Jason D. Kahn - Related publications

Chemistry and Biochemistry University of Maryland, College Park, College Park, MD 
DNA looping, transcription, topology
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50 most relevant papers in past 60 days:
Year Citation  Score
2021 Stracy M, Schweizer J, Sherratt DJ, Kapanidis AN, Uphoff S, Lesterlin C. Transient non-specific DNA binding dominates the target search of bacterial DNA-binding proteins. Molecular Cell. PMID 33621478 DOI: 10.1016/j.molcel.2021.01.039   
2021 Mustafa M, Ali A, Siddiqui SA, Mir AR, Kausar T, Nayeem SM, Abidi M, Habib S. Biophysical characterization of structural and conformational changes in methylmethane sulfonate modified DNA leading to the frizzled backbone structure and strand breaks in DNA. Journal of Biomolecular Structure & Dynamics. 1-14. PMID 33719845 DOI: 10.1080/07391102.2021.1899051   
2021 Neidle S. Beyond the double helix: DNA structural diversity and the PDB. The Journal of Biological Chemistry. 100553. PMID 33744292 DOI: 10.1016/j.jbc.2021.100553   
2021 Monakhova MV, Milakina MA, Savitskaia VY, Romanova EA, Rao DN, Kubareva EA. [MutL Protein from the Neisseria gonorrhoeae Mismatch Repair System: Interaction with ATP and DNA]. Molekuliarnaia Biologiia. 55: 289-304. PMID 33871442 DOI: 10.31857/S0026898421020117   
2021 McCormack LS, Efremov AK, Yan J. Effects of size, cooperativity and competitive binding on protein positioning on DNA. Biophysical Journal. PMID 33771470 DOI: 10.1016/j.bpj.2021.03.016   
2021 Bigman LS, Greenblatt HM, Levy Y. What Are the Molecular Requirements for Protein Sliding along DNA? The Journal of Physical Chemistry. B. 125: 3119-3131. PMID 33754737 DOI: 10.1021/acs.jpcb.1c00757   
2021 Wickhorst PJ, Ihmels H. Berberrubine Phosphate: A Selective Fluorescent Probe for Quadruplex DNA. Molecules (Basel, Switzerland). 26. PMID 33924894 DOI: 10.3390/molecules26092566   
2021 Clauvelin N, Olson WK. Synergy between Protein Positioning and DNA Elasticity: Energy Minimization of Protein-Decorated DNA Minicircles. The Journal of Physical Chemistry. B. 125: 2277-2287. PMID 33635080 DOI: 10.1021/acs.jpcb.0c11612   
2021 Cohan B, Frappier L. Herpesvirus DNA Polymerase Processivity Factors: Not just for DNA Synthesis. Virus Research. 198394. PMID 33775751 DOI: 10.1016/j.virusres.2021.198394   
2021 Kapp JD, Green RE, Shapiro B. A fast and efficient single-stranded genomic library preparation method optimized for ancient DNA. The Journal of Heredity. PMID 33768239 DOI: 10.1093/jhered/esab012   
2021 Wickhorst PJ, Ihmels H. Selective, pH-Dependent Colorimetric and Fluorimetric Detection of Quadruplex DNA with 4-Dimethylamino(phenyl)-Substituted Berberine Derivatives. Chemistry (Weinheim An Der Bergstrasse, Germany). PMID 33855748 DOI: 10.1002/chem.202100297   
2021 Pauszek RF, Lamichhane R, Rajkarnikar Singh A, Millar DP. Single-molecule view of coordination in a multi-functional DNA polymerase. Elife. 10. PMID 33704066 DOI: 10.7554/eLife.62046   
