Kahn Lab Web Site
Department of Chemistry and Biochemistry
University of Maryland, College Park
Research: We are interested in the structure, function, and design of protein-DNA complexes, focusing on the 50-1000 bp length scale. This is the biologically-relevant domain of multi-protein DNA complexes, DNA looping, chromatin, and DNA topology. 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.
Here are two very large PDF files (1) and (2) that outline much of our work in the context of the field. These are informal, not comprehensive; I welcome any feedback you may have. Earlier versions were originally presented at a workshop at the Institute for Mathematics and its Applications (IMA), Univ. of Minnesota.
Practical applications of nucleic acid thermodynamics are done in collaboration with Celadon Laboratories, Inc.
Current publication list including links to collaborators.
General teaching resources: Overheads from several courses, and instructions, examples, and tutorials for Jmol/Rasmol/Pymol-based viewing of biomolecule PDB files.
My official department web page and my slightly less official page on the companion biochemistry-oriented site.
This rather outdated but still illustrative PDF research description, and for historical curiousity an even older brief research description/resume are still available.
Undergraduate research opportunities and advice.
A statement on plagiarism and intellectual honesty.
An archive of past exams for all of my biochemistry courses. Use at your own risk.
Chemistry 271, General Chemistry and Energetics, at Blackboard. Here is a syllabus.
Biochemistry 673, graduate Regulatory Networks = Regulation of Metabolism = Signal transduction, Spring '05.and Fall '07.
Biochemistry 463, undergraduate Biochemistry and Physiology, Spring 2003 and Fall 2002, Summer II 2007 syllabus. And here are some figures.
Biochem 674, graduate Nucleic Acids, Fall '99, Fall '00, Fall '01, Fall '04, Fall '05, Fall '06.
Biochem 465, undergraduate Biochemistry III = Biological Information Processing, Spring '02, Spring '01, Spring '99, and Spring '06.
Undergrad Biochem 461 stuff, most recently Spring '98.
Biochemistry research here at the University of Maryland.
University of Maryland Chem. and Biochem. Department home page. We are part of the College of Chemical and Life Sciences.
The Molecular and Cell Biology Program.
You can reach me at jdkahn@umd.edu
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