HYBRIDIZATION PROBES FOR CONVENTIONAL DNA-FINGERPRINTING USED AS SINGLE PRIMERS IN THE POLYMERASE CHAIN-REACTION TO DISTINGUISH STRAINS OF CRYPTOCOCCUS-NEOFORMANS

In conventional DNA fingerprinting, hypervariable and repetitive seque nces (minisatellite or microsatellite DNA) are detected with hybridiza tion probes. As demonstrated here, these probes can be used as single primers in the polymerase chain reaction (PCR) to generate individual fingerprints. Several conventional DNA fingerprinting probes were used to prime the PCR, yielding distinctive, hypervariable multifragment p rofiles for different strains of Cryptococcus neoformans. PCR fingerpr inting with the oligonucleotide primers (GTG)5, (GACA)4, and the phage M13 core sequence (GAGGGTGGXGGXTCT), but not with (CA), or (CT)8, gen erated DNA polymorphisms with all 42 strains of C. neoformans investig ated. PCR fingerprints produced by priming with (GTG)5, (GACA)4, or th e M13 core sequence differentiated the two varieties of C. neoformans, C neoformans var. neoformans (serotypes A and D) and C neoformans var . gattii (serotypes B and C). Furthermore, strains of serotypes A, D, and B or C could be distinguished from each other by specific PCR fing erprint patterns. These primers, which also successfully amplified hyp ervariable DNA segments from other species, provide a convenient metho d of identification at the species or individual level. Amplification of polymorphic DNA patterns by PCR with these primers offers several a dvantages over classical DNA fingerprinting techniques, appears to be more reliable than other PCR-based methods for detecting polymorphic D NA, such as analysis of random-amplified polymorphic DNA, and should b e applicable to many other organisms.