Photo-irradiation of the FOXRRM-FOXRBE complex led to key observations with potentially wide-ranging consequences: 1) strong cross-linking occurred between U1, G2 and G6 with clusters of amino acids centered around the phenylalanines F126 and F160; 2) very little cross-linking was observed at other uridines in the parent or a mutated FOXRBE (C3/U3, U5 and U7); and 3) amino acids that flank F126 and F160 also cross-linked efficently to U1, G2 and G6, but not to other nucleotides of FOXRBE. Since the NMR structure of FOXRRM-FOXRBE shows that U1 and G2 stack to F126, and that G6 stacks with F160, the data suggested that a stacking interaction is a requirement for cross-linking events in an RNA-protein interaction, at least for this RRM domain. Indeed, other aromatic side chains could substitute for F126 in cross-linking, but incorporation of leucine abolished direct and almost all indirect cross-linking to U1/G2. Other researchers have noted in passing the increased presence of aromatic amino acid side chains in UV cross-linking data sets (see refs ), but have not to our knowledge recognized its role as a trigger for cross-linking, nor distinguished between direct and indirect cross-link events. It is clear that additional factors may also contribute to cross-linking events in RNA-protein sites, including: efficiency of the photo-induced electron transfer, the ability to stabilize free radicals, the flexibility of the system to adopt to the configurations that are required for the radical reactions and the proximity of reactive pairs 63 (Sarnowski et al; in preparation). Furthermore, our findings cannot explain all RNA-protein cross-linking reactions, at least those involving sulphurcontaining amino acids, such as cysteine, which are highly photoreactive and prone to cross-link probably due to the high reactivity of the thiyl radical . However, our results may partly explain why double-stranded RNA cross-links so poorly to proteins , since in a double-stranded RNA πstacking between aromatic amino acids and nucleobases is hindered. Indeed, double-stranded RNAbinding motifs (dsRBM) recognize their substrates mainly by shape and contacts with the sugarphosphate backbone .