The ligase chain reaction (LCR) is an amplification process that differs from polymerase chain reaction (PCR) in that it involves a thermostable ligase to join two probes or other molecules together which can then be amplified by standard PCR cycling.
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.
[1] LCR and PCR may be used to detect gonorrhea and chlamydia, and may be performed on first-catch urine samples, providing easy collection and a large yield of organisms.
Endogenous inhibitors limit the sensitivity, but if this effect could be eliminated, LCR and PCR would have clinical advantages over any other methods of diagnosing gonorrhea and chlamydia.