Fragmentation

One of the limitations of the Next Generation Sequencing is the length of the DNA sample. Current Illumina technology can sequence up to 250 bp. Our genome is a lot longer than that, for example, the longest chromosome, which is chromosome 1 is almost 250 million bp. Therfore, in the sample preparation of NGS, the DNA needs to be fragmented or cut into a smaller size. This step is typically referred to as the fragmentation step.

Shorter DNA samples, for example, ancient DNA sample do not need to be fragmented because they are already partially degraded into approximately 50 bp. Another example is cDNA generated from miRNA (micro RNA), which is also very short.

There are two ways to fragment the DNA

Sonication:

In sonication, the DNA is fragmented by exposing it to sound waves (usually ultrasound). When a powerful sound wave hits the DNA strand it will create double strand breaks cutting the long DNA strand into smaller DNA strands. To get a specific DNA size, the power and the time need to be adjusted.

Enzymatic:

Long DNA strands can also be fragmented using enzymatic reactions. There are several different enzymes that are capable of cutting DNA strands; they can target specific sequences or randomly cut the DNA.