An End-Trimming Method and Its Application to Amplify Adjacent cDNA and Genomic DNA Fragments by PCR

An end-trimming method was developed to amplify adjacent cDNA fragments by PCR (1 ,2 ). In an attempt to clone a novel cDNA, the 5′ and/or 3′ end are often missing. A well-known PCR technique for cloning the missing sequence is a method of rapid amplification of cDNA ends (RACE) (3 ). Although the missing 5′ and 3′ ends of cDNA are amplified using a sequence-matched primer and a dT-primer as in RACE, multiple bands usually appear. This makes it difficult to select the band that contains the desired sequence. We devised an end-trimming method to clone adjacent DNA fragments, which specifically extended from a sequence-matched primer, in the fixed direction in a plasmid vector.