P. Shing Ho, Ph.D. - Related publications

Biochemistry and Biophysics Colorado State University, Fort Collins, CO 
DNA structure and function, Halogen bonding
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50 most relevant papers in past 60 days:
Year Citation  Score
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 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 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 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 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 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 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 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 Arjmand F, Khursheed S, Roisnel T, Siddique HR. Copper (II)-based halogen-substituted chromone antitumor drug entities: Studying biomolecular interactions with ct-DNA mediated by sigma hole formation and cytotoxicity activity. Bioorganic Chemistry. 104: 104327. PMID 33142405 DOI: 10.1016/j.bioorg.2020.104327   
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 Whitaker AM, Freudenthal BD. History of DNA polymerase β X-ray crystallography. Dna Repair. 93: 102928. PMID 33087265 DOI: 10.1016/j.dnarep.2020.102928   
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 Zhang T. DNA origami-based microtubule analogue. Nanotechnology. 31: 50LT01. PMID 33034304 DOI: 10.1088/1361-6528/abb395   
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   
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 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 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 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 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 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 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 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 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 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 Wang D, Yu L, Ji B, Chang S, Song J, Ke Y. Programming the Curvatures in Reconfigurable DNA Domino Origami by Using Asymmetric Units. Nano Letters. PMID 33095024 DOI: 10.1021/acs.nanolett.0c03348   
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 Mingard C, Wu J, McKeague M, Sturla SJ. Next-generation DNA damage sequencing. Chemical Society Reviews. PMID 32968744 DOI: 10.1039/d0cs00647e   
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 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 Mackay RP, Xu Q, Weinberger PM. R-Loop Physiology and Pathology: A Brief Review. Dna and Cell Biology. PMID 33052725 DOI: 10.1089/dna.2020.5906   
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 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 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 Dodd T, Botto M, Paul F, Fernandez-Leiro R, Lamers MH, Ivanov I. Polymerization and editing modes of a high-fidelity DNA polymerase are linked by a well-defined path. Nature Communications. 11: 5379. PMID 33097731 DOI: 10.1038/s41467-020-19165-2   
2020 Gorb L, Pekh A, Nyporko A, Ilchenko MM, Golius A, Zubatiuk TA, Zubatyuk RI, Dubey IY, Hovorun DM, Leszczynski J. Effect of micro-Environment on the Geometrical Structure of d(A) d(T) d(G) d(C) DNA mini-Helixes and Dickerson Dodecamer: A Density Functional Theory Study. The Journal of Physical Chemistry. B. PMID 32975118 DOI: 10.1021/acs.jpcb.0c06154   
2020 He Y, Wang Y, Qin C, Xu Y, Cheng K, Xu H, Tian B, Zhao Y, Wang L, Hua Y. Structural and Functional Characterization of a Unique AP Endonuclease From . Frontiers in Microbiology. 11: 1178. PMID 33117296 DOI: 10.3389/fmicb.2020.01178   
2020 Marshall CJ, Santangelo TJ. Archaeal DNA Repair Mechanisms. Biomolecules. 10. PMID 33113933 DOI: 10.3390/biom10111472   
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 Desai PR, Brahmachari S, Marko JF, Das S, Neuman KC. Coarse-grained modelling of DNA plectoneme pinning in the presence of base-pair mismatches. Nucleic Acids Research. PMID 33045724 DOI: 10.1093/nar/gkaa836   
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 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 Chalikian TV, Liu L, Macgregor RB. Duplex-tetraplex equilibria in guanine- and cytosine-rich DNA. Biophysical Chemistry. 267: 106473. PMID 33031980 DOI: 10.1016/j.bpc.2020.106473   
2020 Ondruš M, Sýkorová V, Bednárová L, Pohl R, Hocek M. Enzymatic synthesis of hypermodified DNA polymers for sequence-specific display of four different hydrophobic groups. Nucleic Acids Research. PMID 33152081 DOI: 10.1093/nar/gkaa999   
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 Unnikrishnan A, Amero C, Yadav DK, Stachowski K, Potter D, Foster MP. DNA binding induces a -to- switch in Cre recombinase to enable intasome assembly. Proceedings of the National Academy of Sciences of the United States of America. PMID 32968014 DOI: 10.1073/pnas.2011448117   
2020 Zacharias M. Base-Pairing and Base-Stacking Contributions to Double-Stranded DNA Formation. The Journal of Physical Chemistry. B. PMID 33156627 DOI: 10.1021/acs.jpcb.0c07670   
2020 Murugan R. A lattice model on the rate of in vivo site-specific DNA-protein interactions. Physical Biology. PMID 33022664 DOI: 10.1088/1478-3975/abbe9a   
2020 Wu R, Gao S, Du T, Cai K, Cheng X, Fan J, Feng J, Shaginian A, Li J, Wan J, Liu G. Exploring Aldol Reactions on DNA and Applications to Produce Diverse Structures: An Example of Expanding Chemical Space of DNA-Encoded Compounds by Diversity-Oriented Synthesis. Chemistry, An Asian Journal. PMID 33119184 DOI: 10.1002/asia.202001105   
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