John A. Tainer, Ph.D.
Department of Molecular Oncology, Division of Discovery Science
About Dr. John A. Tainer
I am an experimental and computational biophysicist. We develop, combine, and apply quantitative experimental and computational methods to define and control molecular structures, interactions, and activities. We fill critical gaps on how dynamic functional complexes orchestrate stress responses for cell viability and genome integrity. My work centers on intertwined fundamental and clinically derived stress responses: 1) DNA replication stress, 2) DNA/RNA damage responses causing stability and instability from nucleotide damage plus transcription, and 3) cancer bioinformatics and precision oncology. We advanced methods, structures, inhibitors, and results to establish probable molecular mechanisms for dsDNA break repair by homologous recombination (HR), non-homologous end joining (NHEJ), alternative end joining (Alt-EJ), reactive oxygen defenses, DNA base and nucleotide excision repair (NER), and replication fork protection and restart. We examine synthetic lethality, therapy resistance, and inflammation from DNA damage and stress response defects.
We focus on mechanisms controlling biological stress outcomes. We identified breakthrough mechanisms informing biological outcomes for reactive oxygen control by superoxide dismutases, nitric oxide synthases, and catalase. We unveiled immune avoidance mechanisms by pathogenic pili and mobility in anti-peptide antibody reactivity. We elucidated field-expanding structure-activity relationships in DNA replication-repair for biology and chemotherapy stress responses.
We aim to advance predictive biology. We determined predictive mechanisms for key reactive oxygen control, inflammation, immune, plus DNA replication, transcription, and repair responses. At Scripps, I solved novel reactive oxygen defense and virulence factor structures, and developed predictive methods for anti-peptide antibodies that recognize intact proteins. I rose to tenured full Professor, and I directed an NSF Computational Center for Macromolecular Structure. At Berkeley Lab, I developed and still direct synchrotron beamline SIBYLS ( S tructurally I ntegrated Biolog Y for L ife S ciences) for Small Angle X-ray Scattering (SAXS) used by ~200 laboratories. When SAXS was worldwide used for shapes, I led in combining high-resolution structural methods with bio-SAXS to examine dynamic functional states at residue resolution. We discovered the first novel X-ray scattering invariant in last 80 years and solved a >40-year-old problem by applying information theory to solve the inverse Fourier transform for X-ray scattering intensity data: these advances improve structures and enable more rigorous and quantitative analyses of dynamic cancer protein and inhibitor complexes in solution.
Present Title & Affiliation
Primary Appointment
Professor, Department of Molecular Oncology, Division of Discovery Science, The University of Texas MD Anderson Cancer Center, Houston, TX
Endowed Distinguished Chair Robert A. Welch Distinguished Professor Chair in Chemistry, Department of Basic Science Research, The University of Texas MD Anderson Cancer Center, Houston, TX
Director, Department of Structural Biology, The University of Texas MD Anderson Cancer Center, Houston, TX
Dual/Joint/Adjunct Appointment, Professor, Department of Cancer Biology, Division of Discovery Science, UT MD Anderson Cancer Center, Houston, TX
Director, Department of Structurally Integrated Biology for Life Sciences (SIBLYS) Synchrotron Beamline and Facilities, Lawrence Berkeley National Lab, Berkeley, CA
Dual/Joint/Adjunct Appointment
Visiting Professor & Director, Department of SIBLYS synchroton beamline, Lawrence Berkeley National Lab, Berkeley, California
Research Interests
I integrate biophysics and biochemistry to help address challenges relevant to medicine and biotechnology. I strive to characterize macromolecular complexes including their conformations and interactions that control biological outcomes to mechanistically inform on cancer biology and treatment strategies. My group does this by developing and employing multi-disciplinary biophysical methods with biological collaborations to join structures to biology. Importantly, my projects inform and cross-pollinate one another, so we are more able to successfully and efficiently understand how macromolecular complexes and pathway intersections impact outcomes in cells and humans. Besides hypothesis-driven research, my laboratory develops advanced technology to bridge the gaps from molecular structure to quantitative, predictive cell biology: we do this by creating, testing, and providing technology for insights on dynamic macromolecular conformations and interactions that impact biological outcomes including structure-based design and microbially-inspired solutions to challenges in human health.
I develop funded programs that focus structural biology on medical relevant challenges, such as my Structural Biology of DNA Repair (SBDR) NCI program project. My RO1 lab projects center on cellular stress responses (DNA repair impacting genome integrity and tumorigenesis, reactive oxygen regulators, pathogenesis factors, metalloenzymes, RNA, plus enzyme and inhibitor design). My research and training includes advanced methods development for technologies defining complexes and conformations in solution and at high resolution. I designed, built, and run the synchrotron beamline SIBYLS at the Advanced Light Source (ALS) to integrate small angle x-ray scattering (SAXS) with high-resolution crystal structures for predictive biology - see www.bl1231.als.lbl.gov/. SIBYLS had ~1200 users in the last 5 years and >15 HHMI groups.
Our work on structural biology and SAXS includes introducing new equations for analyzing X-ray scattering data for flexible macromolecules and complexes. We introduced a novel SAXS invariant, the first discovered since the Porod invariant 60 years ago. Furthermore, we develop new metrics for accurate structures, conformations, and assemblies in solution. Our analyses are providing parameters to better assess flexibility, measure intermolecular distances and data to model agreement, reduce false positives, and define resolution.
The SIBYLS facility I built and run (funded by my IDAT and MINOS programs) supports efficient progress in developing and testing the technologies and in characterizing protein interactions, complexes, and conformations in solution and at high resolution. These resources support our growing interests in applying both solution and single crystal methods to structure-based inhibitor design relevant to developing chemical knockouts to complement genetic knockouts, and as eventual therapeutics. The synergy between basic research and technique advancement is allowing us to contribute to basic knowledge and advances relevant to human diseases.
