Articles - 5dfh mentioned but not cited (1)
- Capturing snapshots of APE1 processing DNA damage. Freudenthal BD, Beard WA, Cuneo MJ, Dyrkheeva NS, Wilson SH. Nat Struct Mol Biol 22 924-931 (2015)
Reviews citing this publication (11)
- Base excision repair of oxidative DNA damage: from mechanism to disease. Whitaker AM, Schaich MA, Smith MR, Flynn TS, Freudenthal BD. Front Biosci (Landmark Ed) 22 1493-1522 (2017)
- Eukaryotic Base Excision Repair: New Approaches Shine Light on Mechanism. Beard WA, Horton JK, Prasad R, Wilson SH. Annu Rev Biochem 88 137-162 (2019)
- APE1: A skilled nucleic acid surgeon. Whitaker AM, Freudenthal BD. DNA Repair (Amst) 71 93-100 (2018)
- The involvement of nucleotide excision repair proteins in the removal of oxidative DNA damage. Kumar N, Raja S, Van Houten B. Nucleic Acids Res 48 11227-11243 (2020)
- Functions of the major abasic endonuclease (APE1) in cell viability and genotoxin resistance. McNeill DR, Whitaker AM, Stark WJ, Illuzzi JL, McKinnon PJ, Freudenthal BD, Wilson DM. Mutagenesis 35 27-38 (2020)
- Molecular Mechanisms Regulating the DNA Repair Protein APE1: A Focus on Its Flexible N-Terminal Tail Domain. López DJ, Rodríguez JA, Bañuelos S. Int J Mol Sci 22 6308 (2021)
- XRCC1 - Strategies for coordinating and assembling a versatile DNA damage response. London RE. DNA Repair (Amst) 93 102917 (2020)
- Understanding APE1 cellular functions by the structural preference of exonuclease activities. Liu TC, Guo KW, Chu JW, Hsiao YY. Comput Struct Biotechnol J 19 3682-3691 (2021)
- Obstacles and opportunities for base excision repair in chromatin. Biechele-Speziale DJ, Sutton TB, Delaney S. DNA Repair (Amst) 116 103345 (2022)
- Not making the cut: Techniques to prevent RNA cleavage in structural studies of RNase-RNA complexes. Jones SP, Goossen C, Lewis SD, Delaney AM, Gleghorn ML. J Struct Biol X 6 100066 (2022)
- Nucleophosmin Plays a Role in Repairing DNA Damage and Is a Target for Cancer Treatment. Sekhar KR, Freeman ML. Cancer Res 83 1573-1580 (2023)
Articles citing this publication (64)
- Oxidative DNA damage is epigenetic by regulating gene transcription via base excision repair. Fleming AM, Ding Y, Burrows CJ. Proc Natl Acad Sci U S A 114 2604-2609 (2017)
- Dynamic basis for dG•dT misincorporation via tautomerization and ionization. Kimsey IJ, Szymanski ES, Zahurancik WJ, Shakya A, Xue Y, Chu CC, Sathyamoorthy B, Suo Z, Al-Hashimi HM. Nature 554 195-201 (2018)
- PARP1 changes from three-dimensional DNA damage searching to one-dimensional diffusion after auto-PARylation or in the presence of APE1. Liu L, Kong M, Gassman NR, Freudenthal BD, Prasad R, Zhen S, Watkins SC, Wilson SH, Van Houten B. Nucleic Acids Res 45 12834-12847 (2017)
- Molecular snapshots of APE1 proofreading mismatches and removing DNA damage. Whitaker AM, Flynn TS, Freudenthal BD. Nat Commun 9 399 (2018)
- Damage sensor role of UV-DDB during base excision repair. Jang S, Kumar N, Beckwitt EC, Kong M, Fouquerel E, Rapić-Otrin V, Prasad R, Watkins SC, Khuu C, Majumdar C, David SS, Wilson SH, Bruchez MP, Opresko PL, Van Houten B. Nat Struct Mol Biol 26 695-703 (2019)
