Amplification of human genomic DNA sequences with polymerase chain reaction using a single oligonucleotide primer

We present two examples of exponential nucleic acid amplification with the polymerase chain reaction (PCR) in the presence of only one amplification p rimer. Cloning and sequencing of the PCR products generated by amplificatio n of human genomic DNA revealed that the amplified sequence contained only one primer and its complement, at the two ends of the PCR product. Although these experiments were performed with primers derived from the sequence of the prostate specific antigen (PSA) gene and the normal epithelial cell-sp ecific 1 gene (NES1), the amplified sequences were novel and had no homolog y with either PSA or NES1 DNA. While both PSA and NES1 genes reside on chro mosome 19q13.3-q13.4, the amplified sequences were found by mapping to resi de on chromosome 5q12 and 5p15.1-p15.3, respectively. When we examined the mechanism of amplification by PCR using one primer in these two cases, we f ound that there was a high homology between the PSA primer or the NES1 prim er and the two regions flanking the amplified sequence of chromosome 5q12 o r 5p15. This indicated that the single PSA or NES1 primer could anneal on b oth strands of the DNA of that region, and mediate the exponential amplific ation. Since this phenomenon occurred to us twice with a limited number of different PCR reactions performed in our laboratory (< 20), we believe that it may represent a common artifact of PCR. Moreover, it appears that the p alindromic primer binding sites can anneal to each other forming DNA crucif orms. J. Clin. Lab. Anal. 13:69-74, 1999. (C) 1999 Wiley-Liss, Inc.