Overall, my group’s research and technology development aims to bridge the gaps from molecular structure to quantitative, mechanistic, and predictive cell biology for organisms. I view this as the age of cell biology with sequencing advances and systems biology opening doors to game changing contributions to fighting human diseases and applying biotechnology. A missing element needed to make current scientific contributions more powerful is a mechanistic understanding at the molecular level that leverages the sequence information and provides a bottom up quantitative and predictive knowledge to objectively link with top down systems biology. I therefore aim to develop tools and technologies to address biology grand challenges, and to connect dynamic structures to biological outcomes. I apply synthetic biology and inhibitor design to learn more about how biological systems work, and to develop useful agents for medicine and nanotechnology. By leveraging my project efforts by strategic collaborations, my goal is to help apply these advances to therapeutics for pathogenesis, degenerative diseases and cancer, and for biotechnology useful for sustainable health in humans.
Education & Training
Degree-Granting Education
| 1982 | Duke University, Durham, North Carolina, US, Biochemistry and Structural Biology, Ph.D |
| 1974 | Trinity College of Arts and Sciences, Duke University, Durham, North Carolina, US, Zoology and Anthropology, BA |
Postgraduate Training
| 1982-1984 | Postdoctoral, Structural Biology, The Scripps Research Institute, La Jolla, California |
Experience & Service
Faculty Academic Appointments
Visiting Professor, Department of Life Sciences, The University of California Lawrence Berkeley National Laboratory, Berkeley, CA, 2000 - 2009
Senior Scientist & Director, Lawrence Berkeley National Lab, Berkeley, California, 2000 - 2015
Professor, The Scripps Research Institute, La Jolla, CA, 1994 - 2015
Associate Professor, The Scripps Research Institute, La Jolla, CA, 1991 - 1994
Administrative Appointments/Responsibilities
Co-Director, Department of Cryo-EM Cancer Observatory, The University of Texas MD Anderson Cancer Center, Houston, Texas, 2023 - Present
Director, Department of Integrated Diffraction Analysis Technologies Program, The University of California Lawrence Berkeley National Laboratory, Berkeley, California, 2004 - 2021
Director, Department of Structural Cell Biology of DNA Repair NCI Program Project, The University of California Lawrence Berkeley National Laboratory, Berkeley, California, 2002 - Present
Director, Department of Structurally Integrated Biology for Life Sciences, The University of California Lawrence Berkeley National Laboratory, Berkeley, California, 2000 - Present
Director, NSF Computational Center for Macromolecular Structure, The Scripps Institute, La Jolla, CA, 1999 - 2004
Program Leader, Department of Metalloprotein Structure and Design, The Scripps Research Institute, La Jolla, California, 1998 - 2006
Director, Scripps NSF Computational Center for Macromolecular Structure, La Jolla, California, 1992 - 2001
Other Professional Positions
Senior Scientist, The University of California Lawrence Berkeley National Laboratory, Berkeley, California, 2009 - 2015
Assistant Member, The Scripps Research Institute, La Jolla, CA, 1984 - 1990
Staff Fellow, The Scripps Research Institute, La Jolla, CA, 1982 - 1984
Research Associate, Duke University, Department of Biochemistry, La Jolla, CA, 1982 - 1982
Editorial Activities
Editor, PNAS-Proceedings of the National Academy of Sciences of the United States of America, 2022
Editor, PNAS-Proceedings of the National Academy of Sciences of the United States of America, 2020
Editor, NAR Cancer, 2019 - Present
Editor, PNAS-Proceedings of the National Academy of Sciences of the United States of America, 2015
Editor, Current Opinion in Structure Biology, 2015 - Present
Editor, PNAS-Proceedings of the National Academy of Sciences of the United States of America, 2011
Editor, PNAS-Proceedings of the National Academy of Sciences of the United States of America, 2009
Editor, PNAS-Proceedings of the National Academy of Sciences of the United States of America, 2007
Honors & Awards
| 2025 | NCI Outstanding Investigator Award, NCI |
| 2021 | UT MDACC Excellence in Science for EXO5-BLM, UT MD Anderson Cancer Center |
| 2021 | UT MDACC Excellence in Science for MRE11-GRB2 2021, UT MD Anderson Cancer Center |
| 2021 | Cancer Biology, Commended Course |
| 2018 - 2024 | NCI Outstanding Investigator Award, NCI |
| 2015 - 2024 | Chamberlain Mentor, UT MD Anderson Cancer Center |
| 2015 - 2024 | Robert A. Welch Distinguished Chair in Chemistry, UT MD Anderson Cancer Center |
| 2015 - 2024 | CPRIT Scholar in Cancer Biology, UT MD Anderson Cancer Center |
| 2012 - 2024 | Faculty of 1000 Biology, F1000 |
| 1982 - 1984 | Walter Winchell Fellow, The Damon Runyon Cancer Research Foundation |
| 1982 - 1983 | Sigma Xi Award, Sigma X Scientific Research Society |
| 1980 - 1982 | NIH Graduate Assistantship, NIH |
| 1974 | Cystic Fibrosis Award, Cystic Fibrosis Foundation |
Professional Memberships
Selected Presentations & Talks
Formal Peers
- 2022. Metalloenzymes – Structure & Mechanism. Visiting. La Jolla, CA, US.
- 2022. X-ray scattering in structural biology. Visiting. La Jolla, CA, US.
- 2022. Defining Dynamic DNA, Helicase, & Nuclease Structures & Inhibitors for Cancer Biology, Chemistry and Structural Biology Departments. Invited, US.
- 2022. Predictive mechanisms for dynamic multifunctional assemblies Fusion-. Visiting. Cancun, MX.
- 2022. DNA Break Repair Nucleaes and Pathway Choice. Visiting, US.
- 2021. Viral Inhibitors. Visiting, US.
- 2019. Shark Tank. Invited. Galveston, TX, US.
- 2019. Defining Dynamic DNA Repair Structures and Mechanisms for Cancer Biology. Invited. Omaha, NE, US.
