Upon initiation of a pulse-chase experiment the medium is switched from medium(1) to medium(2). The two media must only differ in their isotope content. Thereby it is possible to distinguish between RNA molecules already existent before experiment initiation (= RNA molecules grown in medium(1)) and RNA molecules that are newly transcribed after experiment initiation (= RNA molecules grown in medium(2)). This allows the detailed study of modification dynamics in vivo. The supplementation of labeled methionine in either medium(1) or medium(2) allows the tracing of methylation processes. Other isotopically labeled metabolites potentially allow for further modification analysis.
Altogether NAIL-MS enables the investigation of RNA modification dynamics by mass spectrometry. With this technique, enzymatic demethylation has been observed for several RNA damages inside living bacteria.