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Jason D. Kahn - Publications

Affiliations: 
Chemistry and Biochemistry University of Maryland, College Park, College Park, MD 
Area:
DNA looping, transcription, topology
Website:
http://www.chem.umd.edu/jason-kahn/
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57 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2023 Pham TM, Miffin T, Sun H, Sharp KK, Wang X, Zhu M, Hoshika S, Peterson RJ, Benner SA, Kahn JD, Mathews DH. DNA Structure Design Is Improved Using an Artificially Expanded Alphabet of Base Pairs Including Loop and Mismatch Thermodynamic Parameters. Acs Synthetic Biology. PMID 37671922 DOI: 10.1021/acssynbio.3c00358  0.398
2023 Pham TM, Miffin T, Sun H, Sharp KK, Wang X, Zhu M, Hoshika S, Peterson RJ, Benner SA, Kahn JD, Mathews DH. DNA Structure Design Is Improved Using an Artificially Expanded Alphabet of Base Pairs Including Loop and Mismatch Thermodynamic Parameters. Biorxiv : the Preprint Server For Biology. PMID 37333404 DOI: 10.1101/2023.06.06.543917  0.392
2021 Gang O, Kahn J. Designer Nanomaterials through Programmable Assembly. Angewandte Chemie (International Ed. in English). PMID 34128306 DOI: 10.1002/anie.202105678  0.356
2020 Luteran EM, Kahn JD, Paukstelis PJ. Stability of the pH-Dependent Parallel-Stranded d(CGA) Motif. Biophysical Journal. 119: 1580-1589. PMID 32966760 DOI: 10.1016/J.Bpj.2020.09.002  0.463
2020 Zimmermann AC, White IM, Kahn JD. Nucleic acid-cleaving catalytic DNA for sensing and therapeutics. Talanta. 211: 120709. PMID 32070594 DOI: 10.1016/J.Talanta.2019.120709  0.806
2020 Zimmermann AC, Kahn JD, White IM. Isothermal DNAzyme-Mediated Bicyclic Rolling Circle Amplification Enables Simple Colorimetric Detection of a Target Sequence Biophysical Journal. 118: 152a. DOI: 10.1016/J.Bpj.2019.11.949  0.753
2019 Kahn JD, Hustedt JM. Measurement of the Length Dependence of DNA Cyclization using Next Generation Sequencing Biophysical Journal. 116: 500a. DOI: 10.1016/J.Bpj.2018.11.2698  0.817
2017 Wang X, Hoshika S, Peterson RJ, Kim MJ, Benner SA, Kahn JD. The Biophysics of Artificially Expanded Genetic Information Systems. Thermodynamics of DNA Duplexes Containing Matches and Mismatches Involving 2-Amino-3-nitropyridin-6-one (Z) and Imidazo[1,2-a]-1,3,5-triazin-4(8H)one (P). Acs Synthetic Biology. PMID 28094993 DOI: 10.1021/Acssynbio.6B00224  0.489
2016 Brinson RG, Miller JT, Kahn JD, Le Grice SF, Marino JP. Applying Thymine Isostere 2,4-Difluoro-5-Methylbenzene as a NMR Assignment Tool and Probe of Homopyrimidine/Homopurine Tract Structural Dynamics. Methods in Enzymology. 566: 89-110. PMID 26791977 DOI: 10.1016/Bs.Mie.2015.05.009  0.72
2015 Wang X, Sharp KK, Hoshika S, Bellaousov S, Zhang X, Mathews DH, Benner SA, Peterson RJ, Kahn JD. Structure and Thermodynamics of Aegis Nucleotides P and Z in DNA Biophysical Journal. 108: 395a. DOI: 10.1016/J.Bpj.2014.11.2165  0.49
2015 Brinson RG, Miller JT, Kahn JD, Le Grice SFJ, Marino JP. Applying Thymine Isostere 2,4-Difluoro-5-Methylbenzene as a NMR Assignment Tool and Probe of Homopyrimidine/Homopurine Tract Structural Dynamics Methods in Enzymology. DOI: 10.1016/bs.mie.2015.05.009  0.543
