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Emerging evidence suggests that ADPr at the 5\u2032-phosphate terminus of DNA is implicated in the DNA damage response, yet understanding its precise molecular function has been hampered by the lack of structurally defined chemical probes. Here, we report the stereoselective synthesis of deoxynucleotide-phospho-ADPr (dN-P-ADPr) probes, representing native fragments of terminal DNA-ADPr. Our strategy leverages a mild, stereocontrolled glycosylation to construct the challenging ribosyl-phosphate linkage, followed by P(III)\u2013P(V) coupling to establish the pyrophosphate bridge. This robust toolkit enabled the systematic biochemical profiling of DNA-ADPr hydrolases across diverse kingdoms of life. Remarkably, using these newly developed probes, we uncover hydrolases across the diversity of life capable of reversing ADPr modifications at phosphorylated DNA ends. We further show that these enzymes exhibit an absolute preference for the native-like \u03b1-anomer, independent of the identity of the adjacent DNA nucleobase, suggesting that substrate recognition is governed primarily by the ADPr-phosphate linkages rather than the local nucleobase context. Together, these synthetic probes and biochemical insights provide an essential foundation for deciphering the biological landscape of noncanonical ADPr.<\/jats:p>","DOI":"10.1021\/jacs.6c02874","type":"journal-article","created":{"date-parts":[[2026,7,16]],"date-time":"2026-07-16T18:04:02Z","timestamp":1784225042000},"page":"30836-30849","source":"Crossref","is-referenced-by-count":0,"title":["Deciphering the Specificity\nof Reversible DNA-Phosphate\nADP-Ribosylation via the Precise Synthesis and Enzymatic Profiling\nof Nucleotide-Phospho-ADP-Ribosyl Probes"],"prefix":"10.1021","volume":"148","author":[{"given":"Lingxiao","family":"Liu","sequence":"first","affiliation":[{"name":"Southern Medical University , , ,","place":["Guangzhou, China, 510515"]},{"name":"Zhongshan Institute for Drug Discovery , ,","place":["Zhongshan, China, 528400"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yang","family":"Lu","sequence":"additional","affiliation":[{"name":"University of Oxford , , ,","place":["Oxford, U.K., OX1 3RE"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zongxing","family":"Yu","sequence":"additional","affiliation":[{"name":"Southern Medical University , , ,","place":["Guangzhou, China, 510515"]},{"name":"Zhongshan Institute for Drug Discovery , ,","place":["Zhongshan, China, 528400"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Li","family":"Tang","sequence":"additional","affiliation":[{"name":"Zhongshan Institute for Drug Discovery , ,","place":["Zhongshan, China, 528400"]},{"name":"Shanghai Institute of Materia Medica, Chinese Academy of Sciences , , ,","place":["Shanghai, China, 201203"]},{"name":"University of Chinese Academy of Sciences , ,","place":["Beijing, China, 100049"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yidan","family":"Wu","sequence":"additional","affiliation":[{"name":"Zhongshan Institute for Drug Discovery , ,","place":["Zhongshan, China, 528400"]},{"name":"Shanghai Institute of Materia Medica, Chinese Academy of Sciences , , ,","place":["Shanghai, China, 201203"]},{"name":"University of Chinese Academy of Sciences , ,","place":["Beijing, China, 100049"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jim","family":"Voorneveld","sequence":"additional","affiliation":[{"name":"Leiden Institute of Chemistry, Leiden University , , ,","place":["Leiden, The Netherlands, 2300RA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Waghela","family":"Deeksha","sequence":"additional","affiliation":[{"name":"University of Oxford , , ,","place":["Oxford, U.K., OX1 3RE"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dmitri V.","family":"Filippov","sequence":"additional","affiliation":[{"name":"Leiden Institute of Chemistry, Leiden University , , ,","place":["Leiden, The Netherlands, 2300RA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ivan","family":"Ahel","sequence":"additional","affiliation":[{"name":"University of Oxford , , ,","place":["Oxford, U.K., OX1 3RE"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1229-7908","authenticated-orcid":true,"given":"Qiang","family":"Liu","sequence":"additional","affiliation":[{"name":"Southern Medical University , , ,","place":["Guangzhou, China, 510515"]},{"name":"Zhongshan Institute for Drug Discovery , ,","place":["Zhongshan, China, 528400"]},{"name":"Shanghai Institute of Materia Medica, Chinese Academy of Sciences , , ,","place":["Shanghai, China, 201203"]},{"name":"University of Chinese Academy of Sciences , ,","place":["Beijing, China, 100049"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"316","published-online":{"date-parts":[[2026,7,16]]},"reference":[{"issue":"21","key":"2026073021325227800_cit1","doi-asserted-by":"publisher","first-page":"4475","DOI":"10.1016\/j.cell.2023.08.030","article-title":"ADP-ribosylation from\nmolecular mechanisms to therapeutic implications","volume":"186","author":"Suskiewicz","year":"2023","journal-title":"Cell"},{"issue":"5\u20136","key":"2026073021325227800_cit2","doi-asserted-by":"publisher","first-page":"263","DOI":"10.1101\/gad.334631.119","article-title":"(ADP-ribosyl)hydrolases:\nstructure,\nfunction, and biology","volume":"34","author":"Rack","year":"2020","journal-title":"Genes Dev."