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Why should small cut adapter fragments be removed after restriction digest?

Answer and explanation

Correct answer: They can give unwanted competition in ligation reaction

After a restriction digest, small adapter fragments may still be present in the reaction mixture. If they have ends compatible with the target DNA, they can participate in the ligation reaction. This creates unwanted products or uses up ligase, vector ends, or insert ends that should instead join the intended fragments. Their presence can therefore lower the quality and efficiency of the desired construct.

A cleanup or purification step removes these short fragments before ligation. This makes the reaction more selective and reduces background products, although the exact cleanup method depends on fragment sizes and the experimental design. Option A is correct because the fragments can create unwanted competition. They are not DNA ladders, enzyme storage material, or substances that always improve the DNA.

Related tags

Adapter FragmentsCleanupLigation Competition

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