Next, we incubated the RNAs together with FOXRRM and irradiated the complexes at 254 nm at increasing energies. Work-up and analysis by SDS-PAGE for the three NGCAUGU sequence mutants revealed a new slow-migrating band on the gels, similar to that of the wild-type FOXRBE (N=U), consistent with RNA-protein cross-linking (Fig. ). The appearance of a band on an SDS-PAGE confirms that cross-linking occurs, but it does not identify the site of cross-linking nor the composition of the product. In order to determine whether any of the mutants cross-linked at the N1-position, we turned to CLIR-MS. CLIR-MS data for per-labelled *N*G*C*A*U*G*U confirmed that the three FOXRBE mutants exhibit the same cross-linking "fingerprint" as wild type FOXRBE, i.e. in the same two amino acid clusters around positions 126 and 160 (Fig. ). However, in order to differentiate cross-linking of N1 to that from G2 in the 126-cluster, we performed CLIR-MS on the singly labelled sequences (*NGCAUGU). In contrast to U1, cross-linking hardly occured at A1, G1 or C1 (Fig. ), consistent with the systematic presence of G2 in the di-or tri-nucleotides found cross-linked to F126 confirming that only G2 in the mutants can cross-link efficiently to the phenylalanine (Fig. ). This also confirmed the strong bias for uridine photo-reaction , though it was surprising that G1 was unreactive, given the reactivity of G2.