- 2019. Defining Dynamic Replication and Repair DNA Damage Response Structures. Invited. Alberta, CA.
- 2019. DNA Repair Structures and Mechanisms for Cancer Biology. Invited. New Brunswick, NJ, US.
- 2018. X-ray scattering in structural biology. Visiting. La Jolla, CA, US.
- 2018. Metalloenzyme structures and mechanisms. Visiting. La Jolla, CA, US.
- 2018. X-ray scattering and structure analyses. Visiting. La Jolla, CA, US.
- 2017. Flap Endonuclease Employs Phosphate Steering to Insure Specific 5' Flap Incision to Prevent Genome Instability. Invited. Jeddah, SA.
- 2016. Metalloenzymes – Structure & Mechanism. Visiting. La Jolla, CA, US.
- 2016. The Rise of DNA Repair Machines: implications for biology and medicine. Invited. St. Louis, MO, US.
- 2015. Mre11-Rad50-Nbs1 functional interactions with ATM and other partners. Invited. Beijing, CN.
- 2015. SAXS with Crystallography for Accurate Structures of Flexible Complexes in Solution. Invited. Upton, NY, US.
- 2014. Developing Hybrid Methods and Hybrid Nanomaterials for Accurate Solution Structures. Invited. Berkeley, CA, US.
- 2014. DNA damage signaling. Invited. Copenhagen, DK.
- 2014. Science Grand Challenges: Complexes 10-year outlook. Invited. San Diego, CA, US.
- 2013. Bridging the gaps from atomic structures to pathways and biological outcomes for DNA damage responses by combined methods. Invited. Taipei, TW.
- 2013. Macromolecular Complexes Coordinating DNA Damage Responses. Invited. Taipei, TW.
- 2012. Report of the wwPDB Small-Angle Scattering Task Force: Data Requirements for Biomolecular Modeling and the PDB Structure. Invited. Piscataway, NJ, US.
- 2011. Dynamic XPD & Mre11-Rad50-Nbs1 DNA repair complexes. Invited. Albany, NY, US.
- 2011. DNA repair complexes as keys to cell biology, cancer initiation & interventions. Invited. Ithaca, NY, US.
- 2010. DNA Repair Machine Structures, Predictive Biology, and Insights for Cancer Interventions. Invited. Cambridge, MA, US.
- 2010. Accurate structures, conformations, and assemblies of macromolecules in solution by high. Invited. Toronto, CA.
- 2009. Small Angle X-ray Scattering (SAXS) combined with crystallography and computation defining accurate macromolecular structures in solution. Invited. Buffalo, NY, US.
- 2005. Protein machines assembled in response to DNA damage employ common elements. Invited. Albany, NY, US.
- 2005. Damaged DNA and Repair Machines: Damage Recognition, Conformational Changes and the Structural Chemistry for DNA Repair Coordination. Invited. San Diego, CA, US.
- 2003. DNA Damage, Mutations, and the Structural Basis for Genome Maintenance by DNA Repair Machines. Invited. Chapel Hill, NC, US.
- 2001. A Unified Structural Biology for DNA Repair: From Proteins to Pathways. Invited. St. Louis, MO, US.
- 1997. Structural Mechanisms for Cell Cycle Control. Invited. Ames, IA, US.
Grant & Contract Support
| Date: | 2025 - 2032 |
| Title: | Mesoscale and Nanoscale Technologies Integrated by Structures for DNA Repair Complexes (MANTIS-DRC) |
| Funding Source: | NIH/NCI |
| Role: | PI |
| ID: | 2R35CA330430 |
| Date: | 2024 - 2026 |
| Title: | A Plug and Play DOE Approach for Emerging Threats: Taskforce 5 |
| Funding Source: | US Department of Energy |
| Role: | Project Leader |
| ID: | 7729733 |
| Date: | 2022 - 2027 |
| Title: | ALS Efficiently Networking Advanced Beam Line Experiments (ALS-ENABLE) |
| Funding Source: | NIH |
| Role: | Co-I |
| ID: | 2P30GM124169 |
| Date: | 2019 - 2025 |
| Title: | Mesocale and Nanoscale Technologies Integrated by Structures for DNA Repair Complexes (MANTIS-DRC) |
| Funding Source: | NIH/NCI |
| Role: | PI |
| ID: | 1R35CA220430 |
| Date: | 2019 - 2022 |
| Title: | BRCA Answers from Cancer Interactome Structures (BACIS) |
| Funding Source: | Cancer Prevention & Research Institute of Texas (CPRIT) |
| Role: | Co-PI |
| ID: | RP180813 |
| Date: | 2019 - 2022 |
| Title: | Reconstitution of Human Nucleotide Excision Repair at the Single Molecule Level |
| Funding Source: | KAUST |
| Role: | PI |
| Date: | 2017 - 2022 |
| Title: | ALS Efficiently Networking Advanced Beam Line Experiments |
| Funding Source: | NIH/NCI |
| Role: | Co-I |
| ID: | 1P30GM124169-01 |
| Date: | 2017 - 2018 |
| Title: | Molecular Characterization and Inhibition of the IncRNA LINP1, a Key Regulator of DNA Repair om Triple Negative Breast Cancer (TNBC) |
| Funding Source: | UTMDCC, Knowledge Gap |
| Role: | PI |
| Date: | 2017 - 2018 |
| Title: | SAXS-based Crystallography of Lysyl Hydroxylase 2, a Metastasis Driver in KRAS-mutant Lung Cancer |
| Funding Source: | UTMDACC, Petrin KRAS Award |
| Role: | Co-I |
| Date: | 2016 - 2022 |
