{"database":"biostudies-literature","file_versions":[],"scores":null,"additional":{"submitter":["Welp LM"],"funding":["Germany's Excellence Strategy","Ministry of Science, Research and Arts Baden-Württemberg","Deutsche Forschungsgemeinschaft","International Max Planck Research School for Genome Sciences","European Research Council","Alex's Lemonade Foundation Crazy 8 Initiative","Smith Family Foundation","Marie Skłodowska-Curie","Max Planck Society","Federal Ministry of Education and Research","NIGMS NIH HHS","European Union's Horizon 2020","NIH HHS"],"pagination":["gkaf727"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/S-EPMC12359043"],"repository":["biostudies-literature"],"omics_type":["Unknown"],"volume":["53(15)"],"pubmed_abstract":["Ultraviolet (UV) crosslinking with mass spectrometry (XL-MS) has been established for identifying RNA- and DNA-binding proteins along with their domains and amino acids involved. Here, we explore chemical XL-MS for RNA-protein, DNA-protein, and nucleotide-protein complexes in vitro and in vivo. We introduce a specialized nucleotide-protein-crosslink search engine, NuXL, for robust and fast identification of such crosslinks at amino acid resolution. Chemical XL-MS complements UV XL-MS by generating different crosslink species, increasing crosslinked protein yields in vivo almost four-fold, and thus it expands the structural information accessible via XL-MS. Our workflow facilitates integrative structural modelling of nucleic acid-protein complexes and adds spatial information to the describ"],"journal":["Nucleic acids research"],"pubmed_title":["Chemical crosslinking extends and complements UV crosslinking in analysis of RNA/DNA nucleic acid-protein interaction sites by mass spectrometry."],"pmcid":["PMC12359043"],"funding_grant_id":["SFB1565 P12","SFB1565","SFB1565 P15","2067/1-390 729 940","DP2 GM146254","SFB1565 P18","956148","SFB860","945528","ERC-StG 945528 IMAP","DP2GM146254","469281184","FOR1193"],"pubmed_authors":["Siraj A","de A P Schwarzer AC","Wulf A","Bohnsack KE","Ficner R","Urlaub H","Sachsenberg T","Wohlgemuth I","Infante DA","Bohnsack MT","Liepe J","Dickmanns A","Vos SM","Welp LM","Viner R","Horokhovskyi Y","Schmitzova J","Netz E","Dybkov O","Delanghe B","Pasen M","Raabe M","Fritzemeier K","Johannsson S","Walshe JL","Chernev A","Cramer P","He Y","Moshkovskii S","Neumann P","Oberbeckmann E","Kohlbacher O","Gothert H"],"additional_accession":[]},"is_claimable":false,"name":"Chemical crosslinking extends and complements UV crosslinking in analysis of RNA/DNA nucleic acid-protein interaction sites by mass spectrometry.","description":"Ultraviolet (UV) crosslinking with mass spectrometry (XL-MS) has been established for identifying RNA- and DNA-binding proteins along with their domains and amino acids involved. Here, we explore chemical XL-MS for RNA-protein, DNA-protein, and nucleotide-protein complexes in vitro and in vivo. We introduce a specialized nucleotide-protein-crosslink search engine, NuXL, for robust and fast identification of such crosslinks at amino acid resolution. Chemical XL-MS complements UV XL-MS by generating different crosslink species, increasing crosslinked protein yields in vivo almost four-fold, and thus it expands the structural information accessible via XL-MS. Our workflow facilitates integrative structural modelling of nucleic acid-protein complexes and adds spatial information to the describ","dates":{"release":"2025-01-01T00:00:00Z","publication":"2025 Aug","modification":"2026-04-08T15:34:48.344Z","creation":"2026-04-08T05:05:09.711Z"},"accession":"S-EPMC12359043","cross_references":{"pubmed":["40823814"],"doi":["10.1093/nar/gkaf727"]}}