DNAfragmenter

DNAfragmenter is a term used to describe a device, kit, or protocol designed to cleave long DNA molecules into shorter fragments. Fragmentation is a common preparatory step in molecular biology and genomics, facilitating downstream analyses such as sequencing, cloning, and library construction. DNAfragmenters can be automated instruments, benchtop kits, or stepwise protocols used in research, clinical, and forensic laboratories.

Fragmentation can be achieved by enzymatic or physical means. Enzymatic approaches use restriction endonucleases or non-specific nucleases (such as DNase I) to generate fragments with defined or broad size distributions. Physical approaches rely on mechanical forces to shear DNA, including sonication, nebulization, hydrodynamic shearing, and microfluidic methods. A third approach employs transposases, such as tagmentation, which simultaneously cuts and tags DNA and is widely used to prepare sequencing libraries.

Applications primarily involve preparation of DNA libraries for next-generation sequencing (NGS). Fragment size is selected to match platform requirements, commonly in the range of a few hundred base pairs. Size selection and quality control are critical steps to ensure even representation and efficient sequencing. Fragmentation is also used in mapping, structural studies, and cloning workflows where controlled fragment lengths are needed.

Key considerations include fragment size distribution, starting DNA quality and quantity, throughput, and cost. Fragmentation bias may arise from enzymatic preferences or from physical shear profiles. Over- or under-fragmentation can reduce library complexity or sequencing yield. Proper controls, QC, and validation are standard parts of workflows involving DNAfragmenters.

See also: DNA sequencing library preparation, restriction enzyme, DNase I, sonication, transposase, tagmentation.