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DNA fragments have to be cut precisely and then joined with the other fragment by using a ligase.

To begin with, the DNA fragments to be joined should be cut with the same restriction enzyme or should have compatibility to join. Restriction enzymes make cuts at specific recognition sites. Hence restriction digestion with same enzyme for two different DNA fragments yields identical ends.

Two DNA fragments with protruding ends complementary to each other are joined using a Ligase and blunt ended DNA fragments are joined by means of adding additional complementary sequences at their ends with the help of linkers, adapters or by using a terminal transferase for Homopolymer Tailing.

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