Characterization of universal small-subunit rRNA hybridization probes for quantitative molecular microbial ecology studies

Article Abstract:

The universal oligonucleotide hybridization probe S-*-Univ-1390-a-A-18 accurately estimates domain-level community composition of microbes in environmental samples, under low-stringency wash conditions. However, the probe overestimates methanogen rRNA concentrations under high-stringency wash conditions. The universal probe S-*-Univ-1392-a-A-15 gives overestimated results with both high- and low-stringency wash conditions. Defined mixtures of rRNAs from pure cultures and anaerobic digester samples are used for the comparison of the two probes.

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The Oligonucleotide Probe Database

Article Abstract:

The Oligonucleotide Probe Database (OPD) is a data library designed to provide information on probes and primers used in microbial ecology and environmental microbiology. This information include design and characterization data, the standardized probe name, target group, probe sequence and the old probe name or reference. OPD can be accessed via the World Wide Web at http://www.cme.msu.edu/OPD.

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The presence of humic substances and DNA in RNA extracts affects hybridization results

Article Abstract:

Results demonstrate that the contaminating humic substances and extraneous DNA, in the RNA extracts from environmental samples, interfere in the rRNA-targeted oligonucleotide probe hybridization assays. Data suggest that the contaminants either saturate the membrane surface or reduce rRNA target accessibility.

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