Selected Publications
Peer-Reviewed Articles
- BRCA2 C-terminal clamp restructures RAD51 dimers to bind B-DNA for replication fork stability. Longo MA, Ahmed SM, Chen Y, Tsai CL, Namjoshi S, Shen R, Ahmed Z, Wang X, Perera RL, Arvai A, Lee M, Kong LR, Engl W, Ng WS, Zhao ZW, Venkitaraman AR, Tainer JA, Schlacher K.Mol Cell. 2025 Jun 5;85(11):2080-2096.e6. doi: 10.1016/j.molcel.2025.05.010. Epub 2025 May 28. PMID: 40441151
- RNA sculpting by the primordial Helix-clasp-Helix-Strand-Loop (HcH-SL) motif enforces chemical recognition enabling diverse KH domain functions. Tainer JA, Tsutakawa SE. J Biol Chem. 2025 May;301(5):108474. doi: 10.1016/j.jbc.2025.108474. Epub 2025 Apr 2. PMID: 40185232
- Molecular model of TFIIH recruitment to the transcription-coupled repair machinery. Paul T, Yan C, Yu J, Tsutakawa SE, Tainer JA, Wang D, Ivanov I. Nat Commun. 2025 Mar 8;16(1):2341. doi: 10.1038/s41467-025-57593-0. PMID: 40057514
- A predictive chromatin architecture nexus regulates transcription and DNA damage repair. Bhat A, Bhan S, Kabiraj A, Pandita RK, Ramos KS, Nandi S, Sopori S, Sarkar PS, Dhar A, Pandita S, Kumar R, Das C, Tainer JA, Pandita TK. J Biol Chem. 2025 Mar;301(3):108300. doi: 10.1016/j.jbc.2025.108300. Epub 2025 Feb 11. PMID: 39947477
- NADH-bound AIF activates the mitochondrial CHCHD4/MIA40 chaperone by a substrate-mimicry mechanism. Brosey CA, Shen R, Tainer JA. EMBO J. 2025 Feb;44(4):1220-1248. doi: 10.1038/s44318-024-00360-6. Epub 2025 Jan 13. PMID: 39806100
- A goldilocks computational protocol for inhibitor discovery targeting DNA damage responses including replication-repair functions. Moiani D, Tainer JA. Front Mol Biosci. 2024 Nov 28;11:1442267. doi: 10.3389/fmolb.2024.1442267. eCollection 2024. PMID: 39669672
- Molecular architecture and functional dynamics of the pre-incision complex in nucleotide excision repair. Yu J, Yan C, Paul T, Brewer L, Tsutakawa SE, Tsai CL, Hamdan SM, Tainer JA, Ivanov I. Nat Commun. 2024 Oct 1;15(1):8511. doi: 10.1038/s41467-024-52860-y. PMID: 39353945
- BRCA2 C-terminal clamp restructures RAD51 dimers to bind B-DNA for replication fork stability. Longo MA, Ahmed SM, Chen Y, Tsai CL, Namjoshi S, Wang X, Perera RL, Arvai A, Lee M, Kong LR, Engl W, Shyuan W, Zhao ZW, Venkitaraman AR, Tainer JA, Schlacher K. bioRxiv [Preprint]. 2024 Sep 22:2024.09.21.614229. doi: 10.1101/2024.09.21.614229. Update in: Mol Cell. 2025 Jun 5;85(11):2080-2096.e6. doi: 10.1016/j.molcel.2025.05.010. PMID: 39345573
- Chromatin remodeler BRG1 recruits huntingtin to repair DNA double-strand breaks in neurons. Pradhan S, Bush K, Zhang N, Pandita RK, Tsai CL, Smith C, Pandlebury DF, Gaikwad S, Leonard F, Nie L, Tao A, Russell W, Yuan S, Choudhary S, Ramos KS, Elferink C, Wairkar YP, Tainer JA, Thompson LM, Pandita TK, Sarkar PS. bioRxiv [Preprint]. 2024 Sep 20:2024.09.19.613927. doi: 10.1101/2024.09.19.613927. PMID: 39345557
- Enriched G4 forming repeats in the human genome are associated with robust well coordinated transcription and reduced cancer transcriptome variation. De-Paula RB, Bacolla A, Syed A, Tainer JA. J Biol Chem. 2024 Nov;300(11):107822. doi: 10.1016/j.jbc.2024.107822. Epub 2024 Sep 26. PMID: 39341500
- RNA/DNA Binding Protein TDP43 Regulates DNA Mismatch Repair Genes with Implications for Genome Stability. Provasek VE, Bacolla A, Rangaswamy S, Mitra J, Kodavati M, Yusuf IO, Malojirao VH, Vasquez V, Britz GW, Li GM, Xu Z, Mitra S, Garruto RM, Tainer JA, Hegde ML. bioRxiv [Preprint]. 2024 Nov 8:2024.05.16.594552. doi: 10.1101/2024.05.16.594552. PMID: 38798341
