Bacterial community fingerprinting of amplified 16S and 16–23S ribosomal DNA gene sequences and restriction endonuclease analysis(ARDRA)
The 16S and 23S rRNA genes have been utilized for phylogenetic analysis of both prokaryotic and eukaryotic organisms (see Section 3). In addition to direct comparison of the nucleic acid sequences , numerous groups have used the rapid method of polymerase chain reaction (PCR) amplification of this gene  as well as the complete rRNA locus [3, 4, 8] for a simple method for identification of bacterial genera and species. In these latter procedures, the amplified ribosomal gene (rONA) is subjected to restriction endonuclease digestion; this has been termed ARDRA (Amplified Ribosomal DNA Restriction Analysis ). The resulting restriction fragment pattern is then used as a fingerprint for the identification of bacterial genomes. This method is based on the principle that the restriction sites on the RNA operon are conserved according to phylogenetic patterns.
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