Various biological processes depend on the interaction of proteins with nucleic acids. These comprise transcriptional regulation, DNA replication and DNA repair. Conventional methods to study the interaction are either laborious (EMSA, ChIP) or limited to specific targets (EMSA, FP, ChIP).
A novel assay employs the Cy3 fluorophore which increases its fluorescence when being in proximity to proteins: Cy3-labeled oligonucleotides are immobilized on a microplate bottom and the basal fluorescence is measured on a microplate reader. If a protein is added to the microplate well that binds the oligonucleotide, the fluorescence of the fluorophore will increase. This increase can be measured and reports on protein-nucleic acid binding.
This simple and cost-effective assay detects sequence and structure specificities as well as binding constants of nucleic acid:protein liaisions. The change in fluorescence intensity is captured on a huge surface to provide stable measurements. This has been enabled by the well-scan function and high sensitivity of the FLUOstar® Omega.