- Abasic and oxidized ribonucleotides embedded in DNA are processed by human APE1 and not by RNase H2. Malfatti MC, Balachander S, Antoniali G, Koh KD, Saint-Pierre C, Gasparutto D, Chon H, Crouch RJ, Storici F, Tell G. Nucleic Acids Res 45 11193-11212 (2017)
- APE1 senses DNA single-strand breaks for repair and signaling. Lin Y, Raj J, Li J, Ha A, Hossain MA, Richardson C, Mukherjee P, Yan S. Nucleic Acids Res 48 1925-1940 (2020)
- Direct NMR Evidence that Transient Tautomeric and Anionic States in dG·dT Form Watson-Crick-like Base Pairs. Szymanski ES, Kimsey IJ, Al-Hashimi HM. J Am Chem Soc 139 4326-4329 (2017)
- Effects of mono- and divalent metal ions on DNA binding and catalysis of human apurinic/apyrimidinic endonuclease 1. Miroshnikova AD, Kuznetsova AA, Vorobjev YN, Kuznetsov NA, Fedorova OS. Mol Biosyst 12 1527-1539 (2016)
- Small-molecule inhibition of APE1 induces apoptosis, pyroptosis, and necroptosis in non-small cell lung cancer. Long K, Gu L, Li L, Zhang Z, Li E, Zhang Y, He L, Pan F, Guo Z, Hu Z. Cell Death Dis 12 503 (2021)
- Correlation of bistranded clustered abasic DNA lesion processing with structural and dynamic DNA helix distortion. Bignon E, Gattuso H, Morell C, Dehez F, Georgakilas AG, Monari A, Dumont E. Nucleic Acids Res 44 8588-8599 (2016)
- Human Apurinic/Apyrimidinic Endonuclease (APE1) Is Acetylated at DNA Damage Sites in Chromatin, and Acetylation Modulates Its DNA Repair Activity. Roychoudhury S, Nath S, Song H, Hegde ML, Bellot LJ, Mantha AK, Sengupta S, Ray S, Natarajan A, Bhakat KK. Mol Cell Biol 37 e00401-16 (2017)
- Human AP-endonuclease (Ape1) activity on telomeric G4 structures is modulated by acetylatable lysine residues in the N-terminal sequence. Burra S, Marasco D, Malfatti MC, Antoniali G, Virgilio A, Esposito V, Demple B, Galeone A, Tell G. DNA Repair (Amst) 73 129-143 (2019)
- Oxidative stress-mediated epigenetic regulation by G-quadruplexes. Fleming AM, Burrows CJ. NAR Cancer 3 zcab038 (2021)
- Reversal of DNA damage induced Topoisomerase 2 DNA-protein crosslinks by Tdp2. Schellenberg MJ, Perera L, Strom CN, Waters CA, Monian B, Appel CD, Vilas CK, Williams JG, Ramsden DA, Williams RS. Nucleic Acids Res 44 3829-3844 (2016)
- DNA Repair Molecular Beacon assay: a platform for real-time functional analysis of cellular DNA repair capacity. Li J, Svilar D, McClellan S, Kim JH, Ahn EE, Vens C, Wilson DM, Sobol RW. Oncotarget 9 31719-31743 (2018)
- Substrate specificity of human apurinic/apyrimidinic endonuclease APE1 in the nucleotide incision repair pathway. Kuznetsova AA, Matveeva AG, Milov AD, Vorobjev YN, Dzuba SA, Fedorova OS, Kuznetsov NA. Nucleic Acids Res 46 11454-11465 (2018)
- APE1 distinguishes DNA substrates in exonucleolytic cleavage by induced space-filling. Liu TC, Lin CT, Chang KC, Guo KW, Wang S, Chu JW, Hsiao YY. Nat Commun 12 601 (2021)