},{"issue":"12","key":"2026073021325227800_cit3","doi-asserted-by":"publisher","first-page":"2315","DOI":"10.1016\/j.molcel.2022.02.021","article-title":"The expanding universe of PARP1-mediated molecular\nand therapeutic mechanisms","volume":"82","author":"Huang","year":"2022","journal-title":"Mol. 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Am.\nChem. Soc."},{"issue":"21","key":"2026073021325227800_cit25","doi-asserted-by":"publisher","first-page":"4552","DOI":"10.1016\/j.molcel.2021.08.037","article-title":"Reading ADP-ribosylation signaling using chemical biology\nand interaction proteomics","volume":"81","author":"Kliza","year":"2021","journal-title":"Mol. Cell"},{"issue":"4","key":"2026073021325227800_cit26","doi-asserted-by":"publisher","first-page":"431","DOI":"10.1016\/j.chembiol.2017.04.003","article-title":"ADP-Ribosylation\nGoes Normal: Serine\nas the Major Site of the Modification","volume":"24","author":"Liu","year":"2017","journal-title":"Cell\nChem. Biol."},{"issue":"6","key":"2026073021325227800_cit27","doi-asserted-by":"publisher","first-page":"1659","DOI":"10.1002\/anie.201710527","article-title":"A General Approach Towards Triazole-Linked Adenosine\nDiphosphate Ribosylated Peptides and Proteins","volume":"57","author":"Liu","year":"2018","journal-title":"Angew. Chem., Int. Ed. 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Lett."},{"key":"2026073021325227800_cit37","doi-asserted-by":"publisher","first-page":"111","DOI":"10.1007\/978-1-0716-2891-1_8","article-title":"A Simple Method to\nStudy ADP-Ribosylation Reversal:\nFrom Function to Drug Discovery","volume":"2609","author":"Rack","year":"2023","journal-title":"Methods in\nmolecular biology (Clifton, N.J.)"},{"issue":"13","key":"2026073021325227800_cit38","doi-asserted-by":"publisher","first-page":"4140","DOI":"10.1021\/acs.orglett.8b01742","article-title":"Synthetic \u03b1-\nand \u03b2-Ser-ADP-ribosylated\nPeptides Reveal \u03b1-Ser-ADPr as the Native Epimer","volume":"20","author":"Voorneveld","year":"2018","journal-title":"Org. Lett."},{"issue":"9","key":"2026073021325227800_cit39","doi-asserted-by":"publisher","first-page":"1225","DOI":"10.1038\/emboj.2013.51","article-title":"Deficiency\nof terminal ADP-ribose protein glycohydrolase TARG1\/C6orf130 in neurodegenerative\ndisease","volume":"32","author":"Sharifi","year":"2013","journal-title":"Embo J."},{"issue":"18","key":"2026073021325227800_cit40","doi-asserted-by":"publisher","first-page":"10477","DOI":"10.1093\/nar\/gkab771","article-title":"TARG1 protects against toxic DNA\nADP-ribosylation","volume":"49","author":"Tromans-Coia","year":"2021","journal-title":"Nucleic Acids Res."},{"issue":"12","key":"2026073021325227800_cit41","doi-asserted-by":"publisher","first-page":"2526","DOI":"10.1038\/s41594-025-01715-1","article-title":"Filament\nformation and NAD processing by noncanonical human FAM118 sirtuins","volume":"32","author":"Baretic\u0301","year":"2025","journal-title":"Nat. Struct Mol. Biol."},{"issue":"2","key":"2026073021325227800_cit42","doi-asserted-by":"publisher","first-page":"293","DOI":"10.1042\/BJ20141554","article-title":"Processing of protein\nADP-ribosylation by Nudix hydrolases","volume":"468","author":"Palazzo","year":"2015","journal-title":"Biochem.\nJ."},{"key":"2026073021325227800_cit43","doi-asserted-by":"publisher","first-page":"2366","DOI":"10.1016\/j.csbj.2021.04.023","article-title":"ADP-ribosylation\nsystems in bacteria and viruses","volume":"19","author":"Mikolc\u030cevic\u0301","year":"2021","journal-title":"Comput. Struct\nBiotechnol J."},{"key":"2026073021325227800_cit44","doi-asserted-by":"publisher","first-page":"4","DOI":"10.1016\/j.dnarep.2014.05.003","article-title":"Distribution of protein poly(ADP-ribosyl)ation\nsystems across all domains of life","volume":"23","author":"Perina","year":"2014","journal-title":"DNA Repair"},{"issue":"1","key":"2026073021325227800_cit45","doi-asserted-by":"publisher","first-page":"3200","DOI":"10.1038\/s41467-023-38793-y","article-title":"Serine ADP-ribosylation in Drosophila provides insights into the\nevolution of reversible ADP-ribosylation signalling","volume":"14","author":"Fontana","year":"2023","journal-title":"Nat. Commun."},{"issue":"1","key":"2026073021325227800_cit46","doi-asserted-by":"publisher","first-page":"2452","DOI":"10.1038\/s41467-024-46649-2","article-title":"Legionella\nmetaeffector MavL reverses ubiquitin ADP-ribosylation via a conserved\narginine-specific macrodomain","volume":"15","author":"Zhang","year":"2024","journal-title":"Nat. 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