Footprinting Studies with Nucleosome-Bound DNA

Although there have been many studies on the interaction of DNA-binding agents with both natural and synthetic nucleic acids, these have almost exclusively concerned their binding to naked DNA. In contrast, cellular DNA is packed into chromatm, generating higher order structures, which may alter the local DNA conformation and/or mask potential binding sites. This chapter describes the preparation of nucleosome particles containing radiolabeled DNA fragments that can be used as substrates for footprinting experiments.