- The structure of human Nocturnin reveals a conserved ribonuclease domain that represses target transcript translation and abundance in cells. Abshire ET, Chasseur J, Bohn JA, Del Rizzo PA, Freddolino PL, Goldstrohm AC, Trievel RC. Nucleic Acids Res 46 6257-6270 (2018)
- AP-endonuclease 1 sculpts DNA through an anchoring tyrosine residue on the DNA intercalating loop. Hoitsma NM, Whitaker AM, Beckwitt EC, Jang S, Agarwal PK, Van Houten B, Freudenthal BD. Nucleic Acids Res 48 7345-7355 (2020)
- RNA abasic sites in yeast and human cells. Liu Y, Rodriguez Y, Ross RL, Zhao R, Watts JA, Grunseich C, Bruzel A, Li D, Burdick JT, Prasad R, Crouch RJ, Limbach PA, Wilson SH, Cheung VG. Proc Natl Acad Sci U S A 117 20689-20695 (2020)
- Activity of Human Apurinic/Apyrimidinic Endonuclease APE1 Toward Damaged DNA and Native RNA With Non-canonical Structures. Davletgildeeva AT, Kuznetsova AA, Fedorova OS, Kuznetsov NA. Front Cell Dev Biol 8 590848 (2020)
- Nucleotide excision repair of abasic DNA lesions. Kitsera N, Rodriguez-Alvarez M, Emmert S, Carell T, Khobta A. Nucleic Acids Res 47 8537-8547 (2019)
- Molecular and structural characterization of disease-associated APE1 polymorphisms. Whitaker AM, Stark WJ, Flynn TS, Freudenthal BD. DNA Repair (Amst) 91-92 102867 (2020)
- Crystal Structure of Human Nocturnin Catalytic Domain. Estrella MA, Du J, Korennykh A. Sci Rep 8 16294 (2018)
- Crystal structure and functional properties of the human CCR4-CAF1 deadenylase complex. Chen Y, Khazina E, Izaurralde E, Weichenrieder O. Nucleic Acids Res 49 6489-6510 (2021)
- Inferring joint sequence-structural determinants of protein functional specificity. Neuwald AF, Aravind L, Altschul SF. Elife 7 e29880 (2018)
- Binding of AP endonuclease-1 to G-quadruplex DNA depends on the N-terminal domain, Mg2+ and ionic strength. Fleming AM, Manage SAH, Burrows CJ. ACS Bio Med Chem Au 1 44-56 (2021)
- The Role of Active-Site Plasticity in Damaged-Nucleotide Recognition by Human Apurinic/Apyrimidinic Endonuclease APE1. Bulygin AA, Kuznetsova AA, Vorobjev YN, Fedorova OS, A Kuznetsov N. Molecules 25 E3940 (2020)
- Environmental Effects on Guanine-Thymine Mispair Tautomerization Explored with Quantum Mechanical/Molecular Mechanical Free Energy Simulations. Li P, Rangadurai A, Al-Hashimi HM, Hammes-Schiffer S. J Am Chem Soc 142 11183-11191 (2020)
- Shining light on the response to repair intermediates in DNA of living cells. Janoshazi AK, Horton JK, Zhao ML, Prasad R, Scappini EL, Tucker CJ, Wilson SH. DNA Repair (Amst) 85 102749 (2020)
- Small molecule activation of apurinic/apyrimidinic endonuclease 1 reduces DNA damage induced by cisplatin in cultured sensory neurons. Georgiadis MM, Chen Q, Meng J, Guo C, Wireman R, Reed A, Vasko MR, Kelley MR. DNA Repair (Amst) 41 32-41 (2016)
- Thermococcus Eurythermalis Endonuclease IV Can Cleave Various Apurinic/Apyrimidinic Site Analogues in ssDNA and dsDNA. Wang WW, Zhou H, Xie JJ, Yi GS, He JH, Wang FP, Xiao X, Liu XP. Int J Mol Sci 20 E69 (2018)
- APE1 assembles biomolecular condensates to promote the ATR-Chk1 DNA damage response in nucleolus. Li J, Zhao H, McMahon A, Yan S. Nucleic Acids Res 50 10503-10525 (2022)