2021 Li Z, Hua X, Serra-Cardona A, Xu X, Zhang Z. Efficient and strand-specific profiling of replicating chromatin with enrichment and sequencing of protein-associated nascent DNA in mammalian cells. Nature Protocols. PMID 33911256 DOI: 10.1038/s41596-021-00520-6   
2021 Wang S, Zhang Q, Shen Z, He Y, Chen ZH, Li J, Huang DS. Predicting transcription factor binding sites using DNA shape features based on shared hybrid deep learning architecture. Molecular Therapy. Nucleic Acids. 24: 154-163. PMID 33767912 DOI: 10.1016/j.omtn.2021.02.014   
2021 Jiang C, Zhang Y, Wang F, Liu H. Toward Smart Information Processing with Synthetic DNA Molecules. Macromolecular Rapid Communications. e2100084. PMID 33864315 DOI: 10.1002/marc.202100084   
2021 Wan L, Lam SL, Lee HK, Guo P. Effects of Adenine Methylation on the Structure and Thermodynamic Stability of a DNA Minidumbbell. International Journal of Molecular Sciences. 22. PMID 33807305 DOI: 10.3390/ijms22073633   
2021 Sui J, Gandotra N, Xie P, Lin Z, Scharfe C, Javanmard M. Multi-frequency impedance sensing for detection and sizing of DNA fragments. Scientific Reports. 11: 6490. PMID 33753781 DOI: 10.1038/s41598-021-85755-9   
2021 Stefanucci A, Amato J, Brancaccio D, Pagano B, Randazzo A, Santoro F, Mayol L, Learte-Aymamí S, Rodriguez J, Mascareñas JL, Novellino E, Carotenuto A, Mollica A. A novel β-hairpin peptide derived from the ARC repressor selectively interacts with the major groove of B-DNA. Bioorganic Chemistry. 112: 104836. PMID 33812270 DOI: 10.1016/j.bioorg.2021.104836   
2021 Wang H, Elber R. Catalytic Magnesium as a Door Stop for DNA Sliding. The Journal of Physical Chemistry. B. PMID 33819040 DOI: 10.1021/acs.jpcb.1c00122   
2021 Shendi AM, Davenport A. The difference between delivered and prescribed dialysate sodium in haemodialysis machines. Clinical Kidney Journal. 14: 863-868. PMID 33777369 DOI: 10.1093/ckj/sfaa022   
2021 Li Y, Gao H, Qi Z, Huang Z, Ma L, Liu J. Freezing-assisted Conjugation of Unmodified Diblock DNA to Hydrogel Nanoparticles and Monoliths for DNA and Hg2+ Sensing. Angewandte Chemie (International Ed. in English). PMID 33792133 DOI: 10.1002/anie.202102330   
2021 Ujaoney AK, Padwal MK, Basu B. An Interaction Network of DNA-Repair Proteins: A Snapshot at Double Strand Break Repair in . Journal of Proteome Research. PMID 33929844 DOI: 10.1021/acs.jproteome.1c00078   
2021 Cabrero C, Martín-Pintado N, Mazzini S, Gargallo R, Eritja R, Aviñó A, González C. Structural Effects of Incorporation of 2'-Deoxy-2'2'-Difluorodeoxycytidine (Gemcitabine) in A- and B-Form Duplexes. Chemistry (Weinheim An Der Bergstrasse, Germany). PMID 33772916 DOI: 10.1002/chem.202100503   
2021 Begum NA, Haque F, Stanlie A, Husain A, Mondal S, Nakata M, Taniguchi T, Taniguchi H, Honjo T. Phf5a regulates DNA repair in class switch recombination via p400 and histone H2A variant deposition. The Embo Journal. e106393. PMID 33938017 DOI: 10.15252/embj.2020106393   
2021 Thakur B, Arora K, Gupta A, Guptasarma P. The DNA-binding protein HU is a molecular glue that attaches bacteria to extracellular DNA in biofilms. The Journal of Biological Chemistry. 100532. PMID 33713701 DOI: 10.1016/j.jbc.2021.100532   
