Mass Spectrometric Evidence for the Under-represented RNA–Protein Cross-Links

Abstract

In protein–RNA complexes, UVC cross-links proteins predominantly to uracil and other nucleobases to a smaller extent. The cross-linked RNA moieties can be simplified via hydrofluoride digestion and identified via tandem mass spectrometry. While uridine or uracil cross-links have been successfully characterized, concrete evidence for other UVC-cross-linked RNA bases is lacking. Here, I elucidate mass spectrometric signatures of UVC-cross-linked, hydrofluoride-digested guanine, cytidine, and methyladenine. This information can help us capture the native protein–RNA interactions in more detail.