Development of the Non‐Palindromic Adaptor Polymerase Chain Reaction (NPA‐PCR) for the Amplification of Alpha‐and Beta‐Chain T‐Cell Receptor cDNAs

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Abstract
We have developed a highly efficient new method for the amplification of alpha- and beta-chain human T-cell receptor (TCR) cDNAs. This method is designated non-palindromic adaptor polymerase chain reaction (NPA-PCR). cDNA was synthesized from total RNA isolated from mononuclear leucocytes, using either an oligo (dT)15-NotI or a C alpha-NotI or a C beta-NotI primer and RNase H-negative reverse transcriptase. The double-stranded cDNA was ligated with the non-palindromic adaptors EcoRI-XmnI [d(ATTCGAACCCCTTCG)] and XmnI G strand [d(pCGAAGGGGTTCG)] (phosphorylated), which resulted in the addition of the EcoRI-XmnI site in both 5' and 3' ends. These two non-palindromic adaptors, EcoRI-XmnI and XmnI G strand, are complementary to each other and both are required for ligation. The EcoRI-XmnI adaptor was removed from the 3' end by treatment with NotI restriction nuclease, whereas it was retained at the 5' end. The non-palindromic adaptor EcoRI-XmnI was used as the 5' amplification primer. C alpha or C beta constant region primers were used as 3' amplification primers. The amplified cDNAs were cloned and the plasmids were used to transform DH5 alpha competent cells. Over 1000 white colonies per 0.1-0.25 micrograms of total RNA or per 10,000 to 50,000 human peripheral blood mononuclear cells were obtained after amplification of either the alpha- or the beta-chain TCR cDNAs. Between 40 and 62% of the colonies (range from five donors) were positive after screening with either a C alpha or a C beta probe, located 5' to the C alpha and C beta amplification primers. A total of 50 amplified alpha- or beta-chain cDNA positive clones from two normal donors were randomly chosen and sequenced, and the sequences obtained were typical of alpha beta TCR. Two new J alpha gene segments were identified. Approximately 30% of the alpha-chain positive clones have 5' untranslated region, and most of the remaining alpha- or beta-chain TCR clones started from the initiation codon or near the 5' end. NPA-PCR has several advantages over existing PCR methods for the amplification of cDNAs with unknown or variable 5' end, such as the T-cell antigen receptors and the immunoglobulins. Among these advantages is that only one 5' end extension primer is required. Because of the large number of TCR V alpha and V beta families, a large number of different 5' end primers are required for amplification of alpha beta TCR cDNAs by conventional PCR.