Oleg Tsodikov - Related publications

Affiliations: 
Chemistry University of Kentucky, Lexington, KY 
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50 most relevant papers in past 60 days:
Year Citation  Score
2020 Corsi F, Lavery R, Laine E, Carbone A. Multiple protein-DNA interfaces unravelled by evolutionary information, physico-chemical and geometrical properties. Plos Computational Biology. 16: e1007624. PMID 32012150 DOI: 10.1371/journal.pcbi.1007624   
2020 Seckfort D, Lynch GC, Pettitt BM. The lac repressor hinge helix in context: The effect of the DNA binding domain and symmetry. Biochimica Et Biophysica Acta. General Subjects. 129538. PMID 31958546 DOI: 10.1016/j.bbagen.2020.129538   
2020 An J, Choi J, Hwang D, Park J, Pemble CW, Duong THM, Kim KR, Ahn H, Chung HS, Ahn DR. The crystal structure of a natural DNA polymerase complexed with mirror DNA. Chemical Communications (Cambridge, England). PMID 31971182 DOI: 10.1039/c9cc09351f   
2020 Hrabina O, Malina J, Kostrhunova H, Novohradsky V, Pracharova J, Rogers N, Simpson DH, Scott P, Brabec V. Optically Pure Metallohelices That Accumulate in Cell Nuclei, Condense/Aggregate DNA, and Inhibit Activities of DNA Processing Enzymes. Inorganic Chemistry. PMID 32064865 DOI: 10.1021/acs.inorgchem.0c00092   
2020 Chen X, Cui Y, Best RB, Wang H, Zhou ZH, Yang W, Gellert M. Cutting antiparallel DNA strands in a single active site. Nature Structural & Molecular Biology. PMID 32015552 DOI: 10.1038/s41594-019-0363-2   
2020 Lian FM, Yang X, Jiang YL, Yang F, Li C, Yang W, Qian C. New structural insights into the recognition of undamaged splayed-arm DNA with a single pair of non-complementary nucleotides by human nucleotide excision repair protein XPA. International Journal of Biological Macromolecules. PMID 31962067 DOI: 10.1016/j.ijbiomac.2020.01.169   
2020 Alves PS, Mesquita ON, Rocha MS. A Model for DNA Interactions with Proteins and Other Large Ligands: Extracting Physical Chemistry from Pure Mechanical Measurements. The Journal of Physical Chemistry. B. PMID 31961690 DOI: 10.1021/acs.jpcb.0c00155   
2020 Zia A, Imran M, Rashid S. In Silico Exploration of Conformational Dynamics and Novel Inhibitors for Targeting MEF2-Associated Transcriptional Activity. Journal of Chemical Information and Modeling. PMID 32031799 DOI: 10.1021/acs.jcim.0c00008   
2020 Yang W, Deng L. PreDBA: A heterogeneous ensemble approach for predicting protein-DNA binding affinity. Scientific Reports. 10: 1278. PMID 31992738 DOI: 10.1038/s41598-020-57778-1   
2020 Felipe C, Shin J, Loginova Y, Kolomeisky AB. The effect of obstacles in multi-site protein target search with DNA looping. The Journal of Chemical Physics. 152: 025101. PMID 31941320 DOI: 10.1063/1.5135917   
2020 Tondnevis F, Dudenhausen EE, Miller AM, McKenna R, Altschul SF, Bloom LB, Neuwald AF. Deep Analysis of Residue Constraints (DARC): identifying determinants of protein functional specificity. Scientific Reports. 10: 1691. PMID 32015389 DOI: 10.1038/s41598-019-55118-6   
2020 Gong Y, Li S, Li Y, Zhu J, Yang Y, Liu M. Mutation of leucine 20 causes a change of local conformation indirectly impairing the DNA binding of SP_0782 from Streptococcus pneumoniae. Biochemical and Biophysical Research Communications. PMID 31980174 DOI: 10.1016/j.bbrc.2020.01.057   
