for the study of PA properties and PA-DNA interactions.

Chemicals Related in the Paper:

Catalog Number	Product Name	Structure	CAS Number	Price
LPLC83101	Polyamide with Fluorescence			Price

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