Lincoln Scott - Identification of 5-hydroxycytidine at position 2501 concludes characterization of modified nucleotides in E. coli 23S rRNA.

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  J Mol Biol. 2011   Aug 19;411(3):529-36. doi: 10.1016/j.jmb.2011.06.036. Epub 2011   Jun 24.


  Complete characterization of a biomolecule's chemical structure   is crucial in the full understanding of the relations between   their structure and function. The dominating components in   ribosomes are ribosomal RNAs (rRNAs), and the entire rRNA-but a   single modified nucleoside at position 2501 in 23S rRNA-has   previously been characterized in the bacterium Escherichia coli.   Despite a first report nearly 20 years ago, the chemical nature   of the modification at position 2501 has remained elusive, and   attempts to isolate it have so far been unsuccessful. We   unambiguously identify this last unknown modification as   5-hydroxycytidine-a novel modification in RNA. Identification of   5-hydroxycytidine was completed by liquid chromatography under   nonoxidizing conditions using a graphitized carbon stationary   phase in combination with ion trap tandem mass spectrometry and   by comparing the fragmentation behavior of the natural nucleoside   with that of a chemically synthesized ditto. Furthermore, we show   that 5-hydroxycytidine is also present in the equivalent position   of 23S rRNA from the bacterium Deinococcus radiodurans. Given the   unstable nature of 5-hydroxycytidine, this modification might be   found in other RNAs when applying the proper analytical   conditions as described here.

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