Ribosomal RNA Probes for Detection and Identification of Species

Nucleic acid hybridization probes have a wide range of applica tions for the detection, identification, and quantification of microor ganisms, from environmental studies to medical diagnoses (1 ,2 ). They offer unique advantages in terms of sensitivity and specificity, with their potential to recognize the organism of interest in a background of biological material of different origin (3 ). In addition, the technol ogy is particularly well-suited for the development of fast and simple assays carried out on a routine basis on large numbers of biological samples. A first class of DNA probes for the identification of species correspond to cloned DNA fragments highly specific to particular organisms, such as genes involved in toxin production (4 ), or some repetitive DNA families. An alternative, more general approach is to choose a gene represented in a large spectrum of organisms but exhib iting sequence variation among closely related species or groups of species. In this respect, rRNA genes represent a particularly attrac tive system. Although frequently viewed as a paradigm of sequence conservation, rRNA molecules have in fact accumulated a very sub stantial degree of structural diversity during evolution (5 ,6 ). Riboso mal RNAs possess two other essential features for species identification: the multiplicity of their genes (7 ), and their outstand ing sequence homogeneity within a genome and a species (8 ) which allow for easy detection without the limitations inherent to extensive polymorphisms among multigene family members.