LeAnn J. Godderz, Ph.D. - Related publications

2005 University of Oklahoma Health Sciences Center, Oklahoma City, OK, United States 
Biochemistry, Molecular Biology
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50 most relevant papers in past 60 days:
Year Citation  Score
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 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 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 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 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 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 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 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 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 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 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 Qin L, Bdira FB, Sterckx YGJ, Volkov AN, Vreede J, Giachin G, van Schaik P, Ubbink M, Dame RT. Structural basis for osmotic regulation of the DNA binding properties of H-NS proteins. Nucleic Acids Research. PMID 31925429 DOI: 10.1093/nar/gkz1226   
2020 Fan S, Liu H, Liu J, Hua W, Xu S, Li J. Systematic Analysis of the DNA Methylase and Demethylase Gene Families in Rapeseed ( L.) and Their Expression Variations After Salt and Heat stresses. International Journal of Molecular Sciences. 21. PMID 32023925 DOI: 10.3390/ijms21030953   
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 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 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 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 Singh S, Shih SJ, Vaughan ATM. Detection of DNA Double-Strand Breaks and Chromosome Translocations Using Ligation-Mediated PCR and Inverse PCR. Methods in Molecular Biology (Clifton, N.J.). 2102: 271-288. PMID 31989561 DOI: 10.1007/978-1-0716-0223-2_15   
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   
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 Hsu HK, Weng YI, Hsu PY, Huang TH, Huang YW. Detection of DNA Methylation by MeDIP and MBDCap Assays: An Overview of Techniques. Methods in Molecular Biology (Clifton, N.J.). 2102: 225-234. PMID 31989558 DOI: 10.1007/978-1-0716-0223-2_12   
2020 Totoiu CA, Phillips JM, Reese AT, Majumdar S, Girguis PR, Raston CL, Weiss GA. Vortex fluidics-mediated DNA rescue from formalin-fixed museum specimens. Plos One. 15: e0225807. PMID 31999723 DOI: 10.1371/journal.pone.0225807   
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 Do DT, Le NQK. Using extreme gradient boosting to identify origin of replication in Saccharomyces cerevisiae via hybrid features. Genomics. PMID 31987913 DOI: 10.1016/j.ygeno.2020.01.017   
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 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 Deshpande RA, Myler LR, Soniat MM, Makharashvili N, Lee L, Lees-Miller SP, Finkelstein IJ, Paull TT. DNA-dependent protein kinase promotes DNA end processing by MRN and CtIP. Science Advances. 6: eaay0922. PMID 31934630 DOI: 10.1126/sciadv.aay0922   
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 Nakamura J, Nakamura M. DNA-protein crosslink formation by endogenous aldehydes and AP sites. Dna Repair. 88: 102806. PMID 32070903 DOI: 10.1016/j.dnarep.2020.102806   
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 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 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 Jain S, Maini J, Narang A, Maiti S, Brahmachari V. The regulatory function of dIno80 correlates with its DNA binding activity. Gene. 144368. PMID 31954859 DOI: 10.1016/j.gene.2020.144368   
2020 Kadyrova LY, Gujar V, Burdett V, Modrich PL, Kadyrov FA. Human MutLγ, the MLH1-MLH3 heterodimer, is an endonuclease that promotes DNA expansion. Proceedings of the National Academy of Sciences of the United States of America. PMID 32015124 DOI: 10.1073/pnas.1914718117   
2020 Jiang Z, Lai Y, Beaver JM, Tsegay PS, Zhao ML, Horton JK, Zamora M, Rein HL, Miralles F, Shaver M, Hutcheson JD, Agoulnik I, Wilson SH, Liu Y. Oxidative DNA Damage Modulates DNA Methylation Pattern in Human Breast Cancer 1 (BRCA1) Gene via the Crosstalk between DNA Polymerase β and a DNA Methyltransferase. Cells. 9. PMID 31963223 DOI: 10.3390/cells9010225   
2020 McKinney JA, Wang G, Mukherjee A, Christensen L, Subramanian SHS, Zhao J, Vasquez KM. Distinct DNA repair pathways cause genomic instability at alternative DNA structures. Nature Communications. 11: 236. PMID 31932649 DOI: 10.1038/s41467-019-13878-9   
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 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 Lerner LK, Nguyen TV, Castro LP, Vilar JB, Munford V, Le Guillou M, Mohammad MM, Vergé V, Rosselli F, Menck CFM, Sarasin A, Aoufouchi S. Large deletions in immunoglobulin genes are associated with a sustained absence of DNA Polymerase η. Scientific Reports. 10: 1311. PMID 31992747 DOI: 10.1038/s41598-020-58180-7   
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 Ma X, Tang TS, Guo C. Regulation of Translesion DNA Synthesis in Mammalian Cells. Environmental and Molecular Mutagenesis. PMID 31983077 DOI: 10.1002/em.22359   
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 Yamazaki T, Hatano Y, Taniguchi R, Kobayashi N, Yamagata K. Editing DNA Methylation in Mammalian Embryos. International Journal of Molecular Sciences. 21. PMID 31963664 DOI: 10.3390/ijms21020637   
2020 Deng M, Liu Z, Chen B, Cai Y, Wan Y, Wang F. Locus-Specific Regulation of Expression Using the CRISPR-Cas9-Based System. Dna and Cell Biology. PMID 32073884 DOI: 10.1089/dna.2019.4945   
2020 Burleigh K, Maltbaek JH, Cambier S, Green R, Gale M, James RC, Stetson DB. Human DNA-PK activates a STING-independent DNA sensing pathway. Science Immunology. 5. PMID 31980485 DOI: 10.1126/sciimmunol.aba4219   
2020 Zhao J, Cramer SM, McGown LB. Mechanism of sequence-based separation of single-stranded DNA in capillary zone electrophoresis. Electrophoresis. PMID 32031267 DOI: 10.1002/elps.201900418   
2020 Lawarée E, Jankevicius G, Cooper C, Ahel I, Uphoff S, Tang CM. DNA ADP-Ribosylation Stalls Replication and Is Reversed by RecF-Mediated Homologous Recombination and Nucleotide Excision Repair. Cell Reports. 30: 1373-1384.e4. PMID 32023456 DOI: 10.1016/j.celrep.2020.01.014   
2020 McKie SJ, Maxwell A, Neuman KC. Mapping DNA Topoisomerase Binding and Cleavage Genome Wide Using Next-Generation Sequencing Techniques. Genes. 11. PMID 31941152 DOI: 10.3390/genes11010092   
2020 Carvajal-Garcia J, Gales ER, Ramsden DA, Sekelsky J. The Ortholog of RFWD3 Functions Independently of RAD51 During DNA Repair. G3 (Bethesda, Md.). PMID 31900333 DOI: 10.1534/g3.119.400903   
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