Peer-reviewed Papers (undergraduate students are indicated in white)


  1. 42.Kathleen M.Urrutia, Yu Hsuan Chen, Jin Tang, Ta I Hung, Guodong Zhang, Wenyan Xu, Wenxin Zhao, Dylan Tonthat, Chia-en Chang and Linlin Zhao*, DNA Sequence and Lesion-Dependent Mitochondrial Transcription Factor A (TFAM)-DNA Binding Modulates DNA Repair Activities and Products, Nucleic Acids Res, 2024, gkae1144


  1. 41.Wenxin Zhao, Adil S. Hussen, Bret Freudenthal, Zucai Suo and Linlin Zhao*, Mitochondrial transcription factor A (TFAM) has 5’-deoxyribose phosphate lyase activity in vitro, DNA Repair, 2024


  1. 40.Chaoxing Liu, Brandon Le, Wenyan Xu, Ching-Hsin Yang, Yu Hsuan Chen and Linlin Zhao*, Dual chemical labeling enables nucleotide-resolution mapping of DNA abasic sites and common alkylation damage in human mitochondrial DNA,  Nucleic Acids Res, 2023, 51, e73.


  1. 39.Rebecca Hernandez, Junchao Shi, Jingwei Liu, Xiuchun Li, Jake Wu, Linlin Zhao, Tong Zhou, Qi Chen, Changcheng Zhou,  PANDORA-Seq unveils the hidden small noncoding RNA landscape in atherosclerosis of LDL receptor-deficient mice,  J. Lipid Res, 2023, 64, 100352.


  1. 38.Wenxin Zhao, Wenyan Xu, Jin Tang, Shivansh Kaushik, Chia-En A. Chang, Linlin Zhao*, Key amino acid residues of mitochondrial transcription factor A synergize with abasic (AP) site dynamics to facilitate AP-lyase reactions, ACS Chem. Biol. 2023, 18, 5, 1168–1179.


  1. 37.Wenyan Xu, Jin Tang, Linlin Zhao*, DNA-protein cross-links between abasic DNA damage and mitochondrial transcription factor A (TFAM), Nucleic Acids Res, 2023, 1, 41-53.


  1. 36.Wenyan Xu, Linlin Zhao*, An enzyme-linked immunosorbent assay for the detection of mitochondrial DNA-protein cross-links from mammalian cells, DNA, 2022, 2, 264-278.


  1. 35.Jin Tang, Feng Tang, Linlin Zhao*, Facile preparation of model DNA interstrand cross-link repair intermediates using ribonucleotide-containing DNA, DNA Repair, 2022, 111, 103286.


  1. 34.Jin Tang, Linlin Zhao*, Preparation of DNA interstrand cross-link repair intermediates induced by abasic sites, MethodsX, 9, 101687


  1. 33.Kathleen M.Urrutia, Wenyan Xu, Linlin Zhao*,  The 5′-phosphate enhances the DNA-binding and exonuclease activities of human mitochondrial genome maintenance nuclease 1 (MGME1) J. Biol. Chem. 2022, 289, 102306.


  1. 32.Jin Tang, Wenxin Zhao, Nathan G. Hendricks, Linlin Zhao*,  High-Resolution Mapping of Amino Acid Residues in DNA-Protein Cross-Links Enabled by Ribonucleotide-Containing DNA Anal. Chem. 2021, 93, 13398-13406.


  1. 31.Junchao Shi, Yunfang Zhang, Dongmei Tan, Xudong Zhang, Menghong Yan, Ying Zhang, Reuben Franklin, Marta Shahbazi, Kirsty Mackinlay, Shichao Liu, Bernhard Kuhle, Emma R. James, Liwen Zhang, Yongcun Qu, Qiwei Zhai, Wenxin Zhao, Linlin Zhao, Changcheng Zhou, Weifeng Gu, Jernej Murn, Jingtao Guo, Douglas T. Carrell, Yinsheng Wang, Xuemei Chen, Bradley R. Cairns, Xiang-lei Yang, Paul Schimmel, Magdalena Zernicka-Goetz, Sihem Cheloufi*, Ying Zhang*, Tong Zhou*, Qi Chen*, PANDORA-seq expands the repertoire of regulatory small RNAs by overcoming RNA modifications, Nat. Cell Biol. 2021, 23, 424-436.


