PCR-RFLP

Definition

A molecular diagnostic method combining polymerase chain reaction (PCR) amplification of a target DNA region with restriction fragment length polymorphism (RFLP) analysis, in which amplified products are digested with restriction enzymes to produce fragment patterns diagnostic of species, populations, or genotypes. The technique exploits sequence variation at restriction sites to generate discriminating banding profiles without requiring sequencing.

Etymology

Example

In medical entomology, PCR-RFLP of the mitochondrial cytochrome oxidase I gene is routinely used to distinguish cryptic species within the Anopheles gambiae complex, enabling accurate identification of malaria vectors that are morphologically identical but differ in vector competence and geographic distribution.

Synonyms

• PCR–restriction fragment length polymorphism
• amplified fragment length polymorphism (AFLP, related but distinct technique)

Related Terms

• DNA barcoding
• qPCR
• Species complex
• cryptic species
• mitochondrial DNA
• restriction enzyme
• genotyping
• molecular taxonomy
• Sanger sequencing

Usage Notes

Distinguish from AFLP (amplified fragment length polymorphism), which uses selective PCR primers rather than restriction digestion of a specific amplicon. PCR-RFLP is lower resolution than full sequencing but faster and cheaper, making it practical for high-throughput species screening in field studies. Results depend on enzyme choice and primer specificity; incomplete digestion or intraspecific variation at restriction sites can produce ambiguous profiles. The method has been largely superseded by direct sequencing in research contexts but remains valuable for resource-limited surveillance programs and rapid vector identification.