Visualizing DNA Disassociation from the Nucleosome Core Particle

Abstract

The organization of DNA in nucleosome core particles (NCP) is understood to play crucial regulatory roles in transcription, replication, recombination and repair. High resolution crystal structures deliver detailed snapshots of the NCP in its most stable conformations and reveal thousands of electrostatic interactions that mediate the stability of NCPs. However, many of the techniques that have been applied thus far are ill-suited for directly monitoring the intermediary and dissociated conformations of the NCP. To this end, we applied small angle X-ray scattering (SAXS) - a powerful technique for delivering low resolution structural details of biological molecules. Since SAXS studies of protein-nucleic acid complexes are complicated by the differences in scattering lengths between proteins and nucleic acids, we applied a contrast variation approach where we matched the solvent and protein contrasts to effectively probe the DNA component of the NCP alone. We systematically modulated the electrostatic interactions by adjusting the salt concentration of the solvent and visualized the conformational transition of the DNA from a bound to unbound state during NCP disassembly.