- ASCC1 structures and bioinformatics reveal a novel helix-clasp-helix RNA-binding motif linked to a two-histidine phosphodiesterase. Chinnam NB, Thapar R, Arvai AS, Sarker AH, Soll JM, Paul T, Syed A, Rosenberg DJ, Hammel M, Bacolla A, Katsonis P, Asthana A, Tsai MS, Ivanov I, Lichtarge O, Silverman RH, Mosammaparast N, Tsutakawa SE, Tainer JA. J Biol Chem. 2024 Jun;300(6):107368. doi: 10.1016/j.jbc.2024.107368. Epub 2024 May 14. PMID: 38750793
- A prismatic view of the epigenetic-metabolic regulatory axis in breast cancer therapy resistance. Das C, Bhattacharya A, Adhikari S, Mondal A, Mondal P, Adhikary S, Roy S, Ramos K, Yadav KK, Tainer JA, Pandita TK. Oncogene. 2024 Jun;43(23):1727-1741. doi: 10.1038/s41388-024-03054-9. Epub 2024 May 8. PMID: 38719949
- Chemical screening by time-resolved X-ray scattering to discover allosteric probes. Brosey CA, Link TM, Shen R, Moiani D, Burnett K, Hura GL, Jones DE, Tainer JA. Nat Chem Biol. 2024 Sep;20(9):1199-1209. doi: 10.1038/s41589-024-01609-1. Epub 2024 Apr 26. PMID: 38671223
- Synthetic cationic helical polypeptides for the stimulation of antitumour innate immune pathways in antigen-presenting cells. Lee D, Huntoon K, Wang Y, Kang M, Lu Y, Jeong SD, Link TM, Gallup TD, Qie Y, Li X, Dong S, Schrank BR, Grippin AJ, Antony A, Ha J, Chang M, An Y, Wang L, Jiang D, Li J, Koong AC, Tainer JA, Jiang W, Kim BYS. Nat Biomed Eng. 2024 May;8(5):593-610. doi: 10.1038/s41551-024-01194-7. Epub 2024 Apr 19. PMID: 38641710
- Nardilysin-regulated scission mechanism activates polo-like kinase 3 to suppress the development of pancreatic cancer. Fu J, Ling J, Li CF, Tsai CL, Yin W, Hou J, Chen P, Cao Y, Kang Y, Sun Y, Xia X, Jiang Z, Furukawa K, Lu Y, Wu M, Huang Q, Yao J, Hawke DH, Pan BF, Zhao J, Huang J, Wang H, Bahassi EIM, Stambrook PJ, Huang P, Fleming JB, Maitra A, Tainer JA, Hung MC, Lin C, Chiao PJ. Nat Commun. 2024 Apr 11;15(1):3149. doi: 10.1038/s41467-024-47242-3. PMID: 38605037
- Author Correction: Automating data analysis for hydrogen/deuterium exchange mass spectrometry using data-independent acquisition methodology. Filandr F, Sarpe V, Raval S, Crowder DA, Khan MF, Douglas P, Coales S, Viner R, Syed A, Tainer JA, Lees-Miller SP, Schriemer DC. Nat Commun. 2024 Apr 2;15(1):2836. doi: 10.1038/s41467-024-47157-z. PMID: 38565885
- Automating data analysis for hydrogen/deuterium exchange mass spectrometry using data-independent acquisition methodology. Filandr F, Sarpe V, Raval S, Crowder DA, Khan MF, Douglas P, Coales S, Viner R, Syed A, Tainer JA, Lees-Miller SP, Schriemer DC. Nat Commun. 2024 Mar 11;15(1):2200. doi: 10.1038/s41467-024-46610-3. PMID: 38467655
- GRB2 stabilizes RAD51 at reversed replication forks suppressing genomic instability and innate immunity against cancer. Ye Z, Xu S, Shi Y, Cheng X, Zhang Y, Roy S, Namjoshi S, Longo MA, Link TM, Schlacher K, Peng G, Yu D, Wang B, Tainer JA, Ahmed Z. Nat Commun. 2024 Mar 8;15(1):2132. doi: 10.1038/s41467-024-46283-y. PMID: 38459011
- The NS1 protein of influenza B virus binds 5'-triphosphorylated dsRNA to suppress RIG-I activation and the host antiviral response. Woltz R, Schweibenz B, Tsutakawa SE, Zhao C, Ma L, Shurina B, Hura GL, John R, Vorobiev S, Swapna G, Solotchi M, Tainer JA, Krug RM, Patel SS, Montelione GT. bioRxiv [Preprint]. 2024 Jan 24:2023.09.25.559316. doi: 10.1101/2023.09.25.559316. PMID: 38328244
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