 high affinity rna - protein interactions 
 are critical to cellular 
 function , but directly identifying the determinants of binding within 
 these complexes is often difficult . here , we introduce a stable isotope 
 mass labeling technique to assign specific interacting nucleotides 
 in an oligonucleotide - protein complex by photo - cross - linking . 
 the 
 method relies on generating site - specific oxygen-18-labeled phosphodiester 
 linkages in oligonucleotides , such that covalent peptide - oligonucleotide 
 cross - link sites arising from ultraviolet irradiation can be assigned 
 to specific sequence positions in both rna and protein simultaneously 
 by mass spectrometry . using lin28a and a let-7 pre - element rna , 
 we 
 demonstrate that mass labeling permits unambiguous identification 
 of the cross - linked sequence positions in the rna - protein complex . 
Supplementary Material