Return to JDK's lab home page or offical department home page.

You can search for my papers (mostly) at Pubmed with this link, although I do try to keep this one page up to date. The references include links to the journals and to the home pages of present collaborators and former research advisors. The linked abstracts were downloaded from NCBI/Entrez/PubMed or from the journals directly; now that it is so easy to link to the actual journals, I will not generally continue to update abstracts here. Here is my Google Scholar page.

Also, you can click on the button below for my publication list and citation stats as indexed in Web of Science. Note that paper numbering does not agree, because they include meeting abstracts and I include book chapters. If the button does not show up it may be available on my departmental page. I also have not figured out how to keep it up to date. The Google Scholar page is probably more useful. 

54. Kahn, Jason D., Lemke, Edward A. & Pappu, Rohit V. (2021). “Faces, facets, and functions of biomolecular condensates driven by multivalent proteins and nucleic acids.” Biophys. J. 120(7), E1-E4. DOI: 10.1016/j.bpj.2021.03.003. Text. Editorial introduction to a Special Issue on Phase Separation in Nucleic Acid Biochemistry and Signal Transduction.

53. Luteran, Emily M., Kahn, Jason D., & Paukstelis, Paul J. (2020). “Stability of the pH-Dependent Parallel-Stranded d(CGA) Motif.” Biophys. J. 119(8), 1580-1589. DOI: 10.1016/j.bpj.2020.09.002. Abstract.

52. Zimmermann, Alessandra C., White, Ian M., & Kahn, Jason. D. (2020). “Nucleic acid-cleaving catalytic DNA for sensing and therapeutics.” Talanta 211, 120709. DOI: 10.1016/j.talanta.2019.120709. Abstract.

51. Moore, Peter B., Eisenberg, David, & Kahn, Jason (2018). “Donald M. Crothers, 1937-2014.” prepared for the National Academy of Sciences Biographical Memoirs. The PDF of the memoir is available directly. I guess this is not strictly a publication, but helping with it was very much worth doing.

50. Wang, Xiaoyu, Hoshika, Shuichi, Peterson, Raymond J., Kim, Myong-Jung, Benner, Steven A., & Kahn, Jason D. (2017). “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 6, 782-792. DOI: 10.1021/acssynbio.6b00224. Abstract.

49. Brinson, Robert G., Miller, Jennifer T., Kahn, Jason D., Le Grice, Stuart F.J., & Marino John P. (2016). “Chapter Four - Applying Thymine Isostere 2,4-Difluoro-5-Methylbenzene as a NMR Assignment Tool and Probe of Homopyrimidine/Homopurine Tract Structural Dynamics.” In Zvi Kelman, ed., Methods in Enzymology 566, 89-110. DOI:10.1016/bs.mie.2015.05.009. Abstract.

48. Lee, Amy, Karcz, Adam, Akman, Ryan, Zheng, Tai, Kwon, Sara, Chou, Szu-Ting, Sucayan, Sarah, Tricoli, Lucas J., Hustedt, Jason M., Leng, Qixin, Kahn, Jason D., Mixson, A. James, & Seog, Joonil (2014). “Direct Observation of Dynamic Mechanical Regulation of DNA Condensation by Environmental Stimuli.” Angewandte Chemie 53(40), 10807-10811. DOI:10.1002/ange.201403499. Abstract.

47. Kahn, Jason D. (2014). “DNA, Flexibly Flexible.” Biophys. J. 107(2), 282-284. Invited minireview. DOI: 10.1016/j.bpj.2014.06.007. Text.

46. Revalee, Joel D., Blab, Gerhard A., Wilson, Henry D., Kahn, Jason D. & Meiners, Jens-Christian (2014). “Tethered Particle Motion Reveals that LacI-DNA Loops Coexist with a Competitor-Resistant but Apparently Unlooped Conformation.” Biophys. J. 106(3), 705-715. DOI:10.1016/j.bpj.2013.12.024. Abstract.

