DNA-WT1 protein interaction studied by surface-enhanced Raman spectroscopy

Interactions of proteins with DNA play an important role in regulating the biological functions of DNA. Here we propose and demonstrate the detection of protein-DNA binding using surface-enhanced Raman scattering (SERS). In this method, double-stranded DNA molecules with potential protein-binding sites are labeled with dye molecules and immobilized on metal nanoparticles. The binding of proteins protects the DNA from complete digestion by exonuclease and can be detected by measuring the SERS signals before and after the exonuclease digestion. As a proof of concept, this SERS-based protein-DNA interaction assay is validated by studying the binding of a zinc finger transcription factor WT1 with DNA sequences derived from the promoter of the human vascular endothelial growth factor.