Modification of the termini of double-stranded DNA is often necessary to prepare the molecule for cloning. DNA ligases require a 5' monophosphate for adenylation of the donor end, while the acceptor end requires a 3' hydroxyl group. Additionally, the sequences to be joined need to be compatible: either a blunt end being joined to another blunt end, or a cohesive end with a complementary overhang to another cohesive end. End modifications are performed to improve the efficiency of the cloning process, ensure the ends to be joined are compatible, and to optimize the positioning of regulatory and translated sequences.
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