45. Chou, Szu-Ting, Hom, Kellie, Zhang, Daoning, Leng, Qixin, Tricoli, Lucas J., Hustedt, Jason M., Lee, Amy, Shapiro, Michael J., Seog, Joonil, Kahn, Jason D., & Mixson, A. James. (2014). “Enhanced silencing and stabilization of siRNA polyplexes by histidine-mediated hydrogen bonds.” Biomaterials 35, 846-855. DOI: 10.1016/j.biomaterials.2013.10.019. Abstract

44. Gowetski, Daniel B., Kodis, Erin J., & Kahn, Jason D. (2013). “Rationally designed coiled-coil DNA looping peptides control DNA topology.” Nucleic Acids Research. 41(17), 8253-8265. DOI: 10.1093/nar/gkt553. Open Access. Abstract.

43. Goodson, Kathy A., Wang, Zifan, Haeusler, Aaron R., Kahn, Jason D., & English, Douglas S. (2013). “LacI-DNA-IPTG Loops: Equilibria among Conformations by Single-Molecule FRET.” Journal of Physical Chemistry B. 117(16), 4713-4722. DOI: 10.1021/jp308930. Abstract. Part of the Paul Barbara Memorial Issue.

42. Chou, Szu-Ting, Leng, Qixin, Scaria, Puthupparampil, Kahn, Jason D., Tricoli, Lucas J., Woodle, Martin & Mixson, A. James (2013). “Surface-modified HK:siRNA nanoplexes with enhanced pharmacokinetics and tumor growth inhibition.” Biomacromolecules, 14(3), 752-760. DOI: 10.1021/bm30183560. Abstract.

41. Haeusler, Aaron R., Goodson, Kathy A., Lillian, Todd D., Wang, Xiaoyu, Goyal, Sachin, Perkins, Noel C. and Kahn, Jason D. (2012). “FRET studies of a landscape of Lac repressor-mediated DNA loops.” Nucleic Acids Res. 40(10), 4432-4445. Open access. Abstract. Highlighted in Faculty of 1000.

40. Peters, J. P., Becker, N. A., Rueter, E. M., Bajzer, Z., Kahn, J. D., & Maher, L. J. (2011). “Quantitative methods for measuring DNA flexibility in vitro and in vivo.” Methods in Enzymology, 488, 287–335.

39. Bond, L. M., Peters, J. P., Becker, N. A., Kahn, J. D., & Maher, L. J. (2010). “Gene repression by minimal lac loops in vivo.Nucleic Acids Res., 38(22), 8072–8082. doi:10.1093/nar/gkq755

38. Kahn, Jason D., Jenssen, James R., and Vittal, Vasavi (2009). “Useful Intrusions of DNA Topology into Experiments on Protein-DNA Geometry,” in Mathematics of DNA Structure, Function and Interactions, eds. C.J. Benham, S. Harvey, W. K. Olson, D.W.L. Sumners and D. Swigon. The IMA Volumes in Mathematics and its Applications, vol. 150. Springer Science+Business Media, New York, pp. 159-175.

37. Lillian, Todd D., Goyal, Sachin, Kahn, Jason D., Meyhöfer, Edgar, and Perkins, N. C. (2008). “Computational Analysis of Looping of a Large Family of Highly Bent DNA by LacI.” Biophysical Journal 95, 5832-5842. Abstract.

36. Becker, Nicole A., Kahn, Jason D., and Maher, L. James (2008) “Eukaryotic HMGB proteins as replacements for HU in E. coli repression loop formation.” Nucleic Acids Res. 36(12), 4009-4021. Abstract.

35. Leng, Qixin, Kahn, Jason, Zhu, Jingsong, Scaria, Puthapparampil, & Mixson, A. James. (2007) “Needle-like morphology of H2K4b polyplexes associated with increases in transfection in vitro.” Cancer Therapy, 5B, 193-202. Available here.

34. Becker, Nicole A., Kahn, Jason D., and Maher, L. James III. (2007). “Effects of nucleoid proteins on DNA repression loop formation in Escherichia coli.” Nucleic Acids Res., 35, 3988-4000. Open access at NAR.

33. Kahn, Jason D., Cheong, Raymond, Mehta, Ruchi A., Edelman, Laurence M., and Morgan, Michael A. (2006). “Flexibility and Control of Protein-DNA Loops.” Biophysical Reviews and Letters, 1 (4), 327-341. Preprint with supplemental information available at the Digital Repository of the Univ. of Maryland (DRUM), Presented at the Asia and Pacific Workshop on Biological Physics. Official version available here.