- High-Resolution Mapping of Amino Acid Residues in DNA-Protein Cross-Links Enabled by Ribonucleotide-Containing DNA. Tang J, Zhao W, Hendricks NG, Zhao L. Anal Chem 93 13398-13406 (2021)
- Histone H3 Lysine 56 Acetylation Enhances AP Endonuclease 1-Mediated Repair of AP Sites in Nucleosome Core Particles. Rodriguez Y, Horton JK, Wilson SH. Biochemistry 58 3646-3655 (2019)
- Mutational and Kinetic Analysis of APE1 Endoribonuclease Activity. Kuznetsova AA, Gavrilova AA, Novopashina DS, Fedorova OS, Kuznetsov NA. Mol Biol 55 211-224 (2021)
- Polymorphism of apyrimidinic DNA structures in the nucleosome. Osakabe A, Arimura Y, Matsumoto S, Horikoshi N, Sugasawa K, Kurumizaka H. Sci Rep 7 41783 (2017)
- Probing conformational transitions towards mutagenic Watson-Crick-like G·T mismatches using off-resonance sugar carbon R1ρ relaxation dispersion. Rangadurai A, Szymanski ES, Kimsey I, Shi H, Al-Hashimi HM. J Biomol NMR 74 457-471 (2020)
- Letter Structural basis for inhibition of the deadenylase activity of human CNOT6L. Zhang Q, Yan D, Guo E, Ding B, Yang W, Liu R, Yamamoto T, Bartlam M. FEBS Lett 590 1270-1279 (2016)
- The Enigma of Substrate Recognition and Catalytic Efficiency of APE1-Like Enzymes. Davletgildeeva AT, Ishchenko AA, Saparbaev M, Fedorova OS, Kuznetsov NA. Front Cell Dev Biol 9 617161 (2021)
- Altered APE1 activity on abasic ribonucleotides is mediated by changes in the nucleoside sugar pucker. Hoitsma NM, Click TH, Agarwal PK, Freudenthal BD. Comput Struct Biotechnol J 19 3293-3302 (2021)
- Human TDP1, APE1 and TREX1 repair 3'-DNA-peptide/protein cross-links arising from abasic sites in vitro. Wei X, Wang Z, Hinson C, Yang K. Nucleic Acids Res 50 3638-3657 (2022)
- Role of AP-endonuclease (Ape1) active site residues in stabilization of the reactant enzyme-DNA complex. Batebi H, Dragelj J, Imhof P. Proteins 86 439-453 (2018)
- Structural basis for recognition and repair of the 3'-phosphate by NExo, a base excision DNA repair nuclease from Neisseria meningitidis. Silhan J, Zhao Q, Boura E, Thomson H, Förster A, Tang CM, Freemont PS, Baldwin GS. Nucleic Acids Res 46 11980-11989 (2018)
- Comparative Analysis of Exo- and Endonuclease Activities of APE1-like Enzymes. Davletgildeeva AT, Kuznetsova AA, Novopashina DS, Ishchenko AA, Saparbaev M, Fedorova OS, Kuznetsov NA. Int J Mol Sci 23 2869 (2022)
- Insights into Mechanisms of Damage Recognition and Catalysis by APE1-like Enzymes. Bulygin AA, Fedorova OS, Kuznetsov NA. Int J Mol Sci 23 4361 (2022)
- Mechanistic decoupling of exonuclease III multifunctionality into AP endonuclease and exonuclease activities at the single-residue level. Lee D, Oh S, Cho H, Yoo J, Lee G. Nucleic Acids Res 50 2211-2222 (2022)
- Structural and Functional Characterization of a Unique AP Endonuclease From Deinococcus radiodurans. He Y, Wang Y, Qin C, Xu Y, Cheng K, Xu H, Tian B, Zhao Y, Wang L, Hua Y. Front Microbiol 11 1178 (2020)
