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High Sensitivity Measurement of Transcription Factor-DNA Binding Affinities by Competitive Titration Using Fluorescence Microscopy

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A competition assay for DNA binding using the fluorescent probe ANS.

Ian A Taylor¹, G Geoff Kneale

¹Biophysics Laboratories, Institute of Biomedical and Biomolecular Sciences, St Michael's Building, University of Portsmouth, Portsmouth PO1 2DT, UK.

Methods in Molecular Biology (Clifton, N.J.)

|April 21, 2009

Summary

This study demonstrates using the extrinsic fluorescence probe 1-anilinonaphthalene-8-sulphonic acid (1,8-ANS) to effectively study protein-DNA interactions. The probe

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Area of Science:

Biochemistry
Molecular Biology
Biophysical Chemistry

Background:

Fluorescence spectroscopy is a key method for analyzing protein-nucleic acid interactions.
Intrinsic tryptophan fluorescence can be limited for studying proteins with distant binding sites.

Purpose of the Study:

To investigate the utility of an extrinsic fluorescence probe for studying protein-DNA interactions.
To characterize the interaction between the EcoR124I methylase and its DNA target sequences.

Main Methods:

Utilized the environmentally sensitive extrinsic fluorescence probe 1-anilinonaphthalene-8-sulphonic acid (1,8-ANS).
Monitored 1,8-ANS fluorescence emission spectrum changes upon displacement by DNA from the EcoR124I binding site.

Main Results:

DNA binding to EcoR124I caused a red shift and intensity decrease in the 1,8-ANS fluorescence spectrum.
These spectral changes were successfully used to investigate EcoR124I's interaction with DNA target sequences.

Conclusions:

Extrinsic fluorescence probes like 1,8-ANS offer a viable alternative when intrinsic tryptophan fluorescence is insufficient.
This method provides a sensitive approach to study specific protein-DNA recognition events.