2014 Lee A, Karcz A, Akman R, Zheng T, Kwon S, Chou ST, Sucayan S, Tricoli LJ, Hustedt JM, Leng Q, Kahn JD, Mixson AJ, Seog J. Direct observation of dynamic mechanical regulation of DNA condensation by environmental stimuli. Angewandte Chemie (International Ed. in English). 53: 10631-5. PMID 25146232 DOI: 10.1002/Anie.201403499  0.709
2014 Kahn JD. DNA, flexibly flexible. Biophysical Journal. 107: 282-4. PMID 25028868 DOI: 10.1016/J.Bpj.2014.06.007  0.559
2014 Revalee JD, Blab GA, Wilson HD, Kahn JD, Meiners JC. Tethered particle motion reveals that LacI·DNA loops coexist with a competitor-resistant but apparently unlooped conformation. Biophysical Journal. 106: 705-15. PMID 24507611 DOI: 10.1016/J.Bpj.2013.12.024  0.615
2014 Chou ST, Hom K, Zhang D, Leng Q, Tricoli LJ, Hustedt JM, Lee A, Shapiro MJ, Seog J, Kahn JD, Mixson AJ. Enhanced silencing and stabilization of siRNA polyplexes by histidine-mediated hydrogen bonds. Biomaterials. 35: 846-55. PMID 24161165 DOI: 10.1016/J.Biomaterials.2013.10.019  0.745
2013 Gowetski DB, Kodis EJ, Kahn JD. Rationally designed coiled-coil DNA looping peptides control DNA topology. Nucleic Acids Research. 41: 8253-65. PMID 23825092 DOI: 10.1093/Nar/Gkt553  0.844
2013 Goodson KA, Wang Z, Haeusler AR, Kahn JD, English DS. LacI-DNA-IPTG loops: equilibria among conformations by single-molecule FRET. The Journal of Physical Chemistry. B. 117: 4713-22. PMID 23406418 DOI: 10.1021/Jp308930C  0.827
2013 Chou ST, Leng Q, Scaria P, Kahn JD, Tricoli LJ, Woodle M, Mixson AJ. Surface-modified HK:siRNA nanoplexes with enhanced pharmacokinetics and tumor growth inhibition. Biomacromolecules. 14: 752-60. PMID 23360232 DOI: 10.1021/Bm3018356  0.72
2012 Haeusler AR, Goodson KA, Lillian TD, Wang X, Goyal S, Perkins NC, Kahn JD. FRET studies of a landscape of Lac repressor-mediated DNA loops. Nucleic Acids Research. 40: 4432-45. PMID 22307389 DOI: 10.1093/Nar/Gks019  0.816
2011 Peters JP, Becker NA, Rueter EM, Bajzer Z, Kahn JD, Maher LJ. Quantitative methods for measuring DNA flexibility in vitro and in vivo. Methods in Enzymology. 488: 287-335. PMID 21195233 DOI: 10.1016/B978-0-12-381268-1.00012-4  0.621
2011 Kahn JD, Haeusler AR, Goodson KA, English DS. FRET and Sm-FRET Characterization of a Lac Repressor-Dna Looping Landscape Biophysical Journal. 100: 70a-71a. DOI: 10.1016/J.Bpj.2010.12.586  0.837
2010 Bond LM, Peters JP, Becker NA, Kahn JD, Maher LJ. Gene repression by minimal lac loops in vivo. Nucleic Acids Research. 38: 8072-82. PMID 21149272 DOI: 10.1093/Nar/Gkq755  0.647
2010 Haeusler AR, Goodson K, Kahn JD. A LacI-DNA Looping Landscape and Allosteric Effects on the Loop Shapes Biophysical Journal. 98: 72a. DOI: 10.1016/J.Bpj.2009.12.410  0.827
2009 Goodson K, Haeusler AR, English D, Kahn JD. Inducer Effects on Lac Repressor-Mediated DNA Loops: Single-Molecule FRET Studies Biophysical Journal. 96: 418a. DOI: 10.1016/J.Bpj.2008.12.2136  0.832
2008 Lillian TD, Goyal S, Kahn JD, Meyhöfer E, Perkins NC. Computational analysis of looping of a large family of highly bent DNA by LacI. Biophysical Journal. 95: 5832-42. PMID 18931251 DOI: 10.1529/Biophysj.108.142471  0.57
2008 Becker NA, Kahn JD, Maher LJ. Eukaryotic HMGB proteins as replacements for HU in E. coli repression loop formation. Nucleic Acids Research. 36: 4009-21. PMID 18515834 DOI: 10.1093/Nar/Gkn353  0.569
