What Fragmentation Method Can I Use for Library Prep?

Chemical Fragmentation

Suitable for fragmentation of RNA. Typically, heat is applied to RNA in the presence of a divalent metal cation (for example, magnesium or zinc). The length of the resulting fragments can be adjusted by modifying the incubation time.

Enzymatic Fragmentation

A cost-effective alternative to mechanical shearing methods. Depending on the approach, you may expect some amount of sequencing bias, as many enzymatic methods are influenced by sequence context.

Mechanical Fragmentation

Methods include sonication, acoustic shearing, needle shearing, nebulization, and others. Acoustic shearing generally has the tightest size distribution and introduces the least amount of bias compared to other methods. However, some investment in capital equipment is required. Mechanical methods can introduce DNA damage, and you might consider repair methods as part of your library construction process.