Practice question

Sticky ends are produced when restriction enzymes cut asymmetrically within recognition sites, leaving short single-stranded overhangs. Ligation efficiency depends on transient association of fragments before phosphodiester bond sealing by DNA ligase. Cohesive termini can anneal through Watson-Crick hydrogen bonding between complementary bases, forming a stable, pre-aligned substrate that greatly increases effective local concentration of 5' phosphate and 3' hydroxyl groups. Blunt ends lack this stabilization and rely on random collision. Complementary pairing therefore lowers activation energy, improves fidelity and accelerates recombinant formation in cloning.