DNA fragmentation is typically done either mechanically using sonication, or enzymatically through digestion with micrococcal nuclease (MNase).
Sonication is the conventional method for fragment chromatin, utilizing either a standard probe sonicator or more complex water-bath sonicators for precise sonication. While sonication yields randomized chromatin fragments, optimization is necessary for different cell lines and tissues and reproducibility between experiments can be challenging.
MNase is a nuclease enzyme that digests the linker DNA between nucleosomes, resulting in the release of mononucleosomes and shorter DNA fragments. Digesting with micrococcal nuclease enzymatically is highly consistent and suitable for handling multiple samples. However, variations may arise from alterations in enzyme activity and its tendency to target inter-nucleosome regions.
The goal of fragmentation is to produce chromatin fragments sized between 200 to over 1000 base pairs. However, controlling DNA shearing is often difficult.
An alternative method is through chemical agents, like DNAse I. DNase I specifically cleaves phosphodiester bonds within the DNA backbone, resulting in DNA fragmentation.
Another alternative is hydrodynamic shearing. This method involves applying high pressure to force DNA through a narrow space, resulting in shearing of the DNA into smaller fragments. Hydrodynamic shearing is commonly used for large-scale DNA fragmentation.