Fingerprinting sequence variation in ribosomal DNA of parasites by DGGE

Although there is a tendency for rDNA genes within a species to maintain sequence homogeneity, there can be significant levels of variation among rDNA repeat sequences within populations or individuals of a species as a consequence of mutation mechanisms. To date, there have been no practical techniques available in molecular parasitology that allow the extent of sequence variation among the repeats (i.e., number of sequence types) to be displayed visually. In this report, we describe the use of the denaturing gradient gel electrophoresis (DGGE) technique for the rapid screening of parasite rDNA for sequence variation without the need for exhaustive cloning or DNA sequencing. The resolution of this variation by DGGE provides a diagnostic fingerprint for a species.