| Title: | Pharmacological Modulation of Poly(ADP-RIBOSE) Metabolism |
| Funding Source: | NIH/NCI |
| Role: | Co-I |
| ID: | 7R01CA200231-02 |
| Date: | 2016 - 2019 |
| Title: | NO TITLE PROVIDED |
| Funding Source: | UT STARS AWARD |
| Role: | PI |
| Date: | 2015 - 2021 |
| Title: | DNA Repair Inhibitors for Cancer Research and Translation |
| Funding Source: | Cancer Prevention & Research Institute of Texas (CPRIT) |
| Role: | PI |
| ID: | Established Investigator Award |
| Date: | 2015 - 2019 |
| Title: | Solving the Paradox of the Structure Specific 5' Nucleases |
| Funding Source: | KAUST |
| Role: | PI |
| Date: | 2012 - 2016 |
| Title: | MINOS (Macromolecular Insights on Nucleic acids Optimized by Scattering) |
| Funding Source: | NIH/NIGMS |
| Role: | PI |
| ID: | 5R01GM105404-04 |
| Date: | 2006 - 2016 |
| Title: | Structural Biology of XPB and XPD Helicases |
| Funding Source: | NIH/NCI |
| Role: | PI |
| ID: | 5R01CA112093-10 |
| Date: | 2005 - 2011 |
| Title: | Molecular Assemblies |
| Funding Source: | Dept of Energy |
| Role: | PI |
| ID: | DE AC02 05CH11231 |
| Date: | 2005 - 2020 |
| Title: | Mre11/Rad50/Nbs1 Structural Biology for DNA Damage Responses |
| Funding Source: | NIH/NCI |
| Role: | PI |
| ID: | 2R01CA117638 |
| Date: | 2004 - 2019 |
| Title: | IDAT - Integrated diffraction analysis technologies |
| Funding Source: | Dept of Energy |
| Role: | PI |
| ID: | DE AC02 05CH11231 |
| Date: | 2004 - 2009 |
| Title: | Structural Biology of RecQ Helicase |
| Funding Source: | NIH/NCI |
| Role: | PI |
| ID: | R01 CA104660 |
| Date: | 2003 - 2014 |
| Title: | Fen-1 Complexes and Human Genome Stability |
| Funding Source: | NIH/NCI |
| Role: | PI |
| ID: | R01 CA81967 |
| Date: | 2003 - 2009 |
| Title: | Metalloprotein Biosensors |
| Funding Source: | NIH/NIAID |
| Role: | PI |
| ID: | R01 AI054945 |
| Date: | 2002 - 2014 |
| Title: | Structural Biochemistry of DNA Dealkylation |
| Funding Source: | NIH/NCI |
| Role: | PI |
| ID: | 3R01CA097209-10S1 |
| Date: | 2001 - 2026 |
| Title: | Structural Cell Biology of DNA Repair Machines (SBDR) |
| Funding Source: | NIH/NCI |
| Role: | PI |
| ID: | 5P01CA092584 |
| Date: | 2000 - 2006 |
| Title: | DNA Repair Complexes |
| Funding Source: | Dept of Energy |
| Role: | PI |
| ID: | DE AC03 76SF00098 |
| Date: | 1999 - 2005 |
| Title: | Computational Center for Macromolecular Structure |
| Funding Source: | National Science Foundation (NSF) |
| Role: | PI |
| ID: | DBI9904559 |
| Date: | 1998 - 2014 |
| Title: | Superoxide Dismutase Structures and Lou Gehrig’s Disease |
| Funding Source: | NIH/NIGMS |
| Role: | PI |
| ID: | GM39345 |
| Date: | 1997 - 2010 |
| Title: | The Structure of Nitric Oxide Synthase Oxygenase Domain and Inhibitor Complexes |
| Funding Source: | NIH/NHLBI |
| Role: | Co-PI |
| ID: | HL58883-03 |
| Date: | 1993 - 2009 |
| Title: | Metalloprotein Structure and Design |
| Funding Source: | NIH/NIGMS |
| Role: | PI |
| ID: | NIH GM |
| Date: | 1991 - 2014 |
| Title: | Structural Biochemistry of DNA Base Excision Repair |
| Funding Source: | NIH/NIGMS |
| Role: | PI |
| ID: | R01 GM46312 |
| Date: | 1985 - 2013 |
| Title: | Type IV Pili & Related Systems |
| Funding Source: | NIH/NIAID |
| Role: | PI |
| ID: | R01 AI22160 |
Selected Publications
Peer-Reviewed Articles
- Charaka, VK, Pandita, RK, Tsai, C, Wang, X, Chakraborty, S, Ramos, K, Nandi, S, Leonard, F, Singh, V, Sarkar, P, Hunt, C, Tainer, J, Das, C, Pandita, TK. HP1β recruits RING1A to ubiquitinate histone H2A for BRCA1-mediated resection of double-stand breaks. iScience 29(2), 2026. e-Pub 2026. PMID: 41623472.
- 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. RNA/DNA-binding protein TDP43 regulates DNA mismatch repair genes with implications for genome stability. Nucleic Acids Res 53(18), 2025. e-Pub 2025. PMID: 40985771.
- 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. APOL2 Stabilizes Ku80 to Confer NHEJ-Mediated Radioresistance in Gastric Cancer. Adv Sci (Weinh) 12(44):e06294, 2025. e-Pub 2025. PMID: 40953331.
- Rambo, RP, Tainer, J. Information theory optimization of signals from small-angle scattering measurements. Biophysical journal 124(15):2511-2522, 2025. e-Pub 2025. PMID: 40581817.
- 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. Huntingtin preserves mitochondrial genome integrity in neurons, which is impaired in Huntington's disease. bioRxiv, 2025. e-Pub 2025. PMID: 40777236.
- 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. BRCA2 C-terminal clamp restructures RAD51 dimers to bind B-DNA for replication fork stability. Mol Cell 85(11):2080-2096.e6, 2025. e-Pub 2025. PMID: 40441151.
