Lelyveld, Victor S.Björkbom, AndersRansey, ElizabethSliz, PiotrSzostak, Jack2016-02-012015Lelyveld, Victor S., Anders Björkbom, Elizabeth M. Ransey, Piotr Sliz, and Jack W. Szostak. 2015. “Pinpointing RNA-Protein Cross-Links with Site-Specific Stable Isotope-Labeled Oligonucleotides.” Journal of the American Chemical Society 137 (49): 15378-15381. doi:10.1021/jacs.5b10596. http://dx.doi.org/10.1021/jacs.5b10596.0002-7863http://nrs.harvard.edu/urn-3:HUL.InstRepos:24983981High 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.en-USJournal Article2016-02-0110.1021/jacs.5b10596