Thomas D. Tullius, Ph.D. - Related publications

1982-1997 Chemistry Johns Hopkins University, Baltimore, MD 
 1997- Chemistry Boston University, Boston, MA, United States 
General Biophysics, Molecular Biology, Biostatistics Biology
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50 most relevant papers in past 60 days:
Year Citation  Score
2020 Afek A, Shi H, Rangadurai A, Sahay H, Senitzki A, Xhani S, Fang M, Salinas R, Mielko Z, Pufall MA, Poon GMK, Haran TE, Schumacher MA, Al-Hashimi HM, Gordân R. DNA mismatches reveal conformational penalties in protein-DNA recognition. Nature. PMID 33087930 DOI: 10.1038/s41586-020-2843-2   
2020 Chaplin AK, Hardwick SW, Liang S, Kefala Stavridi A, Hnizda A, Cooper LR, De Oliveira TM, Chirgadze DY, Blundell TL. Dimers of DNA-PK create a stage for DNA double-strand break repair. Nature Structural & Molecular Biology. PMID 33077952 DOI: 10.1038/s41594-020-00517-x   
2020 Guan L, Zhao J, Sun W, Deng W, Wang L. -Substituted Thiazole Orange for Selective Fluorescence Detection to G-Quadruplex DNA and Molecular Docking Simulation. Acs Omega. 5: 26056-26062. PMID 33073132 DOI: 10.1021/acsomega.0c03556   
2020 Patel M, Patel D, Datta S, Singh U. An immunochemistry-based screen for chemical inhibitors of DNA-protein interactions and its application to human CGGBP1. Bmc Cancer. 20: 1016. PMID 33081720 DOI: 10.1186/s12885-020-07526-5   
2020 Rodriguez J, Mosquera J, Learte-Aymamı S, Vázquez ME, Mascareñas JL. Stimuli-Responsive DNA Binding by Synthetic Systems. Accounts of Chemical Research. PMID 32997936 DOI: 10.1021/acs.accounts.0c00415   
2020 Mingard C, Wu J, McKeague M, Sturla SJ. Next-generation DNA damage sequencing. Chemical Society Reviews. PMID 32968744 DOI: 10.1039/d0cs00647e   
2020 Zhang XX, Brantley SL, Corcelli SA, Tokmakoff A. DNA minor-groove binder Hoechst 33258 destabilizes base-pairing adjacent to its binding site. Communications Biology. 3: 525. PMID 32963293 DOI: 10.1038/s42003-020-01241-4   
2020 Li S, Tollefsbol TO. DNA methylation methods: global DNA methylation and methylomic analyses. Methods (San Diego, Calif.). PMID 33039572 DOI: 10.1016/j.ymeth.2020.10.002   
2020 Zhao F, Kim W, Kloeber JA, Lou Z. DNA end resection and its role in DNA replication and DSB repair choice in mammalian cells. Experimental & Molecular Medicine. PMID 33122806 DOI: 10.1038/s12276-020-00519-1   
2020 He F, DuPrez K, Hilario E, Chen Z, Fan L. Structural basis of the XPB helicase-Bax1 nuclease complex interacting with the repair bubble DNA. Nucleic Acids Research. PMID 32986831 DOI: 10.1093/nar/gkaa801   
2020 Huang Z, Zhao Y, Liu B, Guan S, Liu J. Stronger Adsorption of Phosphorothioate DNA Oligonucleotides on Graphene Oxide by van der Waals Forces. Langmuir : the Acs Journal of Surfaces and Colloids. PMID 33161721 DOI: 10.1021/acs.langmuir.0c02761   
2020 Sharma D, Singh A, Pathak M, Kaur L, Kumar V, Roy BG, Ojha H. DNA binding and antiradical potential of ethyl pyruvate: Key to the DNA radioprotection. Chemico-Biological Interactions. 109313. PMID 33171137 DOI: 10.1016/j.cbi.2020.109313   