- Paul, T, Yan, C, Yu, J, Tsutakawa, SE, Tainer, J, Wang, D, Ivanov, I. Molecular model of TFIIH recruitment to the transcription-coupled repair machinery. Nature communications 16(1), 2025. e-Pub 2025. PMID: 40057514.
- Brosey, CA, Shen, R, Tainer, J. NADH-bound AIF activates the mitochondrial CHCHD4/MIA40 chaperone by a substrate-mimicry mechanism. EMBO Journal 44(4):1220-1248, 2025. e-Pub 2025. PMID: 39806100.
- Ye, Z, Xu, S, Shi, Y, Cheng, X, Zhang, Y, Roy, S, Namjoshi, S, Longo, M, Link, T, Schlacher, K, Peng, G, Yu, D, Wang, B, Tainer, J, Ahmed, Z. GRB2 stabilizes RAD51 at reversed replication forks suppressing genomic instability and innate immunity against cancer. Nature communications 15(1), 2024. e-Pub 2024. PMID: 38459011.
- Filandr, F, Sarpe, V, Raval, S, Crowder, DA, Khan, MF, Douglas, P, Coales, S, Viner, R, Syed, A, Tainer, J, Lees-Miller, SP, Schriemer, DC. Automating data analysis for hydrogen/deuterium exchange mass spectrometry using data-independent acquisition methodology. Nature communications 15(1), 2024. e-Pub 2024. PMID: 38467655.
- Fu, J, Ling, J, Li, CF, Tsai, C, Yin, W, Hou, J, Chen, P, Cao, Y, Kang, Y, Sun, YC, 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, EI, Stambrook, PJ, Huang, P, Fleming, JB, Maitra, A, Tainer, J, Hung, MC, Lin, C, Chiao, PJ. Nardilysin-regulated scission mechanism activates polo-like kinase 3 to suppress the development of pancreatic cancer. Nature communications 15(1), 2024. e-Pub 2024. PMID: 38605037.
- 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. RNA/DNA Binding Protein TDP43 Regulates DNA Mismatch Repair Genes with Implications for Genome Stability. bioRxiv, 2024. e-Pub 2024. PMID: 38798341.
- De-Paula RB, Bacolla A, Syed A, Tainer JA. Enriched G4 forming repeats in the human genome are associated with robust well-coordinated transcription and reduced cancer transcriptome variation. J Biol Chem 300(11):107822, 2024. e-Pub 2024. PMID: 39341500.
- Yu J, Yan C, Paul T, Brewer L, Tsutakawa SE, Tsai CL, Hamdan SM, Tainer JA, Ivanov I. Molecular architecture and functional dynamics of the pre-incision complex in nucleotide excision repair. Nat Commun 15(1):8511, 2024. e-Pub 2024. PMID: 39353945.
- 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. BRCA2 C-terminal clamp restructures RAD51 dimers to bind B-DNA for replication fork stability. bioRxiv, 2024. e-Pub 2024. PMID: 39345573.
- 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. Chromatin remodeler BRG1 recruits huntingtin to repair DNA double-strand breaks in neurons. bioRxiv, 2024. e-Pub 2024. PMID: 39345557.
- Chris A Brosey, Todd M Link, Runze Shen, Davide Moiani, Kathryn Burnett, Greg L Hura, Darin E Jones, Tainer, JA. Chemical screening by time-resolved X-ray scattering to discover allosteric probes. Nat Chem Biol 20(9)(Sept 2024):1199-1209, 2024. e-Pub 2024. PMID: 38671223.
- Chinnam, NB, Thapar, R, Arvai, AS, Sarker, AH, Soll, JM, Paul, T, Syed, A, Rosenberg, D, Hammel, M, Bacolla, A, Katsonis, P, Asthana, A, Tsai, MS, Ivanov, I, Lichtarge, O, Silverman, RH, Mosammaparast, N, Tsutakawa, SE, Tainer, J. ASCC1 structures and bioinformatics reveal a novel helix-clasp-helix RNA-binding motif linked to a two-histidine phosphodiesterase. Journal of Biological Chemistry 300(6), 2024. e-Pub 2024. PMID: 38750793.
- Lee, DY, Huntoon, K, Wang, Y, Kang, M, Lu, Y, Jeong, S, Link, T, Gallup, T, Qie, Y, Li, X, Dong, S, Schrank, BR, Grippin, A, Antony, A, Ha, JH, Chang, M, An, Y, Wang, L, Jiang, D, Li, J, Koong, A, Tainer, J, Jiang, W, Kim, BY. Synthetic cationic helical polypeptides for the stimulation of antitumour innate immune pathways in antigen-presenting cells. Nature Biomedical Engineering 8(5):593-610, 2024. e-Pub 2024. PMID: 38641710.
- 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. The NS1 protein of influenza B virus binds 5'-triphosphorylated dsRNA to suppress RIG-I activation and the host antiviral response. bioRxiv, 2024. e-Pub 2024. PMID: 38328244.
- Moiani D, Tainer JA. A goldilocks computational protocol for inhibitor discovery targeting DNA damage responses including replication-repair functions. Front Mol Biosci 11:1442267, 2024. e-Pub 2024. PMID: 39669672.
- Yu, J, Yan, C, Dodd, T, Tsai, C, Tainer, J, Tsutakawa, SE, Ivanov, I. Dynamic conformational switching underlies TFIIH function in transcription and DNA repair and impacts genetic diseases. Nature communications 14(1), 2023. e-Pub 2023. PMID: 37179334.
- Longo, M, Roy, S, Chen, Y, Tomaszowski, KH, Arvai, AS, Pepper, JT, Boisvert, RA, Kunnimalaiyaan, S, Keshvani, C, Schild, D, Bacolla, A, Williams, GJ, Tainer, J, Schlacher, K. RAD51C-XRCC3 structure and cancer patient mutations define DNA replication roles. Nature communications 14(1), 2023. e-Pub 2023. PMID: 37488098.
