FRET-based methods to study ATP-dependent changes in chromatin structure

DNA packaging into chromatin imposes several levels of regulation on the central nuclear processes of DNA replication, recombination, repair and transcription. ATP-dependent chromatin-remodeling enzymes play a critical role in this regulation by altering the accessibility of nucleosomal DNA. Remodeling can result in large-scale changes in chromatin, such as the formation of heterochromatin, or smaller changes in exposure or occlusion of specific DNA regions. To understand the mechanisms of chromatin remodeling, we report a FRET-based method to follow remodeling of a single histone octamer on DNA. This technique provides a non-perturbing, solution-based approach to quantitatively track the movement of DNA with respect to the octamer in real-time. The method can easily be altered to examine other conformational changes within the nucleosome, and is applicable to study the enzymatic activity of several classes of chromatin-remodeling complexes.