Selected Publications

A unified catalytic mechanism in bifunctional DNA glycosylases with an evolutionarily conserved aspartate-lysine dyad.Syed A, Serafim LF, Arvai AS, Minko IG, Tang HYH, Huffman JL, Mol CD, Hitomi K, Sarker AH, Parikh S, Tsai CL, Bacolla A, Shin DS, Cunningham RP, Iwai S, Chowdhury D, Lloyd RS, Ivanov I, Tainer JA.Nat Commun. 2026 Jul 15. doi: 10.1038/s41467-026-75471-1. Online ahead of print. PMID: 4245772

PARG Governs a PARylation-Ubiquitination Toggle that Stabilizes RAD51AP1 to Drive Homologous Recombination-Mediated Chemoresistance.
He H, Hu Y, Lu Y, Deng M, Bao Q, Zu D, Zhong Y, Zhang C, You C, Du X, Liu S, He Y, Liu M, Gao L, Gao X, Liu H, Huang Y, Chen Y, Rong D, Tainer JA, Jing J, Shi Y, Shen HM, Ye Z, Cheng X.Cancer Res. 2026 Jun 18. doi: 10.1158/0008-5472.CAN-25-4984. Online ahead of print. PMID: 42314057

Orchestrated metal ion repositioning defines the dynamic catalytic strategy of the essential DNA repair nuclease APE1.
Serafim LF, Tsutakawa SE, Arvai AS, Kossmann BR, Mantha AK, Abbotts R, Wilson DM 3rd, Mitra S, Tainer JA, Ivanov I.bioRxiv [Preprint]. 2026 May 14:2026.05.11.724140. doi: 10.64898/2026.05.11.724140. PMID: 42182258

Characteristics and Clinical Outcomes of BRCA Germline Mutation Carriers with Advanced Breast Cancer Treated with PARP (Poly ADP-Ribose Polymerase) Inhibitors: A Single-Institution Experience.
Akkoc Mustafayev FN, Fountzilas E, Munsell MF, Layman RM, Yam C, Gutierrez AM, Albarracin CT, Ahmed Z, Schlacher K, Tainer JA, Arun BK.Cancers (Basel). 2026 Apr 16;18(8):1258. doi: 10.3390/cancers18081258. PMID: 42073582

DPY30 Is an Epigenetic Decoupler Linking Replication Stress to Immunoediting in Pancreatic Cancer.
Citron F, Cecchetto L, Granato E, Ho IL, Liu Z, Balestrieri C, Yen EY, Perelli L, Zhang L, Castillo Montanez LA, Dyke CA, Shah R, Attanasio S, Srinivasan S, Roy S, Kwon HJ, Blazanin N, Chen Y, Chen KC, Chen Z, Scognamiglio I, Pham N, Jiang S, Pan J, Leung CS, Wang L, Gao S, Carugo A, Wang H, Yao W, Tonon G, Bonini MC, Zal MA, Jeter C, Tainer JA, Heffernan TP, Giuliani V, Lissanu Y, Genovese G, Di Pilato M, Viale A, Schlacher K, Draetta GF.Cancer Res. 2026 Jun 15;86(12):2837-2859. doi: 10.1158/0008-5472.CAN-25-3849. PMID: 41941748

EEPD1 evolved a unique DNA clamping dimer protecting reversed replication forks.
Shen R, Sarker AH, Chen Y, Liu M, Roy S, Arvai AS, Bacolla A, Ahmed Z, Katsonis P, Hammel M, Kuraoka I, Tsai MS, Irie C, Webb L, Lichtarge O, Tsai CL, Tsutakawa SE, Schlacher K, Tainer JA. Nucleic Acids Res. 2026 Feb 24;54(5):gkag188. doi: 10.1093/nar/gkag188. PMID: 41830330

HP1β recruits RING1A to ubiquitinate histone H2A for BRCA1-mediated resection of double-stand breaks.
Charaka V, Pandita RK, Tsai CL, Wang X, Chakraborty S, Ramos KS, Nandi S, Leonard F, Singh V, Sarkar PS, Hunt CR, Tainer JA, Das C, Pandita TK.iScience. 2025 Dec 30;29(2):114582. doi: 10.1016/j.isci.2025.114582. eCollection 2026 Feb 20. PMID: 41623472

Poly(ADP-ribose) glycohydrolase enforces p21 degradation via dePARylation to promote gastric cancer progression.
Hu Y, Bao Q, Huang Y, Wang Y, Zhao X, Nan J, Meng Y, Deng M, Li Y, Zhuang Z, He H, Zu D, Zhong Y, Zhang C, Wang B, Li R, He Y, Wang Q, Liu M, Tainer JA, Shi Y, Cheng X, Jing J, Ye Z.J Clin Invest. 2026 Jan 15;136(5):e195538. doi: 10.1172/JCI195538. eCollection 2026 Mar 2. PMID: 41538291

RNA/DNA-binding protein TDP43 regulates DNA mismatch repair genes with implications for genome stability.
Provasek VE, Bacolla A, Rangaswamy S, Kodavati M, Mitra J, Yusuf IO, Malojirao VH, Vasquez V, Britz GW, Li GM, Xu Z, Mitra S, Garruto RM, Tainer JA, Hegde ML.Nucleic Acids Res. 2025 Sep 23;53(18):gkaf920. doi: 10.1093/nar/gkaf920. PMID: 40985771

APOL2 Stabilizes Ku80 to Confer NHEJ-Mediated Radioresistance in Gastric Cancer.
Zu D, Bao Q, He H, Zhong Y, Deng M, Hu Y, Zhang C, Liang C, Huang Y, Liu H, Li X, He Y, Luo G, Wu W, Guan F, Xu S, Liu M, Bacolla A, Jing J, Du Y, Tainer JA, Shi Y, Ye Z, Cheng X.Adv Sci (Weinh). 2025 Nov;12(44):e06294. doi: 10.1002/advs.202506294. Epub 2025 Sep 15. PMID: 40953331

Huntingtin preserves mitochondrial genome integrity in neurons, which is impaired in Huntington's disease.
Pradhan S, Gaikwad S, Tsai CL, Smith C, Zhang N, Bush K, Chakraborty A, Yuan S, Choudhary S, Keene CD, Ellerby LM, Hazra TK, La Spada AR, Wairkar YP, Ashizawa T, Tainer JA, Pandita TK, Thompson LM, Sarkar PS.bioRxiv [Preprint]. 2025 Jul 24:2025.07.24.666629. doi: 10.1101/2025.07.24.666629. PMID: 40777236

Information theory optimization of signals from small-angle scattering measurements.
Rambo RP, Tainer JA.Biophys J. 2025 Aug 5;124(15):2511-2522. doi: 10.1016/j.bpj.2025.06.031. Epub 2025 Jun 27. PMID: 40581817

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