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FIGURE 13.6. Process of ligase chain reaction (LCR). In LCR, two pairs of oligonucleotide
probes that are complementary to the entire target sequence hybridize to the denatured
DNA strands, such that the 3 ′ end of the first probe is immediately adjacent to the 5 ′ end
of the second probe. A thermostable DNA ligase covalently links the two probes together,
provided that the nucleotides at the junction are perfectly base-paired to the target strand.
The newly ligated probes can then serve as templates for subsequent cycles, leading to
exponential amplification of the DNA target.
amenable to automation (Landegren et al., 1988). One of the advantages of LCR is
that ligation cannot occur unless both probes perfectly hybridize to the target and
no gap between the 5 ′ end of one probe and 3 ′ end of the other probe. Therefore, it
offers better allele specificity for genotyping point mutations and single nucleotide
polymorphisms (SNPs) (Tong et al., 1999).
LCR has been employed for the detection of many microorganisms, such as HIV
(de Mendoza et al., 2002), HBV (Osiowy, 2002), Mycobacterium tuberculosis
(Lumb et al., 1999; Rajo et al., 2002), Chlamydia trachomatis, and Neisseria
gonorrhoeae, in clinical specimens. The LCR assay kits (LCx) for C. trachomatis
and N. gonorrhoeae is marketed by Abbott Laboratories (Abbott Park, IL, USA).
The lower detection limit of the assay for C. trachomatis was revealed to be 32
EB/mL of urine (Blocker et al., 2002). The sensitivity conferred by LCR assay
for C. trachomatis in first-void urine sample is found to be 10–15% higher than
that of urethral or endocervical culture and 15–35% higher compared with nonculture
assays done on urethral or cervical secretions. The overall specificity of
LCR assay is typically over 99% (Lee et al., 1995; Schachter et al., 1995; Ridgway