2007 Becker NA, Kahn JD, Maher LJ. Effects of nucleoid proteins on DNA repression loop formation in Escherichia coli. Nucleic Acids Research. 35: 3988-4000. PMID 17553830 DOI: 10.1093/Nar/Gkm419  0.626
2006 Levin JD, Fiala D, Samala MF, Kahn JD, Peterson RJ. Position-dependent effects of locked nucleic acid (LNA) on DNA sequencing and PCR primers. Nucleic Acids Research. 34: e142. PMID 17071964 DOI: 10.1093/Nar/Gkl756  0.385
2006 Amzallag A, Vaillant C, Jacob M, Unser M, Bednar J, Kahn JD, Dubochet J, Stasiak A, Maddocks JH. 3D reconstruction and comparison of shapes of DNA minicircles observed by cryo-electron microscopy. Nucleic Acids Research. 34: e125. PMID 17012274 DOI: 10.1093/Nar/Gkl675  0.442
2006 McDonald RJ, Kahn JD, Maher LJ. DNA bending by bHLH charge variants. Nucleic Acids Research. 34: 4846-56. PMID 16973898 DOI: 10.1093/Nar/Gkl552  0.539
2006 KAHN JD, CHEONG R, MEHTA RA, EDELMAN LM, MORGAN MA. FLEXIBILITY AND CONTROL OF PROTEIN–DNA LOOPS Biophysical Reviews and Letters. 1: 327-341. DOI: 10.1142/S1793048006000276  0.832
2006 Leng Q, Kahn J, Zhu J, Scaria P, Mixson AJ. 203. Salt Conditions during Polyplex Formation Significantly Alters Transfection Molecular Therapy. 13: S79. DOI: 10.1016/J.Ymthe.2006.08.227  0.388
2005 Morgan MA, Okamoto K, Kahn JD, English DS. Single-molecule spectroscopic determination of lac repressor-DNA loop conformation. Biophysical Journal. 89: 2588-96. PMID 16085773 DOI: 10.1529/Biophysj.105.067728  0.583
2005 Becker NA, Kahn JD, Maher LJ. Bacterial repression loops require enhanced DNA flexibility. Journal of Molecular Biology. 349: 716-30. PMID 15893770 DOI: 10.1016/J.Jmb.2005.04.035  0.603
2005 Becker NA, Kahn JD, Maher LJ. Corrigendum to “Bacterial Repression Loops Require Enhanced DNA Flexibility” [J. Mol. Biol. (2005) 349, 716–730] Journal of Molecular Biology. 353: 924-926. DOI: 10.1016/J.Jmb.2005.09.005  0.579
2004 Lilja AE, Jenssen JR, Kahn JD. Geometric and dynamic requirements for DNA looping, wrapping and unwrapping in the activation of E.coli glnAp2 transcription by NtrC. Journal of Molecular Biology. 342: 467-78. PMID 15327947 DOI: 10.1016/J.Jmb.2004.07.057  0.81
2004 McTigue PM, Peterson RJ, Kahn JD. Sequence-dependent thermodynamic parameters for locked nucleic acid (LNA)-DNA duplex formation. Biochemistry. 43: 5388-405. PMID 15122905 DOI: 10.1021/Bi035976D  0.466
2003 Edelman LM, Cheong R, Kahn JD. Fluorescence resonance energy transfer over approximately 130 basepairs in hyperstable lac repressor-DNA loops. Biophysical Journal. 84: 1131-45. PMID 12547794 DOI: 10.1016/S0006-3495(03)74929-7  0.616
2002 Hardwidge PR, Kahn JD, Maher LJ. Dominant effect of protein charge rather than protein shape in apparent DNA bending by engineered bZIP domains. Biochemistry. 41: 8277-88. PMID 12081476 DOI: 10.1021/Bi020185H  0.578
2002 Kahn JD. DNA topology: Applications to gene expression Current Organic Chemistry. 6: 815-826. DOI: 10.2174/1385272023373897  0.473
2000 Kahn JD. Topological effects of the TATA box binding protein on minicircle DNA and a possible thermodynamic linkage to chromatin remodeling. Biochemistry. 39: 3520-4. PMID 10736150 DOI: 10.1021/Bi992263F  0.576
1999 Kahn JD. Methods for analyzing DNA bending. Methods in Molecular Biology (Clifton, N.J.). 94: 109-23. PMID 12844867 DOI: 10.1385/1-59259-259-7:109  0.54
