Rapid determination of 16S ribosomal RNA sequences for phylogenetic analyses (reverse transcriptase/dideoxynucleotide)

Rapid determination of 16S ribosomal RNA sequences for phylogenetic analyses (reverse transcriptase/dideoxynucleotide)

Vol. 82, pp. 6955–6959, October 1985 | DAVID J. LANE*, BERNADETTE PACE*, GARY J. OLSEN*, DAVID A. STAHL†‡, MITCHELL L. SOGIN†, AND NORMAN R. PACE*§
The article describes a rapid method for generating large blocks of 16S ribosomal RNA (16S rRNA) sequence data without the need for isolation or cloning. The method uses reverse transcriptase and synthetic oligodeoxynucleotide primers complementary to universally conserved 16S rRNA sequences. Three particularly useful priming sites are identified, which provide access to the three major structural domains of 16S rRNA and routinely yield 800-1000 nucleotides of sequence data. The method is evaluated for accuracy, sensitivity to modified nucleotides, and phylogenetic usefulness. The simplicity of this approach is expected to facilitate the rapid expansion of the 16S rRNA sequence collection, making it a valuable tool for phylogenetic analyses. The article also discusses the limitations and inaccuracies of the method, such as band compressions and rearrangements caused by secondary structure interactions, and provides guidelines for aligning and interpreting the sequence data.The article describes a rapid method for generating large blocks of 16S ribosomal RNA (16S rRNA) sequence data without the need for isolation or cloning. The method uses reverse transcriptase and synthetic oligodeoxynucleotide primers complementary to universally conserved 16S rRNA sequences. Three particularly useful priming sites are identified, which provide access to the three major structural domains of 16S rRNA and routinely yield 800-1000 nucleotides of sequence data. The method is evaluated for accuracy, sensitivity to modified nucleotides, and phylogenetic usefulness. The simplicity of this approach is expected to facilitate the rapid expansion of the 16S rRNA sequence collection, making it a valuable tool for phylogenetic analyses. The article also discusses the limitations and inaccuracies of the method, such as band compressions and rearrangements caused by secondary structure interactions, and provides guidelines for aligning and interpreting the sequence data.
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