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問題	可能的原因
質粒 DNA 產量低	細菌培養不新鮮。	培養物應在達到所需細胞密度後及時處理。
	质粒的拷贝数低。	处理更大体积的培养物或在更丰富的培养基中生长。Alternatively, clone DNA sequence of interest into a plasmid possessing a higher copy number, for example, pCORON1000 (~300–500 copies per cell).
	The purification system was overloaded.	在處理前測量培養物的 A₆₀₀，以確保純化柱中的細菌碎片沒有超載（例如、使用 illustra™ plasmidPrep Mini Spin 系統時。
	細胞未充分重悬。
	細胞重懸可藉由渦旋、向上/向下移液，或沿著空移液器吸頭盒的蓋子移動含有細菌細胞的微離心管來實現。
	細胞未充分裂解。	加入鹼性裂解液時，輕輕地但完全地混和、	使用矽基純化格式時，使用高鹽分緩衝液對質粒純化柱進行額外的清洗（在結合質粒 DNA 之後）。這個額外的步驟可以去除殘留的核酸酶和過多的碳水化合物，從而提高質粒 DNA 的產量和品質。或者，使用 EndA^-菌株，如 TOP10 或 DH5α。
質粒 DNA 在瓊脂質凝膠上看起來像一塊塗片	EndA⁺菌株（例如：HB101）擁有核酸酶、	使用矽基純化格式時，使用高鹽分緩衝液對質粒純化柱進行額外的清洗（在結合質粒 DNA 之後）。這個額外的步驟可以去除殘留的核酸酶活性，從而提高質粒 DNA 的產量和品質。或者，使用 EndA^-菌株，如 TOP10 或 DH5α。
质粒 DNA 被基因组 DNA 污染	碱性裂解：加入裂解緩衝液後，樣品混合過於激烈。	加入任一溶液後，倒置樣品10-15次，輕輕地混合。劇烈混和可能會造成基因組 DNA 的剪切，從而促進其與質粒 DNA 的共純化。
質粒 DNA 被 RNA 污染	樣本未經 RNase 處理。	RNase（100 μg/mL）包含在 illustra™ plasmidPrep Mini Spin Kit 的裂解緩衝液中。
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