title: Exonuclease III protection assay with FRET probe for detecting DNA-binding proteins.
abstract: We describe a new method for the assay of sequence-specific DNA-binding proteins in this paper. In this method, the sensitive fluorescence resonance energy transfer (FRET) technology is combined with the common DNA footprinting assay in order to develop a simple, rapid and high-throughput approach for quantitatively detecting the sequence-specific DNA-binding proteins. We named this method as exonuclease III (ExoIII) protection assay with FRET probe. The FRET probe used in this assay was a duplex DNA which was designed to contain one FRET pair in the center and two flanking protein-binding sites. During protein detection, if a target protein exists, it will bind to the two protein-binding sites of the FRET probe and thus protect the FRET pair from ExoIII digestion, resulting in high FRET. However, if the target protein does not exist, the FRET pair on the naked FRET probe will be degraded by ExoIII, resulting in low FRET. Three kinds of recombinant transcription factors including NF-kappaB, SP1 and p50, and the target protein of NF-kappaB in HeLa cell nuclear extracts, were successfully detected by the assay. This assay can be extensively used in biomedical research targeted at DNA-binding proteins.
authors.affiliation: Chien-Shiung Wu Laboratory, Southeast University Nanjing 210096, China.
authors.forename: Jinke
authors.initials: J
authors.lastname: Wang
authors.forename: Tongxiang
authors.initials: T
authors.lastname: Li
authors.forename: Xiaoying
authors.initials: X
authors.lastname: Guo
authors.forename: Zuhong
authors.initials: Z
authors.lastname: Lu
mesh_terms: D002467:Cell Nucleus / Q000737:chemistry; D018983:DNA Footprinting / Q000379:methods*; D015342:DNA Probes / Q000737:chemistry* / Q000378:metabolism; D004268:DNA-Binding Proteins / Q000032:analysis*; D005090:Exodeoxyribonucleases / Q000378:metabolism*; D031541:Fluorescence Resonance Energy Transfer / Q000379:methods*; D005456:Fluorescent Dyes / Q000737:chemistry* / Q000378:metabolism; D006367:HeLa Cells; D006801:Humans; D014157:Transcription Factors / Q000032:analysis
chemical_list: D015342:DNA Probes; D004268:DNA-Binding Proteins; D005456:Fluorescent Dyes; D014157:Transcription Factors; D005090:Exodeoxyribonucleases; C020133:exodeoxyribonuclease III