A Chemical Screen for Biological Small Molecule-RNA Conjugates Reveals CoA-Linked RNA

Compared with the rapidly expanding set of known biological roles for RNA, the known chemical diversity of cellular RNA has remained limited primarily to canonical RNA, 3'-aminoacylated tRNAs, nucleobase-modified RNAs, and 5'-capped mRNAs in eukaryotes. We developed two methods to detect in a broad manner chemically labile cellular small molecule-RNA conjugates. The methods were validated by the detection of known tRNA and rRNA modifications. The first method analyzes small molecules cleaved from RNA by base or nucleophile treatment. Application to Escherichia coli and Streptomyces venezuelae RNA revealed an RNA-linked hydroxyfuranone or succinyl ester group, in addition to a number of other putative small molecule-RNA conjugates not previously reported. The second method analyzes nuclease-generated mononucleotides before and after treatment with base or nucleophile and also revealed a number of new putative small molecule-RNA conjugates, including 3'-dephospho-CoA and its succinyl-, acetyl-, and methylmalonyl-thioester derivatives. Subsequent experiments established that these CoA species are attached to E. coli and S. venezuelae RNA at the 5' terminus. CoA-linked RNA cannot be generated through aberrant transcriptional initiation by E. coli RNA polymerase in vitro, and CoA-linked RNA in E. coli is only found among smaller (approximately < 200 nucleotide) RNAs that have yet to be identified. These results provide examples of small molecule-RNA conjugates and suggest that the chemical diversity of cellular RNA may be greater than previously understood.Chemistry and Chemical Biolog

Photoswitching Mechanism of Cyanine Dyes

Photoswitchable fluorescent probes have been used in recent years to enable super-resolution fluorescence microscopy by single-molecule imaging.1-6 Among these probes are red carbocyanine dyes, which can be reversibly photoconverted between a fluorescent state and a dark state for hundreds of cycles, yielding several thousand detected photons per switching cycle, before permanent photobleaching occurs.7,8 While these properties make them excel-lent probes for super-resolution imaging, the mechanism by which cyanine dyes are photoconverted has yet to be determined. Such an understanding could prove useful for creating new photoswit-chable probes with improved properties. The photoconversion of red cyanine dyes into their dark states occurs upon illumination by red light and is facilitated by a primary thiol in solution,7,9 whereas agents with a secondary thiol do not support photoswitching. These observations suggest that the reactiv

Tiny tags on RNA

The covalent association of CoA with small RNA from bacteria might open the door to a new era of the chemical diversity and biological roles of RNA molecules

LC/MS analysis of cellular RNA reveals NAD-linked RNA

We developed a general method to detect cellular small molecule-RNA conjugates that does not rely on the reactivity of the small molecule, revealing NAD-linked RNA in E. coli and S. venezuelae. Subsequent characterization shows NAD is a 5’ modification of RNA, cannot be installed in vitro through aberrant transcriptional initiation, is only found among smaller cellular RNAs, and is present at a surprisingly high abundance of ~3000 copies per cell.Chemistry and Chemical Biolog