Publisher Summary This chapter focuses on the recently adapted technique of agarose multigel electrophoresis (AME) for analysis of the higher-order nucleoprotein structure of specific genomic loci that have been isolated as native chromatin in unfractionated low-salt nuclear extracts. It also describes how AME can be used as a biophysical method for characterizing specific in vivo –assembled chromatin fragments. The general concepts presented in this chapter are based on the recent studies of genomic murine mammary tumor virus (MMTV) promoters. This approach yields analytical measurements of average macromolecular radii and surface charge density that in turn allows one to evaluate the condensation behavior and conformational flexibility of the chromatin fragment being studied. AME is an easily accessible method that is performed with the commercially available electrophoresis apparatus. In an AME experiment, the sample of interest is first spiked with the spherical bacteriophage T3. The only aspect of the AME approach that is not general is obtaining the specific genomic chromatin fragment of interest in a low-salt nuclear extract. As with any newly introduced technical approach, the ability to accurately interpret AME data have capability to increase in direct proportion to the number of systems that are characterized by this method in the future.