- Syed, A, Filandr, F, Patterson-Fortin, J, Bacolla, A, Ravindranathan, R, Zhou, J, McDonald, D, Albuhluli, ME, Verway-Cohen, A, Newman, JA, Tsai, MS, Jones, DE, Schriemer, DC, D’Andrea, AD, Tainer, J. Novobiocin blocks nucleic acid binding to Polθ and inhibits stimulation of its ATPase activity. Nucleic acids research 51(18):9920-9937, 2023. e-Pub 2023. PMID: 37665033.
- Swift, ML, Zhou, R, Syed, A, Moreau, LA, Tomasik, B, Tainer, J, Konstantinopoulos, PA, D’Andrea, AD, He, YJ, Chowdhury, D. Dynamics of the DYNLL1–MRE11 complex regulate DNA end resection and recruitment of Shieldin to DSBs. Nature Structural and Molecular Biology 30(10):1456-1467, 2023. e-Pub 2023. PMID: 37696958.
- Townley, BA, Buerer, L, Tsao, N, Bacolla, A, Mansoori, F, Rusanov, T, Clark, N, Goodarzi, N, Schmidt, N, Srivatsan, SN, Sun, H, Sample, RA, Brickner, JR, McDonald, D, Tsai, MS, Walter, MJ, Wozniak, DF, Holehouse, AS, Pena, V, Tainer, J, Fairbrother, W, Mosammaparast, N. A functional link between lariat debranching enzyme and the intron-binding complex is defective in non-photosensitive trichothiodystrophy. Molecular cell 83(13):2258-2275.e11, 2023. e-Pub 2023. PMID: 37369199.
- LeBleu, V, Dai, J, Tsutakawa, SE, MacDonald, B, Alge, JL, Sund, M, Xie, L, Sugimoto, H, Tainer, J, Zon, LI, Kalluri, R. Identification of unique α4 chain structure and conserved antiangiogenic activity of α3NC1 type IV collagen in zebrafish. Developmental Dynamics 252(7):1046-1060, 2023. e-Pub 2023. PMID: 37002899.
- Zhou R, Swift ML, Syed A, Huang K, Moreau L, Tainer JA, Konstantinopoulos PA, Da Andrea AD, He YJ, Chowdhury D. Dynamics of the DYNLL1/MRE11 complex regulates DNA end resection and recruitment of the Shieldin complex to DSBs. bioRxiv, 2023. e-Pub 2023. PMID: 37034578.
- Das, C, Adhikari, S, Bhattacharya, A, Chakraborty, S, Mondal, P, Yadav, SS, Adhikary, S, Hunt, C, Yadav, KK, Pandita, S, Roy, S, Tainer, J, Ahmed, Z, Pandita, TK. Epigenetic-Metabolic Interplay in the DNA Damage Response and Therapeutic Resistance of Breast Cancer. Cancer Research 83(5):657-666, 2023. e-Pub 2023. PMID: 36661847.
- Bralić, A, Tehseen, M, Sobhy, MA, Tsai, C, Alhudhali, L, Yi, G, Yu, J, Yan, C, Ivanov, I, Tsutakawa, SE, Tainer, J, Hamdan, SM. A scanning-to-incision switch in TFIIH-XPG induced by DNA damage licenses nucleotide excision repair. Nucleic acids research 51(3):1019-1033, 2023. e-Pub 2023. PMID: 36477609.
- Fan, C, Chen, K, Wang, Y, Ball, EV, Stenson, PD, Mort, M, Bacolla, A, Kehrer-Sawatzki, H, Tainer, J, Cooper, DN, Zhao, H. Profiling human pathogenic repeat expansion regions by synergistic and multi-level impacts on molecular connections. Human genetics 142(2):245-274, 2023. e-Pub 2023. PMID: 36344696.
- Fan C, Chen K, Wang Y, Ball EV, Stenson PD, Mort M, Bacolla A, Kehrer-Sawatzki H, Tainer JA, Cooper DN, Zhao H. Profiling human pathogenic repeat expansion regions by synergistic and multi-level impacts on molecular connections. Hum Genet, 2022. e-Pub 2022.
- Kim, M, Kim, HS, D’Souza, A, Gallagher, K, Jeong, E, Topolska-Wós, A, Le Meur, KO, Tsai, C, Tsai, MS, Kee, M, Tainer, J, Yeo, JE, Chazin, WJ, Schärer, OD. Two interaction surfaces between XPA and RPA organize the precision complex in nucleotide excision repair. Proceedings of the National Academy of Sciences of the United States of America 119(34), 2022. e-Pub 2022. PMID: 35969784.
- Kim M, Kim HS, D'Souza A, Gallagher K, Jeong E, Topolska-Wós A, Ogorodnik Le Meur K, Tsai CL, Tsai MS, Kee M, Tainer JA, Yeo JE, Chazin WJ, Schärer OD. Two interaction surfaces between XPA and RPA organize the preincision complex in nucleotide excision repair. Proc Natl Acad Sci U S A 119(34), 2022. e-Pub 2022.
- Yuan X, Duan Y, Xiao Y, Sun K, Qi Y, Zhang Y, Ahmed Z, Moiani D, Yao J, Li H, Zhang L, Yuzhalin AE, Li P, Zhang C, Badu-Nkansah A, Saito Y, Liu X, Kuo WL, Ying H, Sun SC, Chang JC, Tainer JA, Yu D. Vitamin E Enhances Cancer Immunotherapy by Reinvigorating Dendritic Cells via Targeting Checkpoint SHP1. Cancer Discov 12(7):1743-1759, 2022. e-Pub 2022. PMID: 35420681.
- Qi M, Stenson PD, Ball EV, Tainer JA, Bacolla A, Kehrer-Sawatzki H, Cooper DN, Zhao H. Distinct sequence features underlie microdeletions and gross deletions in the human genome. Hum Mutat 43(3):328-346, 2022. e-Pub 2021. PMID: 34918412.