32. Levin, Joshua D., Fiala, Dean, Samala, Meinrado F., Kahn, Jason D., Peterson, Raymond J. “Position-Dependent Effects of Locked Nucleic Acid (LNA) on DNA Sequencing and PCR Primers.” Nucleic Acids Res., 34, e142. DOI:10.1093/nar/gkl756. Open access:

31. Amzallag, Arnaud, Vaillant, Cedric, Jacob, Mathews, Unser, Michael, Bednar, Jan, Kahn, Jason, Stasiak, Andrzej, Dubochet, Jacques, and Maddocks, John (2006).“3-D Reconstruction and Comparison of Shapes of DNA Minicircles Observed by Cryo-Electron Microscopy.” Nucleic Acids Res., 34, e125. DOI:10.1093/nar/gkl675. Open access: Journal cover:

30. McDonald, Robert J., Kahn, Jason D., Maher, L. James III (2006). “DNA bending by bHLH charge variants.” Nucleic Acids Res., 34, 4846-4856. DOI: 10.1093/nar/gkl552. Open access:

29. Morgan, Michael A. Okamoto, Kenji, Kahn, Jason D. and English, Douglas S. (2005). "Single-Molecule Spectroscopic Determination of Lac Repressor-DNA Loop Conformation." Biophys. J., 89, 2588-2596.DOI:10.1529/biophysj.105.067728. Available here. Michael Morgan was a graduate student with me.

28. Becker, Nicole A., Kahn, Jason D., and Maher, L. James III. (2005). “Bacterial Repression Loops Require Enhanced DNA Flexibility.” J. Mol. Biol., 349, 716-730. DOI:10.1016/j.jmb.2005.04.035. Available through Science Direct at the JMB page, or this link will take you there directly.

27. Lilja, Anders E., Jenssen, James R., and Kahn, Jason D. (2004). “Geometric and Dynamic Requirements for DNA Looping, Wrapping and Unwrapping in the Activation of E. coli glnAp2 Transcription by NtrC." J. Mol. Biol., 342, 467-478. DOI:10.1016/j.jmb.2004.07.057. Available through Science Direct at the JMB page, or this link will take you there directly. Anders Lilja and Jim Jenssen were grad students in the group.

26. McTigue, Patricia M., Peterson, Raymond J., and Kahn, Jason D. (2004). “Sequence-Dependent Thermodynamic Parameters for Locked Nucleic Acid (LNA)-DNA Duplex Formation.Biochemistry, 43, 5388-5405. DOI: 10.1021/bi035976d. Available on the Biochemistry web page here.

25. Edelman, Laurence M., Cheong, Raymond, and Kahn, Jason D. (2003). “Fluorescence Resonance Energy Transfer over ~130 Basepairs in Hyperstable Lac Repressor-DNA Loops.Biophysical Journal, 84(Feb), 1131-1145. Available on the Biophys. J. web site here. Larry Edelman and Raymond Cheong were undergraduate researchers in the lab.

24. Kahn, Jason D. (2002). “DNA Topology: Applications to Gene Expression.” Current Organic Chemistry, 6(9), 815-827 (invited review).

23. Hardwidge, Philip R., Kahn, Jason D., and Maher, L. James III. (2002). "Dominant effect of protein charge rather than protein shape in apparent DNA bending by engineered bZIP domains." Biochemistry, 41, 8277-8288. Available on the Biochemistry web page here.

22. Kahn, Jason D. (2000). "Topological Effects of the TATA Box Binding Protein on Minicircle DNA and a Possible Thermodynamic Linkage to Chromatin Remodeling." Biochemistry 39, 3520-3524. Available on the Biochemistry web page here.

21. Mehta, Ruchi A. and Kahn, Jason D. (1999). "Designed Hyperstable Lac Repressor-DNA Loop Topologies Suggest Alternative Loop Geometries." J. Mol. Biol. 294, 67-77. Ruchi Mehta was a graduate student with me.

20. Davis, Natalie A., Majee, Sangita S., and Kahn, Jason D. (1999). "TATA Box DNA Deformation with and without the TATA Box Binding Protein." J. Mol. Biol. 291, 249-265. Natalie Davis was a graduate student and Sangita Majee was a post-doc.

19. Hockings, Susan C., Kahn, Jason D., and Crothers, Donald M. (1998). "Characterization of the ATF/CREB Site and its complex with GCN4." Proc. Natl. Acad. Sci. USA 95, 1410-1415.

