Dependence of polymerase chain reaction product inactivation protocols on amplicon length and sequence composition

Abstract

Specific diagnostic test results generated by polymerase chain reaction (PCR) depend upon control of amplicon contamination in the clinical laboratory. We compared photochemical (isopsoralen [IP]) and enzymatic (uracil N-glycosylase [UNG]) methods for their ability to prevent carryover of amplicons generated from genomic targets of five viruses. PCR products (amplicons) (herpes simplex virus, 342 bp; cytomegalovirus, 250 bp; Epstein- Barr virus, 240 bp) exposed to UV light in the presence of various concentrations of IP compound 10 (IP-10) resulted in apparent increased molecular sizes of the products, as indicated by migration patterns after gel electrophoresis, and were predictive of inactivation by the agent. For amplicons of ≤100 bp, IP-10-induced electrophoretic shifts were related to the guanidine-cytidine (G+C) content of the PCR product; no apparent shift and no inactivation were observed for a 92-bp herpes simplex virus amplicon (G+C content, 65%), whereas the 100-bp human papillomavirus product (G+C content, 42%) showed a concentration-dependent shift (25 to 100 μg/ml) in electrophoretic migration and was partially inactivated. UNG effectively controlled amplicon carryover for target DNA of ≥240 bp; however, this treatment did not inactivate the two amplicons of ≤100 bp, regardless of the G+C content of the product. Larger products were inactivated efficiently by both methods, regardless of their G+C contents. We concluded that both IP and UNG effectively inactivate PCR amplicons but not short amplicons of ≤100 bp. We recommend that with the adoption of PCR technology in clinical laboratories, primers should be designed to produce amplicons of at least 240 to 350 bp (depending on G+C content) and that at least one effective method of controlling carryover contamination should be incorporated into each PCR protocol.