PCR amplification introduces errors into mononucleotide and dinucleotide repeat sequences

The polymerase chain reaction (PCR) is used universally for accurate expone ntial amplification of DNA. We describe a high error rate at mononucleotide and dinucleotide repeat sequence motifs. Subcloning of PCR products allowe d sequence analysis of individual DNA molecules from the product pool and r evealed that: (1) monothymidine repeats longer than 11 bp are amplified wit h decreasing accuracy, (2) repeats generally contract during PCR because of the loss of repeat units, (3) Taq and proofreading polymerase Pfu generate similar errors at mononucleotide and dinucleotide repeats, and (4) unlike the parent PCR product pool, individual clones containing a single repeat l ength produce no "shadow bands". These data demonstrate that routine PCR am plification alters mononucleotide and dinucleotide repeat lengths. Such seq uences are common components of genetic markers, disease genes, and introni c splicing motifs, and the amplification errors described here can be mista ken for polymorphisms or mutations.