Significance Many of the important functions in the cell are performed by high-molecular-weight complexes that contain both protein and nucleic acid components. Although developments in solution NMR spectroscopy have facilitated the study of the protein portions of these complexes, similar quantitative studies of the nucleic acids have proven challenging. Here we describe an approach for labeling DNA molecules with methyl-group probes at specific sites, followed by the use of optimized NMR methods to obtain high-quality data in studies of these large molecular complexes. Studies of both the DNA and protein components of the nucleosome core particle are presented, including an investigation of how CpG methylation, an important epigenetic mark, affects the structural dynamics of the particle.