The Chemistry of PCR Primers: Concept and Application

DNA is a typical organic compound with marked differences from other chemicals and biopolymers because DNA can be amplified by the enzyme polymerase. DNA can be, in principle, amplified from a single copy by the polymerase chain reaction (PCR). In this review, we focus our attention on the chemistry of PCR primers. Because PCR is basic technology in biology research fields, we sometimes use chemically labeled primers without any awareness of the chemistry they leave behind. We would like to emphasize that chemically labeled primers contain a lot of potential for different chemistry ideas and much study is still necessary to advance PCR for single-nucleotide polymorphism (SNP) typing, genetic diagnosis, and other fields. Two categories of primers, affinity-capture primers and signaling primers, are discussed from the viewpoints of their chemical concepts and applications. Affinity-capture primers are used for purification, isolation, and manipulation of PCR products by high specificity and affinity to the cognate molecules by moleculemolecule interactions, whereas signaling primers report the hybridization and/or progress of PCR amplification by a signal change, in most cases by a fluorescence change. The content of this review may be useful for a better understanding of the chemistry of PCR primers and, more importantly, for the invention of novel PCR chemistry.