18. Kahn, Jason D. and Crothers, Donald M. (1998). "Measurement of the DNA Bend Angle Induced By the Catabolite Activator Protein Using Monte Carlo Simulation of Cyclization Kinetics." J. Mol. Biol. 276, 287-309.

17. Kahn, Jason D. (1997, or 1999). "Methods for Analyzing DNA Bending", in Protocols in DNA Topology and DNA Topoisomerases, eds. M.-A. Bjornsti and N. Osheroff. Methods in Molecular Biology Series, vol. 94. Humana Press, Totawa, NJ., pp. 109-125.

16. Kahn, Jason D. and Jarvis, Bruce B. (1997). "Synthesis of Sulfonate-Linked DNA. Defining the Interactions Between DNA and the Exonuclease Domains of DNA Polymerases."Chemtracts--Organic Chemistry 10, 5-9.

15. Widlund, Hans R., Cao, Hui, Simonsson, Stina, Magnussion, Elisabet, Simonsson, Tomas, Nielsen, Peter E., Kahn, Jason D., Crothers, Donald M., and Kubista, Mikael. (1997). "Identification and Characterization of Genomic Nucleosome-positioning Sequences." J. Mol. Biol. 267, 807-817.

14. Manning, Robert S., Maddocks, John H., and Kahn, Jason D. (1996). "A continuum rod model of sequence-dependent DNA structure." J. Chem. Phys. 105, 5626-5646.

13. Haran, Tali E., Kahn, Jason D., and Crothers, Donald M. (1994). "Sequence elements responsible for DNA curvature." J. Mol Biol. 244, 135-143.

12. Kahn, Jason D., Yun, Elizabeth, and Crothers, Donald M. (1994). "Identification of localized DNA flexibility." Nature 368, 163-166.

11. Kahn, Jason D. and Crothers, Donald M. (1993). "DNA bending in transcription initiation." Cold Spring Harbor Symp. in Quant. Biol. 58, 115-122.

10. Henriquez, Vitalia, Milisavljevic, Vladana, Kahn, Jason D., and Gennaro, Maria L. (1993). "Sequence and structure of cmp, the replication enhancer of the Staphylococcus aureus plasmid pT181." Gene 134, 93-98.

9. Kahn, Jason D. and Crothers, Donald M. (1992). "Protein-induced bending and DNA cyclization." Proc. Natl. Acad. Sci. USA 89(14), 6343-6347.

8. Crothers, Donald M., Drak, Jacqueline, Kahn, Jason D., and Levene, Stephen D. (1992). "DNA bending, flexibility, and helical repeat by cyclization kinetics." Methods Enzymol. 212, 1-29.

7. Kahn, Jason D. (1990). "Reversibility of nucleotide incorporation and the fidelity of RNA polymerase, mechanistic studies of transcription initiation and elongation, and the interaction of RecA protein with psoralen-modified DNA." Dissertation, University of California, Berkeley.

6. Monforte, Joseph A., Kahn, Jason D., and Hearst, John E. (1990). "RNA folding during transcription by Escherichia coli RNA polymerase analyzed by RNA self-cleavage." Biochemistry 29(34), 7882-7890.

5. Kahn, Jason D. and Hearst, John E. (1989). "Reversibility of nucleotide incorporation by E. Coli RNA polymerase and its effect on fidelity." J. Mol. Biol. 205(2), 291-314.

4. Kahn, Jason D., Haag, Armin, and Schleyer, Paul v. R. (1988). "Mass spectrometry of gas-phase lithium alkoxides." J. Phys. Chem. 92(1), 212-220.

3. Spielmann, H. Peter, Kahn, Jason D., and Hearst, John E. (1986). "New methods for probing nucleic acids." BioEssays 5(5), 232-234.

2. Bergsma, John P., Coladonato, Mark H., Edelsten, Pamela M., Kahn, Jason D., Wilson, Kent R., and Fredkin, Donald R. (1986). "Transient x-ray scattering calculated from molecular dynamics." J. Chem. Phys. 84(11), 6151-6160.

1. Bado, Philippe, Berens, Peter H., Bergsma, John P., Coladonato, Mark H., Dupuy, Charles G., Edelsten, Pamela M., Kahn, Jason D., Wilson, Kent R., and Fredkin, Donald R. (1983). "Molecular dynamics of chemical reactions in solution." Laser Chem. 3, 231-247.