2020 Berroyer A, Kim N. The Functional Consequences of Eukaryotic Topoisomerase 1 Interaction with G-Quadruplex DNA. Genes. 11. PMID 32059547 DOI: 10.3390/genes11020193   
2020 An SQ, Valvano MA, Yu YH, Webb JS, Campos GL. An improved bind-n-seq strategy to determine protein-DNA interactions validated using the bacterial transcriptional regulator YipR. Bmc Microbiology. 20: 1. PMID 31896348 DOI: 10.1186/s12866-019-1672-7   
2020 Shepherd JW, Greenall RJ, Probert MIJ, Noy A, Leake MC. The emergence of sequence-dependent structural motifs in stretched, torsionally constrained DNA. Nucleic Acids Research. PMID 31930331 DOI: 10.1093/nar/gkz1227   
2020 Bores C, Pettitt BM. Structure and the role of filling rate on model dsDNA packed in a phage capsid. Physical Review. E. 101: 012406. PMID 32069548 DOI: 10.1103/PhysRevE.101.012406   
2020 Singh I, Luxami V, Paul K. Synthesis of naphthalimide-phenanthro[9,10-d]imidazole derivatives: In vitro evaluation, binding interaction with DNA and topoisomerase inhibition. Bioorganic Chemistry. 96: 103631. PMID 32036164 DOI: 10.1016/j.bioorg.2020.103631   
2020 McMahon SA, Zhu W, Graham S, Rambo R, White MF, Gloster TM. Structure and mechanism of a Type III CRISPR defence DNA nuclease activated by cyclic oligoadenylate. Nature Communications. 11: 500. PMID 31980625 DOI: 10.1038/s41467-019-14222-x   
2020 Shahabadi N, Zendehcheshm S. Evaluation of ct-DNA and HSA binding propensity of antibacterial drug chloroxine: Multi-spectroscopic analysis, atomic force microscopy and docking simulation. Spectrochimica Acta. Part a, Molecular and Biomolecular Spectroscopy. 230: 118042. PMID 31972466 DOI: 10.1016/j.saa.2020.118042   
2020 Yamada N, Kuntala PK, Pugh BF, Mahony S. ChExMix: A Method for Identifying and Classifying Protein-DNA Interaction Subtypes. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. PMID 32023130 DOI: 10.1089/cmb.2019.0466   
2020 Tiwari P, Chapagain PP, Seddek A, Annamalai T, Üren A, Tse-Dinh YC. Covalent Complex of DNA and Bacterial Topoisomerase: Implications in Antibacterial Drug Development. Chemmedchem. PMID 32043806 DOI: 10.1002/cmdc.201900721   
2020 Suskiewicz MJ, Zobel F, Ogden TEH, Fontana P, Ariza A, Yang JC, Zhu K, Bracken L, Hawthorne WJ, Ahel D, Neuhaus D, Ahel I. HPF1 completes the PARP active site for DNA damage-induced ADP-ribosylation. Nature. PMID 32028527 DOI: 10.1038/s41586-020-2013-6   
2020 Schneider M, Trummer C, Stengl A, Zhang P, Szwagierczak A, Cardoso MC, Leonhardt H, Bauer C, Antes I. Systematic analysis of the binding behaviour of UHRF1 towards different methyl- and carboxylcytosine modification patterns at CpG dyads. Plos One. 15: e0229144. PMID 32084194 DOI: 10.1371/journal.pone.0229144   
2020 Zhang D, Yan Y, Que H, Yang T, Cheng X, Ding S, Zhang X, Cheng W. CRISPR/Cas12a-mediated Interfacial Cleaving of Hairpin DNA Reporter for Electrochemical Nucleic Acids Sensing. Acs Sensors. PMID 32013399 DOI: 10.1021/acssensors.9b02461   
2020 Kumar R, Chand K, Bhowmik S, Das RN, Bhattacharjee S, Hedenström M, Chorell E. Subtle structural alterations in G-quadruplex DNA regulate site specificity of fluorescence light-up probes. Nucleic Acids Research. PMID 31912160 DOI: 10.1093/nar/gkz1205   