- Structural basis for APE1 processing DNA damage in the nucleosome. Weaver TM, Hoitsma NM, Spencer JJ, Gakhar L, Schnicker NJ, Freudenthal BD. Nat Commun 13 5390 (2022)
- Structural dynamics of wild type and mutated forms of human L1 endonuclease and insights into its sequence specific nucleic acid binding mechanism: A molecular dynamics study. Rajagopalan M, Balasubramanian S, Ramaswamy A. J Mol Graph Model 76 43-55 (2017)
- Abasic site-peptide cross-links are blocking lesions repaired by AP endonucleases. Yudkina AV, Bulgakov NA, Kim DV, Baranova SV, Ishchenko AA, Saparbaev MK, Koval VV, Zharkov DO. Nucleic Acids Res 51 6321-6336 (2023)
- Characterizing inhibitors of human AP endonuclease 1. Pidugu LS, Servius HW, Sevdalis SE, Cook ME, Varney KM, Pozharski E, Drohat AC. PLoS One 18 e0280526 (2023)
- Cysteine Oxidation to Sulfenic Acid in APE1 Aids G-Quadruplex Binding While Compromising DNA Repair. Howpay Manage SA, Fleming AM, Chen HN, Burrows CJ. ACS Chem Biol 17 2583-2594 (2022)
- Key Amino Acid Residues of Mitochondrial Transcription Factor A Synergize with Abasic (AP) Site Dynamics To Facilitate AP-Lyase Reactions. Zhao W, Xu W, Tang J, Kaushik S, Chang CA, Zhao L. ACS Chem Biol 18 1168-1179 (2023)
- Processing oxidatively damaged bases at DNA strand breaks by APE1. Whitaker AM, Stark WJ, Freudenthal BD. Nucleic Acids Res 50 9521-9533 (2022)
- APE1 promotes non-homologous end joining by initiating DNA double-strand break formation and decreasing ubiquitination of artemis following oxidative genotoxic stress. Zhang Q, Yang L, Gao H, Kuang X, Xiao H, Yang C, Cheng Y, Zhang L, Guo X, Zhong Y, Li M. J Transl Med 21 183 (2023)
- Conformational Rearrangements Regulating the DNA Repair Protein APE1. Komaniecka N, Porras M, Cairn L, Santas JA, Ferreiro N, Penedo JC, Bañuelos S. Int J Mol Sci 23 8015 (2022)
- Development of a DNAzyme Walker for the Detection of APE1 in Living Cancer Cells. Tao J, Zhang H, Weinfeld M, Le XC. Anal Chem 95 14990-14997 (2023)
- Functional importance and divergence of plant apurinic/apyrimidinic endonucleases in somatic and meiotic DNA repair. Li J, Wang C, Liang W, Zhang J, Jiang CK, Liu Y, Ren Z, Ci D, Chang J, Han S, Deng XW, Wang Y, Qian W. Plant Cell 35 2316-2331 (2023)
- Mechanistic insight into AP-endonuclease 1 cleavage of abasic sites at stalled replication fork mimics. Hoitsma NM, Norris J, Khoang TH, Kaushik V, Chadda R, Antony E, Hedglin M, Freudenthal BD. Nucleic Acids Res 51 6738-6753 (2023)
- Molecular basis for processing of topoisomerase 1-triggered DNA damage by Apn2/APE2. Williams JS, Wojtaszek JL, Appel DC, Krahn J, Wallace BD, Walsh E, Kunkel TA, Williams RS. Cell Rep 41 111448 (2022)
- Structural dissection of sequence recognition and catalytic mechanism of human LINE-1 endonuclease. Miller I, Totrov M, Korotchkina L, Kazyulkin DN, Gudkov AV, Korolev S. Nucleic Acids Res 49 11350-11366 (2021)
- Thermococcus kodakarensis TK0353 is a novel AP lyase with a new fold. Caffrey PJ, Eckenroth BE, Burkhart BW, Zatopek KM, McClung CM, Santangelo TJ, Doublié S, Gardner AF. J Biol Chem 300 105503 (2023)