2020 Inagawa T, Wennink T, Lebbink JHG, Keijzers G, Florea BI, Verkaik NS, van Gent DC. C-Terminal Extensions of Ku70 and Ku80 Differentially Influence DNA End Binding Properties. International Journal of Molecular Sciences. 21. PMID 32937838 DOI: 10.3390/ijms21186725   
2020 Hammel M, Rosenberg DJ, Bierma J, Hura GL, Lees-Miller SP, Tainer JA. Visualizing functional dynamicity in the DNA-dependent protein kinase holoenzyme DNA-PK complex by integrating SAXS with cryo-EM. Progress in Biophysics and Molecular Biology. PMID 32966823 DOI: 10.1016/j.pbiomolbio.2020.09.003   
2020 Sui Z, An R, Komiyama M, Liang X. Stepwise strategy for one-pot synthesis of single-stranded DNA rings from multiple short fragments. Chembiochem : a European Journal of Chemical Biology. PMID 33124728 DOI: 10.1002/cbic.202000738   
2020 Lin MG, Li YC, Hsiao CD. Characterization of Streptococcus pneumoniae PriA helicase and its ATPase and unwinding activities in DNA replication restart. The Biochemical Journal. PMID 32985663 DOI: 10.1042/BCJ20200269   
2020 Marshall CJ, Santangelo TJ. Archaeal DNA Repair Mechanisms. Biomolecules. 10. PMID 33113933 DOI: 10.3390/biom10111472   
2020 Wang L, Song K, Qu Y, Chang Y, Li Z, Dong C, Liu M, Brennan J, Li Y. Engineering Micrometer-sized DNA Tracks for High-Speed DNA Synthesis and Biosensing. Angewandte Chemie (International Ed. in English). PMID 33007137 DOI: 10.1002/anie.202010693   
2020 Sparks MA, Burgers PM, Galletto R. Pif1, RPA and FEN1 modulate the ability of DNA polymerase δ to overcome protein barriers during DNA synthesis. The Journal of Biological Chemistry. PMID 32913126 DOI: 10.1074/jbc.RA120.015699   
2020 Stützer A, Welp LM, Raabe M, Sachsenberg T, Kappert C, Wulf A, Lau AM, David SS, Chernev A, Kramer K, Politis A, Kohlbacher O, Fischle W, Urlaub H. Analysis of protein-DNA interactions in chromatin by UV induced cross-linking and mass spectrometry. Nature Communications. 11: 5250. PMID 33067435 DOI: 10.1038/s41467-020-19047-7   
2020 Schnepf M, von Reutern M, Ludwig C, Jung C, Gaul U. Transcription Factor Binding Affinities and DNA Shape Readout. Iscience. 23: 101694. PMID 33163946 DOI: 10.1016/j.isci.2020.101694   
2020 Li C, Li H, Jie G. Click chemistry reaction-triggered DNA walker amplification coupled with hyperbranched DNA nanostructure for versatile fluorescence detection and drug delivery to cancer cells. Mikrochimica Acta. 187: 625. PMID 33095314 DOI: 10.1007/s00604-020-04580-5   
2020 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. Progress in Biophysics and Molecular Biology. PMID 33035590 DOI: 10.1016/j.pbiomolbio.2020.09.010   
2020 Bhatia DD, Wunder C, Johannes L. Self-assembled, programmable DNA nanodevices for biological and biomedical applications. Chembiochem : a European Journal of Chemical Biology. PMID 32961015 DOI: 10.1002/cbic.202000372   
2020 Li Y, Huang Q, Yao G, Wang X, Zhang F, Wang T, Shao C, Zheng X, Jing X, Zhou H. Remodeling Chromatin Induces Z-DNA Conformation Detected through Fourier Transform Infrared Spectroscopy. Analytical Chemistry. PMID 33085464 DOI: 10.1021/acs.analchem.0c02432   