2020 Janel-Bintz R, Kuhn L, Frit P, Chicher J, Wagner J, Haracska L, Hammann P, Cordonnier AM. Proteomic Analysis of DNA Synthesis on a Structured DNA Template in Human Cellular Extracts: Interplay Between NHEJ and Replication-Associated Proteins. Proteomics. e1900184. PMID 31999075 DOI: 10.1002/pmic.201900184   
2020 Chen X, He Z, Wu X, Mao D, Feng C, Zhang J, Chen G. Comprehensive study of the interaction between Puerariae Radix flavonoids and DNA: From theoretical simulation to structural analysis to functional analysis. Spectrochimica Acta. Part a, Molecular and Biomolecular Spectroscopy. 231: 118109. PMID 32062512 DOI: 10.1016/j.saa.2020.118109   
2020 Li C, Zhao X, Liu W, Yin F, Hu J, Zhang G, Chen G. DNA Structural Distortions Induced by a Monofunctional Trinuclear Platinum Complex with Various Cross-Links Using Molecular Dynamics Simulation. Journal of Chemical Information and Modeling. PMID 32096984 DOI: 10.1021/acs.jcim.0c00002   
2020 Khan S, Ahmad R, Naseem I. Elucidating the interaction of aminophylline with calf thymus DNA using multispectroscopic and molecular docking approach. Journal of Biomolecular Structure & Dynamics. 1-10. PMID 31994973 DOI: 10.1080/07391102.2020.1722240   
2020 Ghosh S, Goldgur Y, Shuman S. Mycobacterial DNA polymerase I: activities and crystal structures of the POL domain as apoenzyme and in complex with a DNA primer-template and of the full-length FEN/EXO-POL enzyme. Nucleic Acids Research. PMID 32034423 DOI: 10.1093/nar/gkaa075   
2020 Ghosh D, Datta LP, Govindaraju T. Molecular architectonics of DNA for functional nanoarchitectures. Beilstein Journal of Nanotechnology. 11: 124-140. PMID 31976202 DOI: 10.3762/bjnano.11.11   
2020 Isogawa A, Fuchs RP, Fujii S. Chromatin Pull-Down Methodology Based on DNA Triple Helix Formation. Methods in Molecular Biology (Clifton, N.J.). 2119: 183-199. PMID 31989525 DOI: 10.1007/978-1-0716-0323-9_16   
2020 Nano A, Bailis JM, Mariano NF, Pham ED, Threatt SD, Barton JK. Cell-Selective Cytotoxicity of a Fluorescent Rhodium Metalloinsertor Conjugate Results from Irreversible DNA Damage at Base Pair Mismatches. Biochemistry. PMID 31967788 DOI: 10.1021/acs.biochem.9b01037   
2020 Olina A, Kuzmenko A, Ninova M, Aravin AA, Kulbachinskiy A, Esyunina D. Genome-wide DNA sampling by Ago nuclease from the cyanobacterium . Rna Biology. 1-12. PMID 32013676 DOI: 10.1080/15476286.2020.1724716   
2020 Ryu Y, Hong CA, Song Y, Beak J, Seo BA, Lee JJ, Kim HS. Modular protein-DNA hybrid nanostructures as a drug delivery platform. Nanoscale. PMID 32057052 DOI: 10.1039/c9nr08519j   
2020 Connelly JC, Cholewa-Waclaw J, Webb S, Steccanella V, Waclaw B, Bird A. Absence of MeCP2 binding to non-methylated GT-rich sequences in vivo. Nucleic Acids Research. PMID 32064528 DOI: 10.1093/nar/gkaa102   
2020 Kribelbauer JF, Loker RE, Feng S, Rastogi C, Abe N, Rube HT, Bussemaker HJ, Mann RS. Context-Dependent Gene Regulation by Homeodomain Transcription Factor Complexes Revealed by Shape-Readout Deficient Proteins. Molecular Cell. PMID 32053778 DOI: 10.1016/j.molcel.2020.01.027   