2021 Hong CA, Park JC, Na H, Jeon H, Nam YS. Short DNA-catalyzed formation of quantum dot-DNA hydrogel for enzyme-free femtomolar specific DNA assay. Biosensors & Bioelectronics. 182: 113110. PMID 33812283 DOI: 10.1016/j.bios.2021.113110   
2021 Del Prado A, Salas M. Strand Displacement and Unwinding Assays to Study the Concerted Action of the DNA Polymerase and SSB During Phi29 TP-DNA Replication. Methods in Molecular Biology (Clifton, N.J.). 2281: 333-342. PMID 33847970 DOI: 10.1007/978-1-0716-1290-3_22   
2021 Shen BW, Quispe JD, Luyten Y, McGough BE, Morgan RD, Stoddard BL. Coordination of phage genome degradation versus host genome protection by a bifunctional restriction-modification enzyme visualized by CryoEM. Structure (London, England : 1993). PMID 33826880 DOI: 10.1016/j.str.2021.03.012   
2021 Wang P, Roider E, Coulter ME, Walsh CA, Kramer CS, Beuning PJ, Giese RW. DNA Adductomics by Mass Tag Prelabeling. Rapid Communications in Mass Spectrometry : Rcm. e9095. PMID 33821547 DOI: 10.1002/rcm.9095   
2021 Lee J, Jo I, Ahn J, Hong S, Jeong S, Kwon A, Ha NC. Crystal structure of the nuclease and capping domain of SbcD from Staphylococcus aureus. Journal of Microbiology (Seoul, Korea). PMID 33877576 DOI: 10.1007/s12275-021-1012-0   
2021 Hai H, Chen C, Chen D, Li P, Shan Y, Li J. A sensitive electrochemiluminescence DNA biosensor based on the signal amplification of ExoIII enzyme-assisted hybridization chain reaction combined with nanoparticle-loaded multiple probes. Mikrochimica Acta. 188: 125. PMID 33723966 DOI: 10.1007/s00604-021-04777-2   
2021 Galindo-Murillo R, Cheatham TE. Ethidium bromide interactions with DNA: an exploration of a classic DNA-ligand complex with unbiased molecular dynamics simulations. Nucleic Acids Research. PMID 33764383 DOI: 10.1093/nar/gkab143   
2021 Aparicio Casado T, Gautier J. DNA Damage Response in Xenopus laevis Cell-Free Extracts. Methods in Molecular Biology (Clifton, N.J.). 2267: 103-144. PMID 33786788 DOI: 10.1007/978-1-0716-1217-0_8   
2021 Hu Y, Lacroix B, Citovsky V. Modulation of plant DNA damage response gene expression during Agrobacterium infection. Biochemical and Biophysical Research Communications. 554: 7-12. PMID 33774281 DOI: 10.1016/j.bbrc.2021.03.044   
2021 Lu CH, Lan WH, Li HW. Single-Molecule Tethered Particle Motion Studies on the DNA Recombinase Filament Assembly and Disassembly. Methods in Molecular Biology (Clifton, N.J.). 2281: 135-149. PMID 33847956 DOI: 10.1007/978-1-0716-1290-3_8   
2021 Ueda S, Yamashita S, Watanabe SI, Wakabayashi M, Motoi N, Noguchi M, Sekine S, Sato Y, Ushijima T. Influence of degree of DNA degradation in formalin-fixed and paraffin-embedded tissue samples on accuracy of genome-wide DNA methylation analysis. Epigenomics. PMID 33820444 DOI: 10.2217/epi-2020-0431   
2021 Robertson WE, Funke LFH, de la Torre D, Fredens J, Wang K, Chin JW. Creating custom synthetic genomes in Escherichia coli with REXER and GENESIS. Nature Protocols. PMID 33903757 DOI: 10.1038/s41596-020-00464-3   