  1. 30.Krystie Chew; Linlin Zhao*, Interactions of mitochondrial transcription factor A with DNA damage: mechanistic insights and functional implications, Genes, 2021, 12(8), 1246.


  1. 29.Jacob L. Perkins, Linlin Zhao*, The N-terminal domain of uracil-DNA glycosylase: Roles for disordered regions, DNA Repair, 2021, 103077


  1. 28.Linlin Zhao, Sumberaz, Phlip, Mitochondrial DNA damage: Prevalence, biological consequence and emerging pathways, Chem. Res. Toxicol. 2020, 33, 10, 2491-2502.


  1. 27.Wenyan Xu, Riley M. Boyd; Maya O. Tree , Faris Samkari; Linlin Zhao*, Mitochondrial transcription factor A promotes DNA strand cleavage at abasic sites, PNAS. 2019, 116, 17792-17799.


  1. 26.Zhao, L*, Mitochondrial DNA degradation: A quality control measure for mitochondrial genome maintenance and stress response, The Enzymes. 2019, 45, 311-341.


  1. 25.Xu W, Zhao W; Morehouse, N; Tree MO, Zhao, L*, Divalent cations alter the rate-limiting step of PrimPol-catalyzed DNA elongation, J Mol. Biol. 2019, 431, 673-686.


  1. 24.Yockey OP; Jha V; Ghodke PP; Xu, T; Xu, W; Ling, H; Pradeepkumar, PI; Zhao L* Mechanism of error-free DNA replication past lucidin-derived DNA damage by human DNA polymerase κ, Chem. Res. Toxicol. 2017, 30, 2023-2032.


  1. 23.Zhao, L*; Washington MT Translesion synthesis: insights into the selection and switching of DNA polymerases, Genes, 2017, 8, 24.


  1. 22.Xu, W; Kool, D; O’Flaherty, DK; Keating AM; Sacre L; Egli, M; Noronha A; Wilds, CJ; Zhao, L* O6-2’-deoxyguanosine-butylene-O6-2’-deoxyguanosine DNA interstrand cross-links are replication-blocking and mutagenic DNA lesions, Chem. Res. Toxicol. 2016, 29, 1872-1882.


  1. 22.Xu, W; Ouellette AM; Ghosh S; O’Neil TC; Greenberg MM; Zhao, L* Mutagenic bypass of an oxidized abasic lesion-induced DNA interstrand cross-link analogue by human translesion synthesis DNA polymerases. Biochemistry, 2015, 54, 7409-7422.


  1. 20.Xu, W; Ouellette AM; Wawrzak, Z; Shriver S; Anderson, SM; Zhao, L* Kinetic and structural mechanisms of (5’S)-8,5’-cyclo-2’-deoxyguanosine-induced DNA replication stalling. Biochemistry, 2015, 54, 639-651.


  1. 19.Zhao, L*; Pence, M; Eoff, R; Yuan S; Fercu, C; Guengerich, FP*. Elucidation of kinetic mechanisms of human tranlesion DNA polymerase kappa using tryptophan mutants. FEBS J, 2014, 281, 4394–4410.

 

Peer-reviewed Papers


  1. 17.Chang, SC; Fedeles, BI; Wu, J; Delaney, JC; Li, D; Zhao, L; Christov, PP; Yau, E; Singh, V; Jost, M; Drennan, C; Marnett, LJ; Rizzo, CJ; Levine, SS; Guengerich, FP; Essigmann, JM. Next-generation sequencing reveals the biological significance of the N2,3-ethenoguanine lesion in vivo. Nucl. Acids Res. 2015, 43, 5489-5500. (NAR Breakthrough Article)


  1. 16.Guengerich FP; Zhao, L; Pence, MG; Egli M, Structure and function of the translesion DNA polymerases and interactions with damaged DNA. Perspect. Sci., 2015, 4, 24-31.


  1. 15.Maddukuri, L; Shuck, SC; Eoff, RL; Zhao, L; Rizzo, CJ; Guengerich, FP; Marnett, LJ. N6-Oxopropenyl-2'-deoxyadenosine bypass by Y-family human DNA polymerases eta, kappa and iota, Biochemistry, 2013, 52, 8766–8776.