2020 Wang X, Yang X. A Simple Blocking PCR-Based Method for the Synthesis of High-Copy dsDNA Tandem Repeats. Small (Weinheim An Der Bergstrasse, Germany). e2003671. PMID 33006262 DOI: 10.1002/smll.202003671   
2020 Wang X, Yang X. A Simple Blocking PCR-Based Method for the Synthesis of High-Copy dsDNA Tandem Repeats. Small (Weinheim An Der Bergstrasse, Germany). e2003671. PMID 33006262 DOI: 10.1002/smll.202003671   
2020 Hakim HM, Khan HO, Lalung J, Nelson BR, Chambers GK, Edinur HA. Autosomal STR Profiling and Databanking in Malaysia: Current Status and Future Prospects. Genes. 11. PMID 32977385 DOI: 10.3390/genes11101112   
2020 Heintz N, Gong S. Growth of and Preparation of DNA. Cold Spring Harbor Protocols. 2020: pdb.prot098145. PMID 33004551 DOI: 10.1101/pdb.prot098145   
2020 Chan RWY, Serpas L, Ni M, Volpi S, Hiraki LT, Tam LS, Rashidfarrokhi A, Wong PCH, Tam LHP, Wang Y, Jiang P, Cheng ASH, Peng W, Han DSC, Tse PPP, et al. Plasma DNA Profile Associated with DNASE1L3 Gene Mutations: Clinical Observations, Relationships to Nuclease Substrate Preference, and In Vivo Correction. American Journal of Human Genetics. PMID 33022220 DOI: 10.1016/j.ajhg.2020.09.006   
2020 Nye TM, Fernandez NL, Simmons LA. A positive perspective on DNA methylation: regulatory functions of DNA methylation outside of host defense in Gram-positive bacteria. Critical Reviews in Biochemistry and Molecular Biology. 1-16. PMID 33059472 DOI: 10.1080/10409238.2020.1828257   
2020 Sullivan ED, Longley MJ, Copeland WC. Polymerase γ efficiently replicates through many natural template barriers but stalls at the HSP1 quadruplex. The Journal of Biological Chemistry. PMID 33077518 DOI: 10.1074/jbc.RA120.015390   
2020 Ramakrishnan S, Subramaniam S, Kielar C, Grundmeier G, Stewart AF, Keller A. Protein-Assisted Room-Temperature Assembly of Rigid, Immobile Holliday Junctions and Hierarchical DNA Nanostructures. Molecules (Basel, Switzerland). 25. PMID 33153073 DOI: 10.3390/molecules25215099   
2020 Ly E, Kugel JF, Goodrich JA. Single molecule studies reveal that p53 tetramers dynamically bind response elements containing one or two half sites. Scientific Reports. 10: 16176. PMID 32999415 DOI: 10.1038/s41598-020-73234-6   
2020 Ouaray Z, Benner SA, Georgiadis MM, Richards NGJ. Building better DNA polymerases: Engineering the replication of expanded genetic alphabets. The Journal of Biological Chemistry. PMID 33004440 DOI: 10.1074/jbc.REV120.013745   
2020 Obi I, Rentoft M, Singh V, Jamroskovic J, Chand K, Chorell E, Westerlund F, Sabouri N. Stabilization of G-quadruplex DNA structures in Schizosaccharomyces pombe causes single-strand DNA lesions and impedes DNA replication. Nucleic Acids Research. PMID 33045725 DOI: 10.1093/nar/gkaa820   
2020 Kosek D, Hickman AB, Ghirlando R, He S, Dyda F. Structures of ISCth4 transpososomes reveal the role of asymmetry in copy-out/paste-in DNA transposition. The Embo Journal. e105666. PMID 33006208 DOI: 10.15252/embj.2020105666   
