Nanoparticle based detection of multiprotein complexes on DNA

Protein‐DNA interactions as well as protein‐protein interactions play critical roles in biological processes and have been extensively studied using solution‐based assays. These assays, however, often lack the ability to be introduced in vivo due to the lack of proper experimental methods, and are limited both in the distances which can be probed and the number of partners which can be investigated. We are developing novel approaches to studying protein‐DNA interactions involving multi‐protein complexes, with applications to cell biology and drug discovery. Our approach relies on the energy transfer between single metallic nanoparticles positioned onto DNA, site specifically and terminally, and dye‐labeled proteins. This energy transfer process is efficient over longer distances than classical FRET methods enhancing our ability to monitor protein‐DNA interactions and is readily applicable to multiplexing (probing multiple proteins binding to the same DNA molecule). Our initial experiments have involved well‐known DNA binding proteins such as restriction endonucleases and zinc fingers. Based on previous work demonstrating the cellular acceptance of both fluorescent dyes and nanoparticles, we are developing this technology to probe protein/DNA interactions in the cell and for drug screening applications.