Labeling of Amine-Modified RNA

RNA labeling enables high-contrast visualization and quantitative measurements. This chapter describes practical guidance for fluorescent dye labeling of RNA via the NHS ester-amine coupling. We detail reaction setup, cleanup by ethanol precipitation, and evaluation of labeling efficiency by absorbance spectrum analysis or by high-performance liquid chromatography (HPLC). Notes summarize common failure modes and remedies, and RNase-free practice is emphasized throughout. Although the workflow demonstrates fluorescent labeling of 3'-amine-modified RNA, the protocol is broadly applicable to 5'-end or internal amine modifications and can also be used to introduce functional groups such as DBCO, used in click chemistry reactions.