Selective labeling and detection of specific RNAs in an RNA mixture

Quantitative detection of previously characterized syntrophic bacteria in anaerobic wastewater treatment systems by sequence-specific rRNA cleavage method

Quantitative monitoring method of two important trophic groups of bacteria in methanogenic communities was established and applied to six different anaerobic processes. The method we employed was based upon our previous sequence-specific rRNA cleavage method that allows quantification of rRNA of target groups so that the populations reflecting in situ activity could be determined. We constructed a set of scissor probes targeting the Chloroflexi group known as 'semi-syntrophic' heterotrophic bacteria and fatty acid-oxidizing syntrophs to determine their relative abundance in the processes. By using the method, we found that several reactors harbored a large amount of organisms belonging to the phylum Chloroflexi accounting for up to 20% of the total prokaryotic populations. Propionate-oxidizing syntrophs, Syntrophobacter, Smithella and Pelotomaculum were also found to be significant comprising up to 3.9% of the total populations, but their distribution is highly dependent on the process examined. This is the first clear, non-PCR based quantitative evidence that those organisms play active roles under in situ methanogenic conditions.

RNA labeling, conjugation and ligation

Advances in RNA nanotechnology will depend on the ability to manipulate, probe the structure and engineer the function of RNA with high precision. This article reviews current abilities to incorporate site-specific labels or to conjugate other useful molecules to RNA either directly or indirectly through post-synthetic labeling methodologies that have enabled a broader understanding of RNA structure and function. Readily applicable modifications to RNA can range from isotopic labels and fluorescent or other molecular probes to protein, lipid, glycoside or nucleic acid conjugates that can be introduced using combinations of synthetic chemistry, enzymatic incorporation and various conjugation chemistries. These labels, conjugations and ligations to RNA are quintessential for further investigation and applications of RNA as they enable the visualization, structural elucidation, localization, and biodistribution of modified RNA.

Selective labeling and detection of specific mRNA in a total-RNA sample

We report a unique approach to selectively label and detect specific RNA using its internal sequence, without separation, reverse transcription, and/or polymerase chain reaction. This approach is especially useful for individual mRNA labeling and detection. To expose mRNA internal sequence for selective labeling and detection, RNase H digestion is used to remove the 3(')-common sequences. We have designed a DNA-2(')-O-Me-RNA hybrid as the template for both RNase H digestion and Klenow extension and have found buffer conditions for both enzymes. Sharing the same template and buffer by these two enzymes largely simplifies experimental procedures. Using this approach, lacZ mRNA was selectively labeled and detected in the presence of thousands of mRNAs. We have successfully demonstrated for the first time the direct labeling and detection of an individual mRNA in a total-RNA sample. The detection sensitivity can reach up to attomole level (5 x 10(-18)mole). This method has great potential in RNA decay and metabolic regulation studies via individual mRNA labeling and in methodology of mRNA direct detection on microchip and direct gene expression profiling, without reverse transcription and polymerase chain reactions.