Why should DNA ends be close for ligation?

Correct answer: So ligase can form a bond between them

The direct answer is option A: DNA ends must be close so that ligase can form a bond between them. DNA ligase seals a break in the sugar-phosphate backbone by joining a nearby 3-prime hydroxyl end to a 5-prime phosphate end, when the ends are properly aligned and reaction conditions are suitable. Bringing compatible ends close first may involve complementary base pairing, especially with sticky ends. Option A is correct because physical proximity and correct alignment are needed for bond formation. Option B is wrong because ligation is not meant to burn DNA. Option C is wrong because protein digestion is unrelated to joining DNA ends. Option D is wrong because the gel is only a separation medium and does not disappear as a result of ligation. Compatible ends, active ligase, suitable buffer, and required energy all support the reaction, but distance or poor alignment can prevent it. Memory cue: ligase is a molecular sealant; the ends must meet before it can seal.