- Berroyer A, Bacolla A, Tainer JA, Kim N. Cleavage-defective Topoisomerase I mutants sharply increase G-quadruplex-associated genomic instability. Microb Cell 9(3):52-68, 2022. e-Pub 2022. PMID: 35291312.
- Qi M, Stenson PD, Ball EV, Tainer JA, Bacolla A, Kehrer-Sawatzki H, Cooper DN, Zhao H. Distinct sequence features underlie microdeletions and gross deletions in the human genome. Distinct sequence features underlie microdeletions and gross deletions in the human genome. Hum Mutat 43(3):328-346, 2022. e-Pub 2022.
- Mondal A, Bhattacharya A, Singh V, Pandita S, Bacolla A, Pandita RK, Tainer JA, Ramos KS, Pandita TK, Das C. Stress Responses as Master Keys to Epigenomic Changes in Transcriptome and Metabolome for Cancer Etiology and Therapeutics. Mol Cell Biol 42(1):e0048321, 2022. e-Pub 2022. PMID: 34748401.
- Bacolla A, Tainer JA. Robust Computational Approaches to Defining Insights on the Interface of DNA Repair with Replication and Transcription in Cancer. Methods Mol Biol 2444:1-13, 2022. e-Pub 2022.
- Chinnam NB, Syed A, Burnett KH, Hura GL, Tainer JA, Tsutakawa SE. Universally Accessible Structural Data on Macromolecular Conformation, Assembly, and Dynamics by Small Angle X-Ray Scattering for DNA Repair Insights. Methods Mol Biol 2444:43-68, 2022. e-Pub 2022.
- Alexander LT, Lepore R, Kryshtafovych A, Adamopoulos A, Alahuhta M, Arvin AM, Bomble YJ, Böttcher B, Breyton C, Chiarini V, Chinnam NB, Chiu W, Fidelis K, Grinter R, Gupta GD, Hartmann MD, Hayes CS, Heidebrecht T, Ilari A, Joachimiak A, Kim Y, Linares R, Lovering AL, Lunin VV, Lupas AN, Makbul C, Michalska K, Moult J, Mukherjee PK, Nutt WS, Oliver SL, Perrakis A, Stols L, Tainer JA, Topf M, Tsutakawa SE, Valdivia-Delgado M, Schwede T. Target highlights in CASP14: Analysis of models by structure providers. Proteins 89(12):1647-1672, 2021. e-Pub 2021. PMID: 34561912.
- Twayana S, Bacolla A, Barreto-Galvez A, De-Paula RB, Drosopoulos WC, Kosiyatrakul ST, Bouhassira EE, Tainer JA, Madireddy A, Schildkraut CL. Translesion polymerase eta both facilitates DNA replication and promotes increased human genetic variation at common fragile sites. Proc Natl Acad Sci U S A 118(48), 2021. e-Pub 2021. PMID: 34815340.
- Tsao N, Brickner JR, Rodell R, Ganguly A, Wood M, Oyeniran C, Ahmad T, Sun H, Bacolla A, Zhang L, Lukinovic V, Soll JM, Townley BA, Casanova AG, Tainer JA, He C, Vindigni A, Reynoird N, Mosammaparast N. Aberrant RNA methylation triggers recruitment of an alkylation repair complex. Mol Cell 81(20):4228-4242.e8, 2021. e-Pub 2021. PMID: 34686315.
- Lees-Miller JP, Cobban A, Katsonis P, Bacolla A, Tsutakawa SE, Hammel M, Meek K, Anderson DW, Lichtarge O, Tainer JA, Lees-Miller SP. Uncovering DNA-PKcs ancient phylogeny, unique sequence motifs and insights for human disease. Prog Biophys Mol Biol S0079-6107(20):30097-3, 2021. e-Pub 2021. PMID: 33035590.
- Wilson DM, Deacon AM, Duncton MAJ, Pellicena P, Georgiadis MM, Yeh AP, Arvai AS, Moiani D, Tainer JA, Das D. Fragment- and structure-based drug discovery for developing therapeutic agents targeting the DNA Damage Response. Prog Biophys Mol Biol S0079-6107(20):30111-5, 2021. e-Pub 2021. PMID: 33115610.
- Nguyen MT, Moiani D, Ahmed Z, Arvai AS, Namjoshi S, Shin DS, Fedorov Y, Selvik EJ, Jones DE, Pink J, Yan Y, Laverty DJ, Nagel ZD, Tainer JA, Gerson SL. An effective human uracil-DNA glycosylase inhibitor targets the open pre-catalytic active site conformation. Prog Biophys Mol Biol 163:143-159, 2021. e-Pub 2021. PMID: 33675849.
- Zhang X, Blundell T, Tainer JA. The renaissance in biophysics and molecular biology enabled by the interface of DNA repair and replication with cancer. Prog Biophys Mol Biol 163:1-4, 2021. e-Pub 2021. PMID: 33798567.
- Rashid I, Hammel M, Sverzhinsky A, Tsai MS, Pascal JM, Tainer JA, Tomkinson AE. Direct interaction of DNA repair protein tyrosyl DNA phosphodiesterase 1 and the DNA ligase III catalytic domain is regulated by phosphorylation of its flexible N-terminus. J Biol Chem 297(2):100921, 2021. e-Pub 2021. PMID: 34181949.
- Ye Z, Xu S, Shi Y, Bacolla A, Syed A, Moiani D, Tsai CL, Shen Q, Peng G, Leonard PG, Jones DE, Wang B, Tainer JA, Ahmed Z. GRB2 enforces homology-directed repair initiation by MRE11. Sci Adv 7(32), 2021. e-Pub 2021. PMID: 34348893.
- Hammel M, Rosenberg DJ, Bierma J, Hura GL, Thapar R, Lees-Miller SP, Tainer JA. Visualizing functional dynamicity in the DNA-dependent protein kinase holoenzyme DNA-PK complex by integrating SAXS with cryo-EM. Prog Biophys Mol Biol S0079-6107(20):30091-2, 2021. e-Pub 2021. PMID: 32966823.