2020 Miura M, Chen H. CUT&RUN detects distinct DNA footprints of RNA polymerase II near the transcription start sites. Chromosome Research : An International Journal On the Molecular, Supramolecular and Evolutionary Aspects of Chromosome Biology. PMID 33070289 DOI: 10.1007/s10577-020-09643-0   
2020 Yang A, Zhang W, Wang J, Yang K, Han Y, Zhang L. Review on the Application of Machine Learning Algorithms in the Sequence Data Mining of DNA. Frontiers in Bioengineering and Biotechnology. 8: 1032. PMID 33015010 DOI: 10.3389/fbioe.2020.01032   
2020 Copp W, Wilds CJ. O -Alkylguanine DNA Alkyltransferase Mediated Disassembly of a DNA Tetrahedron. Chemistry (Weinheim An Der Bergstrasse, Germany). PMID 32543755 DOI: 10.1002/chem.202002565   
2020 Tong ZB, Ai HS, Li JB. The Mechanism of Chromatin Remodeler SMARCAD1/Fun30 in Response to DNA Damage. Frontiers in Cell and Developmental Biology. 8: 560098. PMID 33102471 DOI: 10.3389/fcell.2020.560098   
2020 Gaullier G, Roberts G, Muthurajan UM, Bowerman S, Rudolph J, Mahadevan J, Jha A, Rae PS, Luger K. Bridging of nucleosome-proximal DNA double-strand breaks by PARP2 enhances its interaction with HPF1. Plos One. 15: e0240932. PMID 33141820 DOI: 10.1371/journal.pone.0240932   
2020 De Riso G, Fiorillo DFG, Fierro A, Cuomo M, Chiariotti L, Miele G, Cocozza S. Modeling DNA Methylation Profiles through a Dynamic Equilibrium between Methylation and Demethylation. Biomolecules. 10. PMID 32899254 DOI: 10.3390/biom10091271   
2020 Bignon E, Claerbout VEP, Jiang T, Morell C, Gillet N, Dumont E. Nucleosomal embedding reshapes the dynamics of abasic sites. Scientific Reports. 10: 17314. PMID 33057206 DOI: 10.1038/s41598-020-73997-y   
2020 Majumder K, Boftsi M, Whittle FB, Wang J, Fuller MS, Joshi T, Pintel DJ. The NS1 protein of the parvovirus MVM Aids in the localization of the viral genome to cellular sites of DNA damage. Plos Pathogens. 16: e1009002. PMID 33064772 DOI: 10.1371/journal.ppat.1009002   
2020 Wan Y, Wang H, Ji J, Kang K, Yang M, Huang Y, Su Y, Ma K, Zhu L, Deng S. Zippering DNA Tetrahedral Hyperlink for Ultrasensitive Electrochemical MicroRNA Detection. Analytical Chemistry. PMID 33119272 DOI: 10.1021/acs.analchem.0c03553   
2020 Zilio N, Ulrich HD. Exploring the SSBreakome: genome-wide mapping of DNA single-strand breaks by next-generation sequencing. The Febs Journal. PMID 32965079 DOI: 10.1111/febs.15568   
2020 Paul D, Mu H, Tavakoli A, Dai Q, Chen X, Chakraborty S, He C, Ansari A, Broyde S, Min JH. Tethering-facilitated DNA 'opening' and complementary roles of β-hairpin motifs in the Rad4/XPC DNA damage sensor protein. Nucleic Acids Research. PMID 33119737 DOI: 10.1093/nar/gkaa909   
2020 Furtwängler A, Neukamm J, Böhme L, Reiter E, Vollstedt M, Arora N, Singh P, Cole ST, Knauf S, Calvignac-Spencer S, Krause-Kyora B, Krause J, Schuenemann VJ, Herbig A. Comparison of target enrichment strategies for ancient pathogen DNA. Biotechniques. PMID 33135465 DOI: 10.2144/btn-2020-0100   
2020 Weaver TM, Cortez LM, Khoang TH, Washington MT, Agarwal PK, Freudenthal BD. Visualizing Rev1 catalyze protein-template DNA synthesis. Proceedings of the National Academy of Sciences of the United States of America. PMID 32999062 DOI: 10.1073/pnas.2010484117