  1. 14.Pan, S; Li, D; Zhao, L; Schenkman, JB; Rusling, JF. Genotoxicity-related chemistry of human metabolites of benzo[ghi]perylene (B[ghi]P) investigated using electro-optical arrays and DNA/microsome biocolloid reactors with LC-MS/MS, Chem. Res. Toxicol. 2013, 26, 1229–1239. 


  1. 13.Patra A; Harp J; Pallan, PS; Zhao, L; Herdewijn, P; Egli, M. Structure, stability and function of 5-chlorouracil modified G:U and A:U base pairs, Nucleic Acids Res. 2013, 41, 2689-2697.


  1. 12.Zhao, L; Pence, MG; Christov, PP; Wawrzak, Z; Choi, JY; Rizzo, CJ; Egli, M; Guengerich, FP. Basis of miscoding of the DNA adduct N2,3-ethenoguanine by human Y-family DNA polymerases, J. Biol. Chem., 2012, 287, 33516-33526. (FEATURED ON THE COVER)


  1. 11.Zhao, L; Christov, PP; Kozekov, ID; Pence, MG; Pallan, PS; Rizzo, CJ; Egli, M; Guengerich, FP. Replication of N2,3-ethenoguanine by DNA polymerases, Angew. Chem. Int. Ed., 2012, 51, 5466-5469.


  1. 10.Pan, S; Zhao, L; Rusling, JF. Evaluation of electrochemiluminescent metabolic toxicity screening arrays using a multiple compound set, Anal. Chem. 2011, 83, 2754-2760.


  1. 9.Krishnan, S; Wasalathanthri, D; Zhao, L; Schenkman, JB; Rusling, JF. Efficient bioelectronic actuation of the natural catalytic pathway of human metabolic cytochrome P450s, J. Am. Chem. Soc. 2011, 133, 1459–1465.


  1. 8.Zhao, L; Schenkman JB; Rusling, JF. High throughput genotoxicity screening using magnetic bioreactors with LC-MS/MS, Anal. Chem., 2010, 82, 10172-10178.


  1. 7.Zhao, L; Schenkman JB; Rusling, J. F. Screening for reactive metabolites using electro-optical arrays featuring human liver cytosol and microsomal enzyme sources and DNA, Chem. Comm., 2009, 5386-5388. (HIGHLIGHTED AS  HOT ARTICLE)


  1. 6.Zhao, L; Krishnan, S; Zhang, Y; Schenkman, JB; Rusling, JF.  Differences in metabolite-mediated toxicity of tamoxifen in rodents versus humans elucidated with DNA/microsome electro-optical arrays and nanoreactors, Chem. Res. Toxicol. 2009, 22, 341-347.


  1. 5.Bajrami, B; Zhao, L; Schenkman, JB; Rusling, JF. Rapid LC-MS drug metabolite profiling using enzyme bioreactors in a parallel processing format, Anal. Chem., 2009, 81, 9921-9929.


  1. 4.Benbow, EM; Kelly, SP; Zhao, L.; Reutenauer, JW; Suib, SL. Oxygen reduction properties of bifunctional α-manganese oxide electrocatalysts in aqueous and organic electrolytes, J. Phys. Chem. C, 2011, 115, 22009–22017.


  1. 3.Liu, Z; Xing, Y; Chen, C; Zhao, L; Suib, SL. Framework doping of indium in manganese oxide materials: synthesis, characterization, and electrocatalytic reduction of oxygen, Chem. Mater., 2008, 20, 2069-2071.


  1. 2.Xu, L; Ding, Y; Chen, C; Zhao, L; Rimkus, C; Joesten, R; Suib, SL. 3D flowerlike alpha-nickel hydroxide with enhanced electrochemical activity synthesized by microwave-assisted hydrothermal method, Chem. Mater., 2008, 20, 308-316. 


Book Chapters


  1. 1.Zhao, L; Bajrami, B; Rusling, JF. Rapid LC-MS drug metabolite profiling using bioreactor particles, Cytochrome P450 Protocols 3rd edition, for Methods in Molecular Biology Series. Editors: Ian R. Phillips, Paul Ortiz de Montellano, Elizabeth Shephard. Humana. 2013, 129-134.

 

Ph.D. and postdoctoral training

Copyright 2013-2022 Zhao Lab | Contact: linlin.zhao@ucr.edu

Independent career

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Edited Books


18. The Enzymes: DNA Repair. Edited by Linlin Zhao, Laurie S. Kaguni, Elsevier, 2019