- Brosey CA, Houl JH, Katsonis P, Balapiti-Modarage LPF, Bommagani S, Arvai A, Moiani D, Bacolla A, Link T, Warden LS, Lichtarge O, Jones DE, Ahmed Z, Tainer JA. Targeting SARS-CoV-2 Nsp3 macrodomain structure with insights from human poly(ADP-ribose) glycohydrolase (PARG) structures with inhibitors. Prog Biophys Mol Biol 163:171-186, 2021. e-Pub 2021. PMID: 33636189.
- Hambarde S, Tsai CL, Pandita RK, Bacolla A, Maitra A, Charaka V, Hunt CR, Kumar R, Limbo O, Le Meur R, Chazin WJ, Tsutakawa SE, Russell P, Schlacher K, Pandita TK, Tainer JA. EXO5-DNA structure and BLM interactions direct DNA resection critical for ATR-dependent replication restart. Mol Cell 81(14):2989-3006.e9, 2021. e-Pub 2021. PMID: 34197737.
- Banday S, Pandita RK, Mushtaq A, Bacolla A, Mir US, Singh DK, Jan S, Bhat KP, Hunt CR, Rao G, Charaka VK, Tainer JA, Pandita TK, Altaf M. Autism-Associated Vigilin Depletion Impairs DNA Damage Repair. Mol Cell Biol 41(7):e0008221, 2021. e-Pub 2021. PMID: 33941620.
- Zhou J, Gelot C, Pantelidou C, Li A, Yücel H, Davis RE, Farkkila A, Kochupurakkal B, Syed A, Shapiro GI, Tainer JA, Blagg BSJ, Ceccaldi R, D'Andrea AD. A first-in-class Polymerase Theta Inhibitor selectively targets Homologous-Recombination-Deficient Tumors. Nat Cancer 2(6):598-610, 2021. e-Pub 2021. PMID: 34179826.
- Guo HF, Bota-Rabassedas N, Terajima M, Leticia Rodriguez B, Gibbons DL, Chen Y, Banerjee P, Tsai CL, Tan X, Liu X, Yu J, Tokmina-Roszyk M, Stawikowska R, Fields GB, Miller MD, Wang X, Lee J, Dalby KN, Creighton CJ, Phillips GN, Tainer JA, Yamauchi M, Kurie JM. A collagen glucosyltransferase drives lung adenocarcinoma progression in mice. Commun Biol 4(1):482, 2021. e-Pub 2021. PMID: 33875777.
- Walker RG, Kattamuri C, Goebel EJ, Zhang F, Hammel M, Tainer JA, Linhardt RJ, Thompson TB. Heparin-mediated dimerization of follistatin. Exp Biol Med (Maywood) 246(4):467-482, 2021. e-Pub 2021. PMID: 33197333.
- Hammel M, Rashid I, Sverzhinsky A, Pourfarjam Y, Tsai MS, Ellenberger T, Pascal JM, Kim IK, Tainer JA, Tomkinson AE. An atypical BRCT-BRCT interaction with the XRCC1 scaffold protein compacts human DNA Ligase IIIα within a flexible DNA repair complex. Nucleic Acids Res 49(1):306-321, 2021. e-Pub 2021. PMID: 33330937.
Review Articles
- Tainer, J, Tsutakawa, SE. RNA sculpting by the primordial Helix-clasp-Helix–Strand-Loop (HcH–SL) motif enforces chemical recognition enabling diverse KH domain functions. Journal of Biological Chemistry 301(5), 2025. e-Pub 2025. PMID: 40185232.
- Bhat, A, Bhan, S, Kabiraj, A, Pandita, RK, Ramos, K, Nandi, S, Sopori, S, Sarkar, PS, Dhar, A, Pandita, S, Kumar, R, Das, C, Tainer, J, Pandita, TK. A predictive chromatin architecture nexus regulates transcription and DNA damage repair. Journal of Biological Chemistry 301(3), 2025. e-Pub 2025. PMID: 39947477.
- Das, C, Bhattacharya, A, Adhikari, S, Mondal, A, Mondal, P, Adhikary, S, Roy, S, Ramos, K, Yadav, KK, Tainer, J, Pandita, TK. A prismatic view of the epigenetic-metabolic regulatory axis in breast cancer therapy resistance. Oncogene 43(23):1727-1741, 2024. e-Pub 2024. PMID: 38719949.
- Hammel M, Tainer JA. X-ray scattering reveals disordered linkers and dynamic interfaces in complexes and mechanisms for DNA double-strand break repair impacting cell and cancer biology. Protein Sci 30(9):1735-1756, 2021. e-Pub 2021. PMID: 34056803.
Other Articles
- Filandr, F, Sarpe, V, Raval, S, Crowder, DA, Khan, MF, Douglas, P, Coales, S, Viner, R, Syed, A, Tainer, J, Lees-Miller, SP, Schriemer, DC Correction to. Nature communications 15(1), 2024. PMID: 38565885.
- Thapar, R, Wang, JL, Hammel, M, Ye, R, Liang, K, Sun, C, Hnizda, A, Liang, S, Maw, SS, Lee, L, Villarreal, H, Forrester, I, Fang, S, Tsai, MS, Blundell, TL, Davis, AJ, Lin, C, Lees-Miller, SP, Strick, TR, Tainer, J Erratum. Nucleic acids research 49(2):1199-1200, 2021. PMID: 33337499.
Editorials
- Tainer JA. Preface. Methods Enzymol 678:xv-xix, 2023. PMID: 36641219.
Patents
- DNA glycosylases and their use. Patent Number: 6,713,294.
- Metal binding proteins. Patent Number: 5,665,865.
- DNA glycosylases and their use II. Patent Number: 7,662,601 B2.
Patient Reviews
CV information above last modified March 12, 2026