We present a simple and general affinity method, based on size fractionation and nucleic acid complementarity, to isolate sufficient amounts of native RNA molecules for further physicochemical studies, such as modification state of nucleotides. In the case presented here, we purified four micrograms of dendritic neuronal BC1 RNA from 130 grams of mouse brain (initially yielding a total of 200 mg RNA). Directly combined liquid chromatography-electrospray ionization mass spectrometry (LC/MS) analysis revealed no base or sugar backbone modifications in native BC1 RNA, despite earlier indications that C-54 could be methylated in vitro (Cm5, position 54).