title: Fluorescence recovery assay for the detection of protein-DNA binding.
abstract: We report a novel and straightforward fluorescence recovery assay which enables the detection of protein-DNA interactions and simultaneously determines relative binding affinities of sequence-specific DNA-binding proteins for a variety of DNA sequences in a multiplexed format. The detection of protein-DNA binding is accomplished by monitoring fluorescence recovery during exonuclease digestion of DNA sequences that are modified with fluorophore-quencher pairs. Retardation of fluorescence recovery occurs with binding of the protein to the putative DNA binding element, which arrests exonuclease digestion. The assay detects protein-DNA binding in a homogeneous solution simply, quickly, and reliably without using radioisotopes. Multiplexing is possible by labeling different DNA sequences with spectrally distinct dyes, allowing simultaneous analysis of experimental and control binding reactions in the same mixture.
authors.affiliation: Department of Chemistry and International Institute for Nanotechnology, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208-3113, USA.
authors.forename: Xiaoyang
authors.initials: X
authors.lastname: Xu
authors.forename: Zhen
authors.initials: Z
authors.lastname: Zhao
authors.forename: Lidong
authors.initials: L
authors.lastname: Qin
authors.forename: Wei
authors.initials: W
authors.lastname: Wei
authors.forename: Jon E
authors.initials: JE
authors.lastname: Levine
authors.forename: Chad A
authors.initials: CA
authors.lastname: Mirkin
mesh_terms: D004247:DNA / Q000032:analysis* / Q000378:metabolism*; D047628:Estrogen Receptor alpha / Q000032:analysis* / Q000378:metabolism*; D005453:Fluorescence; D008163:Luminescent Measurements / Q000379:methods*; D011485:Protein Binding; D018167:Receptors, Calcitriol / Q000032:analysis* / Q000378:metabolism*
chemical_list: D047628:Estrogen Receptor alpha; D018167:Receptors, Calcitriol; D004247:DNA