2020 Hu Y, He Y, Lin Z. Biochemical and structural characterization of the Holliday junction resolvase RuvC from Pseudomonas aeruginosa. Biochemical and Biophysical Research Communications. PMID 32085896 DOI: 10.1016/j.bbrc.2020.02.062   
2020 Hayes JA, Hilbert BJ, Gaubitz C, Stone NP, Kelch BA. A thermophilic phage uses a small terminase protein with a fixed helix-turn-helix geometry. The Journal of Biological Chemistry. PMID 32014998 DOI: 10.1074/jbc.RA119.012224   
2020 Lin CC, Chen YP, Yang WZ, Shen JCK, Yuan HS. Structural insights into CpG-specific DNA methylation by human DNA methyltransferase 3B. Nucleic Acids Research. PMID 32083663 DOI: 10.1093/nar/gkaa111   
2020 Li J, Wang J, Fan J, Huang G, Yan L. Binding characteristics of aflatoxin B with free DNA in vitro. Spectrochimica Acta. Part a, Molecular and Biomolecular Spectroscopy. 230: 118054. PMID 32006841 DOI: 10.1016/j.saa.2020.118054   
2020 Chernikova EY, Ruleva AY, Tsvetkov VB, Fedorov YV, Novikov VV, Aliyeu TM, Pavlov AA, Shepel NE, Fedorova OA. Cucurbit[7]uril-driven modulation of ligand-DNA interactions by ternary assembly. Organic & Biomolecular Chemistry. PMID 31912862 DOI: 10.1039/c9ob02543j   
2020 Hoff K, Halpain M, Garbagnati G, Edwards JS, Zhou W. Enzymatic Synthesis of Designer DNA Using Cyclic Reversible Termination and a Universal Template. Acs Synthetic Biology. PMID 31895546 DOI: 10.1021/acssynbio.9b00315   
2020 Zhang F, Liu B, Lopez A, Wang S, Liu J. Opposite salt-dependent stability of i-motif and duplex reflected in a single DNA hairpin nanomachine. Nanotechnology. PMID 31978920 DOI: 10.1088/1361-6528/ab6fdf   
2020 Guarra F, Busto N, Guerri A, Marchetti L, Marzo T, García B, Biver T, Gabbiani C. Cytotoxic Ag(I) and Au(I) NHC-carbenes bind DNA and show TrxR inhibition. Journal of Inorganic Biochemistry. 205: 110998. PMID 31981769 DOI: 10.1016/j.jinorgbio.2020.110998   
2020 Liao N, Liu J, Chai Y, Yuan R, Zhuo Y. DNA Structure Transition-induced Affinity Switch for Biosensing Based on the Strong Electrochemiluminescence Platform from Organic Microcrystals. Analytical Chemistry. PMID 32037802 DOI: 10.1021/acs.analchem.9b05433   
2020 Paoletti F, El-Sagheer AH, Allard J, Brown T, Dushek O, Esashi F. Molecular flexibility of DNA as a key determinant of RAD51 recruitment. The Embo Journal. e103002. PMID 31943278 DOI: 10.15252/embj.2019103002   
2020 Jamroskovic J, Doimo M, Chand K, Obi I, Kumar R, Brännström K, Hedenström M, Nath Das R, Akhunzianov A, Deiana M, Kasho K, Sulis Sato S, Pourbozorgi PL, Mason JE, Medini P, et al. Quinazoline Ligands Induce Cancer Cell Death through Selective STAT3 Inhibition and G-Quadruplex Stabilization. Journal of the American Chemical Society. PMID 31990532 DOI: 10.1021/jacs.9b11232   
2020 Salem MA, Ragab A, El-Khalafawy A, Makhlouf AH, Askar AA, Ammar YA. Design, synthesis, in vitro antimicrobial evaluation and molecular docking studies of indol-2-one tagged with morpholinosulfonyl moiety as DNA gyrase inhibitors. Bioorganic Chemistry. 96: 103619. PMID 32036161 DOI: 10.1016/j.bioorg.2020.103619   
2020 Anindya R. Single-stranded DNA damage: Protecting the single-stranded DNA from chemical attack. Dna Repair. 87: 102804. PMID 31981739 DOI: 10.1016/j.dnarep.2020.102804