PMID: 2413450Oct 1, 1985

Rapid determination of 16S ribosomal RNA sequences for phylogenetic analyses

Proceedings of the National Academy of Sciences of the United States of America
D J LaneN R Pace

Abstract

Although the applicability of small subunit ribosomal RNA (16S rRNA) sequences for bacterial classification is now well accepted, the general use of these molecules has been hindered by the technical difficulty of obtaining their sequences. A protocol is described for rapidly generating large blocks of 16S rRNA sequence data without isolation of the 16S rRNA or cloning of its gene. The 16S rRNA in bulk cellular RNA preparations is selectively targeted for dideoxynucleotide-terminated sequencing by using reverse transcriptase and synthetic oligodeoxynucleotide primers complementary to universally conserved 16S rRNA sequences. Three particularly useful priming sites, which provide access to the three major 16S rRNA structural domains, routinely yield 800-1000 nucleotides of 16S rRNA sequence. The method is evaluated with respect to accuracy, sensitivity to modified nucleotides in the template RNA, and phylogenetic usefulness, by examination of several 16S rRNAs whose gene sequences are known. The relative simplicity of this approach should facilitate a rapid expansion of the 16S rRNA sequence collection available for phylogenetic analyses.

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Related Concepts

Study, Methodological
Ribosomal RNA
Phylogeny
Avian myeloblastosis virus
Sequencing
Ribosomes
Nucleotides
Genetic Template
15S RNA
Ribosomal RNA Location

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