Atomic Force Microscope Measurements of Nucleosome Cores Assembled along Defined DNA Sequences

We have found that the atomic force microscope (AFM) can be used to image the “beads-on-a-string” chromatin structure in a normal air environment following adsorption onto a cover glass substrate. Individual nucleosome cores and linker DNA could be resolved clearly along chromatin fibers that were reconstituted using histone octamers and a tandemly repeated 208-bp nucleosome positioning DNA sequence (208–18). AFM measurements showed that the compaction of the 3780-bp DNA by different loadings of histone octamers was consistent with 146 bp of DNA wrapped 1.75 turns about the histone octamer to form the 11-nm nucleosome core. Precise internucleosome core spacing measurements could be performed along the chromatin fiber axis. In other experiments, AFM images of chromatin reconstituted using closed circular DNA showed highly tangled beaded fibers, as expected. These images and measurements demonstrate that AFM can provide useful high-resolution structural information about chromatin that can be used to complement other more established techniques such as electron microscopy.