End repair

Fragmented DNA (either artificially fragmented or partially degraded) typically have sticky ends, implying that one strand is longer than the other strand (see Figure 1). DNA with sticky ends will ligate easily to other DNA with complementary sticky ends. To prevent DNA with these sticky ends from pairing with other DNA, we need to create blunt ends (see Figure 1).

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

End-repair enzymes

Two enzymes are typically used for repairing DNA with sticky ends (see Figure 2).

• Polymerase: Polymerase fills in the missing bases for the strand from the 5' to the 3' direction. The resulting double stranded DNA will be the same length as the original longest DNA strand.
• Exonuclease: Exonuclease removes the 3' overhangs. The resulting double stranded DNA will be the same length as the original shortest DNA strand.

Figure 2. The Polymerase adding nucleotides in the 5' → 3' direction, and the exonuclease removing nucleotides at the 3' overhangs.

End repair is used in NGS sample preparation, and it is essential to have blunt ends for the following Adenylation step.