I have 4 pcr products which were purified using Qiaspin pcr purification. I sequenced the product with a set of primers, results are good. Then I use topo cloning kit to clone these 4 pcr products, the colonies looks good. Then I did RCA(rolling circle amplification), and did sequence with the same set of primers. But for most colonies only vector primers(M13f and r) have good result and few designed primers have good sequence result. What could be the problem? thanks for reply.
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