2021 Pellanda P, Dalsass M, Filipuzzi M, Loffreda A, Verrecchia A, Castillo Cano V, Thabussot H, Doni M, Morelli MJ, Soucek L, Kress T, Mazza D, Mapelli M, Beaulieu ME, Amati B, et al. Integrated requirement of non-specific and sequence-specific DNA binding in Myc-driven transcription. The Embo Journal. e105464. PMID 33792944 DOI: 10.15252/embj.2020105464   
2021 Singh RK, Mukherjee A. Molecular Mechanism of the Intercalation of the SOX-4 Protein into DNA Inducing Bends and Kinks. The Journal of Physical Chemistry. B. 125: 3752-3762. PMID 33848164 DOI: 10.1021/acs.jpcb.0c11496   
2021 Petruseva I, Naumenko N, Kuper J, Anarbaev R, Kappenberger J, Kisker C, Lavrik O. The Interaction Efficiency of XPD-p44 With Bulky DNA Damages Depends on the Structure of the Damage. Frontiers in Cell and Developmental Biology. 9: 617160. PMID 33777931 DOI: 10.3389/fcell.2021.617160   
2021 Farhana FZ, Umer M, Saeed A, Pannu AS, Husaini S, Sonar P, Firoz SH, Shiddiky MJA. -MagnetoMethyl IP: a magnetic nanoparticle-mediated immunoprecipitation and electrochemical detection method for global DNA methylation. The Analyst. PMID 33949437 DOI: 10.1039/d1an00345c   
2021 Schurr JM. A quantitative model of a cooperative two-state equilibrium in DNA: experimental tests, insights, and predictions. Quarterly Reviews of Biophysics. 54: e5. PMID 33722316 DOI: 10.1017/S0033583521000032   
2021 Glaser M, Deb S, Seier F, Agrawal A, Liedl T, Douglas S, Gupta MK, Smith DM. The Art of Designing DNA Nanostructures with CAD Software. Molecules (Basel, Switzerland). 26. PMID 33920889 DOI: 10.3390/molecules26082287   
2021 Ma N, Dai L, Chen Z, Ji M, Wang Y, Tian Y. Environment-Resistant DNA Origami Crystals Bridged by Rigid DNA Rods with Adjustable Unit Cells. Nano Letters. PMID 33821653 DOI: 10.1021/acs.nanolett.1c00607   
2021 He L, Mu J, Gang O, Chen X. Rationally Programming Nanomaterials with DNA for Biomedical Applications. Advanced Science (Weinheim, Baden-Wurttemberg, Germany). 8: 2003775. PMID 33898180 DOI: 10.1002/advs.202003775   
2021 Loveless TB, Grotts JH, Schechter MW, Forouzmand E, Carlson CK, Agahi BS, Liang G, Ficht M, Liu B, Xie X, Liu CC. Lineage tracing and analog recording in mammalian cells by single-site DNA writing. Nature Chemical Biology. PMID 33753928 DOI: 10.1038/s41589-021-00769-8   
2021 Lo YMD, Han DSC, Jiang P, Chiu RWK. Epigenetics, fragmentomics, and topology of cell-free DNA in liquid biopsies. Science (New York, N.Y.). 372. PMID 33833097 DOI: 10.1126/science.aaw3616   
2021 Cheng M, Shu X, Cao J, Gao M, Xiang S, Wang F, Wang Y, Liu J. A Mutation-based Method for Pinpointing a DNA N6-methyladenine Methyltransferase's Modification Site at Single Base Resolution. Chembiochem : a European Journal of Chemical Biology. PMID 33779011 DOI: 10.1002/cbic.202100088   
2021 Dilley K, Pagan F, Chapman B. Methods for ensuring the highest DNA concentration and yield in future and retrospective trace DNA extracts. Science & Justice : Journal of the Forensic Science Society. 61: 193-197. PMID 33736853 DOI: 10.1016/j.scijus.2020.11.005   
2021 Vemulapalli S, Hashemi M, Kolomeisky AB, Lyubchenko YL. DNA Looping Mediated by Site-Specific SfiI-DNA Interactions. The Journal of Physical Chemistry. B. PMID 33914533 DOI: 10.1021/acs.jpcb.1c00763