Jason Kahn
Associate Professor

jdkahn@umd.edu
phone: 301.405.0058
fax: 301.405.9376

Lab web site

Chem. and Biochem. web home

Jason Kahn is interested in large scale DNA structure, on the biologically relevant length scale of 20-1000 base pairs. We study the shapes of protein-nucleic acid complexes and DNA loops, the functional consequences of changes in shape, and the design and control of DNA and protein-DNA shape. We use molecular biology techniques like DNA ring closure, electrophoretic mobility shift assays, and footprinting to guide hypotheses, and then move on to characterization with fluorescence resonance energy transfer (FRET), single-molecule FRET, and atomic force microscopy (AFM). Accomplishments in this area include the identification of negatively supercoiled minicircles upon ring closure of short fragments bound by the TATA box binding protein (TBP), which led to a proposal on the coupling between chromatin remodeling during transcriptional activation and enhanced TBP binding. We also showed that DNA loops anchored by the Lac repressor can exist in at least two conformations that are distinguishable by bulk and single-molecule FRET. Functional studies of gene regulation in bacteria complement our in vitro work. Currently we are most excited about designing DNA and proteins to form self-assembled protein-DNA nanostructures. Finally, we have applied interests in the hybridization thermodynamics of oligonucleotides containing modified chemistries, with an eye to improving the use of nucleic acids in diagnostics and therapeutics.

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.

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

Becker, Nicole A., Kahn, Jason D., and Maher, L. James (2007) “Effects of nucleoid proteins on DNA repression loops in E. coli.” Nucleic Acids Res. 35(12), 3988-4000.

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.

Levin, Joshua D., Fiala, Dean, Samala, Meinrado F., Kahn, Jason D., Peterson, Raymond J. (2006) “Position-Dependent Effects of Locked Nucleic Acid (LNA) on DNA Sequencing and PCR Primers.” Nucleic Acids Res., 34 (20), e142.

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 (18), e125.

McDonald, Robert J., Kahn, Jason D., Maher, L. James III (2006). “DNA bending by bHLH charge variants.” Nucleic Acids Res., 34, 4846-4856.

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.

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.

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.

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.

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, 1131-1145.

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.

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.

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.