1999 Mehta RA, Kahn JD. Designed hyperstable Lac repressor.DNA loop topologies suggest alternative loop geometries. Journal of Molecular Biology. 294: 67-77. PMID 10556029 DOI: 10.1006/Jmbi.1999.3244  0.823
1999 Davis NA, Majee SS, Kahn JD. TATA box DNA deformation with and without the TATA box-binding protein. Journal of Molecular Biology. 291: 249-65. PMID 10438619 DOI: 10.1006/Jmbi.1999.2947  0.651
1998 Kahn JD, Crothers DM. Measurement of the DNA bend angle induced by the catabolite activator protein using Monte Carlo simulation of cyclization kinetics. Journal of Molecular Biology. 276: 287-309. PMID 9514724 DOI: 10.1006/Jmbi.1997.1515  0.719
1998 Hockings SC, Kahn JD, Crothers DM. Characterization of the ATF/CREB site and its complex with GCN4. Proceedings of the National Academy of Sciences of the United States of America. 95: 1410-5. PMID 9465028 DOI: 10.1073/Pnas.95.4.1410  0.631
1997 Widlund HR, Cao H, Simonsson S, Magnusson E, Simonsson T, Nielsen PE, Kahn JD, Crothers DM, Kubista M. Identification and characterization of genomic nucleosome-positioning sequences. Journal of Molecular Biology. 267: 807-17. PMID 9135113 DOI: 10.1006/Jmbi.1997.0916  0.596
1996 Manning RS, Maddocks JH, Kahn JD. A continuum rod model of sequence-dependent DNA structure Journal of Chemical Physics. 105: 5626-5646. DOI: 10.1063/1.472373  0.482
1994 Kahn JD, Yun E, Crothers DM. Detection of localized DNA flexibility. Nature. 368: 163-6. PMID 8139661 DOI: 10.1038/368163A0  0.735
1994 Haran TE, Kahn JD, Crothers DM. Sequence elements responsible for DNA curvature. Journal of Molecular Biology. 244: 135-43. PMID 7966325 DOI: 10.1006/Jmbi.1994.1713  0.731
1993 Henriquez V, Milisavljevic V, Kahn JD, Gennaro ML. Sequence and structure of cmp, the replication enhancer of the Staphylococcus aureus plasmid pT181. Gene. 134: 93-8. PMID 8244037 DOI: 10.1016/0378-1119(93)90179-7  0.57
1993 Kahn JD, Crothers DM. DNA bending in transcription initiation. Cold Spring Harbor Symposia On Quantitative Biology. 58: 115-22. PMID 7956021 DOI: 10.1101/Sqb.1993.058.01.015  0.707
1992 Crothers DM, Drak J, Kahn JD, Levene SD. DNA bending, flexibility, and helical repeat by cyclization kinetics. Methods in Enzymology. 212: 3-29. PMID 1518450 DOI: 10.1016/0076-6879(92)12003-9  0.804
1992 Kahn JD, Crothers DM. Protein-induced bending and DNA cyclization. Proceedings of the National Academy of Sciences of the United States of America. 89: 6343-7. PMID 1321436 DOI: 10.1073/Pnas.89.14.6343  0.699
1990 Monforte JA, Kahn JD, Hearst JE. RNA folding during transcription by Escherichia coli RNA polymerase analyzed by RNA self-cleavage. Biochemistry. 29: 7882-90. PMID 1702018 DOI: 10.1021/Bi00486A015  0.548
1989 Kahn JD, Hearst JE. Reversibility of nucleotide incorporation by Escherichia coli RNA polymerase, and its effect on fidelity. Journal of Molecular Biology. 205: 291-314. PMID 2467002 DOI: 10.1016/0022-2836(89)90342-2  0.571
1986 Spielmann HP, Kahn JD, Hearst JE. New methods for probing nucleic acids. Bioessays : News and Reviews in Molecular, Cellular and Developmental Biology. 5: 232-4. PMID 2434078 DOI: 10.1002/Bies.950050512  0.726
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