The ligase chain reaction (LCR) is a method of DNA amplification. The ligase chain reaction (LCR) is an amplification process that differs from PCR in that it involves a thermostable ligase to join two probes or other molecules together which can then be amplified by standard polymerase chain reaction (PCR) cycling (Barany, 1991). Each cycle results in a doubling of the target nucleic acid molecule. A key advantage of LCR is greater specificity as compared to PCR.^[1] Thus, LCR requires two completely different enzymes to operate properly: ligase, to join probe molecules together, and a thermostable polymerase (e.g., Taq polymerase) to amplify those molecules involved in successful ligation. The probes involved in the ligation are designed such that the 5′ end of one probe is directly adjacent to the 3′ end of the other probe, thereby providing the requisite 3′-OH and 5′-PO4 group substrates for the ligase.

LCR was originally developed to detect point mutations; a single base mismatch at the junction of the two probe molecules is all that is needed to prevent ligation. By performing the ligation right at the Tm of the oligonucleotide probe, only perfectly matched primer:template duplexes will be tolerated. LCR can also be used to amplify template molecules that have been successfully ligated for the purpose of assessing ligation efficiency and producing a large amount of product with even greater specificity than PCR. Thus, LCR is not necessarily an alternative, but rather a complement, to PCR.