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End-repair

Fragmented DNA (either artificially fragmented or partially degraded) typically have sticky ends, implying that 1 of the strand is longer than the other strand (see Figure 1).

There are two strands of DNA each showing an example of a DNA end type. The first showing blunt ends, and the second showing sticky ends. The first strand of DNA has the sequence T, C, C, T on the top backbone, and the sequence A, G, G, A on the bottom backbone. In the example of the blunt end, the DNA is cut vertically to form two pieces. Each piece has a T A base pair and a C G base pair. The second strand of DNA has the sequence G, A, A, T, T, C on the top backbone, and the sequence C, T, T, A, A, G. In the example of the sticky end, the cut starts between G and A on the top backbone, cuts down vertically, then cuts horizontally between the four A T and T A base pairs, and then cuts down vertically to end between the A and G on the bottom backbone. This creates two pieces. One piece of the top backbone, A, A, T, T, and the end C G base pair. The other piece of the start G C base pair and the bottom backbone, T, T, A, A.

Figure 1. Blunt ends DNA with both of the strands having the same length vs. sticky ends DNA with one strand being longer than the other strand.

DNA with sticky ends will ligate easily to other DNA that has complementary sticky ends. To prevent DNA with these sticky ends from pairing with another DNA, we need to modify them into blunt-ended DNA(see Figure 1). One of the steps in the NGS sample preparation is to repair these sticky ends and create DNA with blunt ends. This is important for the next step, the A-overhang.

See also: End-repair enzymes

Referred from:

Article
Next Generation Sequencing
Article
Adapter ligation
Article
A-tailing
Article
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