Selected Publications

Peer-Reviewed Articles

1. 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.
2. 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.
3. 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 2020. PMID: 32966823.
4. 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.
5. 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.
6. 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.
7. 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.
8. Bacolla A, Sengupta S, Ye Z, Yang C, Mitra J, De-Paula RB, Hegde ML, Ahmed Z, Mort M, Cooper DN, Mitra S, Tainer JA. Heritable pattern of oxidized DNA base repair coincides with pre-targeting of repair complexes to open chromatin. Nucleic Acids Res 49(1):221-243, 2021. PMID: 33300026.
9. Ye Z, Shi Y, Lees-Miller SP, Tainer JA. Function and Molecular Mechanism of the DNA Damage Response in Immunity and Cancer Immunotherapy. Front Immunol 12:797880, 2021. e-Pub 2021. PMID: 34970273.
10. Tsutakawa SE, Bacolla A, Katsonis P, Bralic A, Hamdan SM, Lichtarge O, Tainer JA, Tsai CL. Decoding Cancer Variants of Unknown Significance for Helicase-Nuclease-RPA Complexes Orchestrating DNA Repair During Transcription and Replication. Front Mol Biosci 8:791792, 2021. e-Pub 2021. PMID: 34966786.
11. Moiani D, Link TM, Brosey CA, Katsonis P, Lichtarge O, Kim Y, Joachimiak A, Ma Z, Kim IK, Ahmed Z, Jones DE, Tsutakawa SE, Tainer JA. An efficient chemical screening method for structure-based inhibitors to nucleic acid enzymes targeting the DNA repair-replication interface and SARS CoV-2. Methods Enzymol 661:407-431, 2021. e-Pub 2021. PMID: 34776222.
12. 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 JA. Mechanism Of Efficient Double-Strand Break Repair By a Long Non-Coding RNA. Nucleic Acids Res 48(19):10953-10972, 2020. PMID: 33045735.
13. Hou J, Zhao R, Xia W, Chang CW, You Y, Hsu JM, Nie L, Chen Y, Wang YC, Liu C, Wang WJ, Wu Y, Ke B, Hsu JL, Huang K, Ye Z, Yang Y, Xia X, Li Y, Li CW, Shao B, Tainer JA, Hung MC. PD-L1-mediated gasdermin C expression switches apoptosis to pyroptosis in cancer cells and facilitates tumour necrosis. Nat Cell Biol 22(10):1264-1275, 2020. e-Pub 2020. PMID: 32929201.
14. Eckelmann BJ, Bacolla A, Wang H, Ye Z, Guerrero EN, Jiang W, El-Zein R, Hegde ML, Tomkinson AE, Tainer JA, Mitra S. XRCC1 promotes replication restart, nascent fork degradation and mutagenic DNA repair in BRCA2-deficient cells. NAR Cancer 2(3):zcaa013, 2020. e-Pub 2020. PMID: 32776008.
15. Tsutakawa SE, Sarker AH, Ng C, Arvai AS, Shin DS, Shih B, Jiang S, Thwin AC, Tsai MS, Willcox A, Her MZ, Trego KS, Raetz AG, Rosenberg D, Bacolla A, Hammel M, Griffith JD, Cooper PK, Tainer JA. Human XPG nuclease structure, assembly, and activities with insights for neurodegeneration and cancer from pathogenic mutations. Proc Natl Acad Sci U S A 117(25):14127-14138, 2020. e-Pub 2020. PMID: 32522879.
16. Houl JH, Ye Z, Brosey CA, Balapiti-Modarage LPF, Namjoshi S, Bacolla A, Laverty D, Walker BL, Pourfarjam Y, Warden LS, Babu Chinnam N, Moiani D, Stegeman RA, Chen MK, Hung MC, Nagel ZD, Ellenberger T, Kim IK, Jones DE, Ahmed Z, Tainer JA. Selective small molecule PARG inhibitor causes replication fork stalling and cancer cell death. Nat Commun 10(1):5654, 2019. e-Pub 2019. PMID: 31827085.
17. Shibata A, Moiani D, Arvai AS, Perry J, Harding SM, Genois MM, Maity R, van Rossum-Fikkert S, Kertokalio A, Romoli F, Ismail A, Ismalaj E, Petricci E, Neale MJ, Bristow RG, Masson JY, Wyman C, Jeggo PA, Tainer JA. DNA double-strand break repair pathway choice is directed by distinct MRE11 nuclease activities. Mol Cell 53(1):7-18, 2014. e-Pub 2013. PMID: 24316220.
18. Rambo RP, Tainer JA. Accurate assessment of mass, models and resolution by small-angle scattering. Nature 496(7446):477-81, 2013. PMID: 23619693.
19. 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. e-Pub 2022. PMID: 35420681.

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