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because you need the phosphate of the foreign DNA fragment for ligation. If not inactivated before you add the fragment, SAP will imediately remove the phosphate form your fregment too leaving you with two dephosphorylated fragments that are not easy to ligate..

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Q: Why is it important to inactivate the shrimp alkaline phosphatase before ligating your EcoRI cut pBluescript plasmid to a foreign DNA fragment?
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