Concatemer chain reaction: A taq DNA polymerase-mediated mechanism for generating long tandemly repetitive DNA sequences

Abstract

The concatemer chain reaction (CCR) uses Taq DNA polymerase to synthesize double- or single-stranded DNA concatemers whose length and yield can be controlled by varying the number of thermal cycling steps. Although the reactions which occur in CCR are slower and more complex than in polymerase chain reaction (PCR), the practical application of the CCR technique is simple. The CCR technique is less expensive, faster, and easier than conventional methods for producing concatemers and gives greatly improved yields. The templates used in CCR may be: (i) double-stranded concatemer templates produced by ligation, (ii) double-stranded concatemers from previous CCRs, or (iii) single-stranded oligonucleotides consisting of one copy of the sense strand repeat and a complementary but overlapping repeat for the antisense strand. Different molar ratios and lengths (masses) of the two strands of the helix may be obtained. We have used both single-stranded and double-stranded concatemers as targets for RNA hybridization. Applications of this concatemer technology are discussed, including the use of concatemers as hybridization probes or targets in applications such as run-on transcription or analysis of repetitive DNA sequences.