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.