Links to official web pages:

• My official department web page, my slightly less official page on the companion biochemistry-oriented site, and a short page at the College of Computer, Mathematical, and Natural Sciences.

• 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.

• More detail: 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. This rather outdated but still illustrative PDF research description, and for historical curiousity an even older brief research description/resume are still available.

• Practical applications of nucleic acid thermodynamics are done in collaboration with Celadon Laboratories, Inc.

• I mentored a Gemstone team, Genes to Fuels, that investigated the application of phytohormones to improving algal biofuel yield.

• Current publication list including links to collaborators.

• Undergraduate research opportunities and advice.

I teach several general chemistry, biochemistry, and special interest courses. Here is a collection of general teaching resources, including figures created for several courses, and instructions, examples, and tutorials for Jmol/Rasmol/Pymol-based viewing of biomolecule PDB files. For recent courses, lecture notes and other resources are available mainly through the ELMS system.

• Cuurent Teaching:

  Chemistry 271, General Chemistry and Energetics: Syllabus.This is a course covering the traditional material for the second half of general chemistry, but given in the fourth semester of the undergraduate series, after organic chemistry instead of before. I also include special topics applications like DNA hybridization thermodynamics and the redox reactions driving anaerobic metabolism.

  We have converted our graduate Nucleic Acids class to two 2-credit half-semester modules, Biochemistry 661 and 662, co-taught with Paul Paukstelis.

• An archive of past exams for all of my chemistry and biochemistry courses. Use at your own risk.

• A statement on plagiarism and intellectual honesty. Advice for success and failure (pdf) in coursework.

  Past courses:

  I do not actively maintain links on these older pages, and some course materials were provided primarily through Blackboard and are not available here.

  • Chemistry 271, General Chemistry and Energetics, at Blackboard. Here is the 2007 syllabus, and the 2009. Spring 2010 was similar.
  • Honors 228J, Nanotechnology: Fact, Hyperbole, and Fiction, at Blackboard. Here is a syllabus. The seminar course was given as part of the Honors Program (now College) on campus.
  • 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, Summer II 2208 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, Spring '06, and Fall '08 (syllabus).
  • Undergrad Biochem 461 stuff, most recently Spring '98.
  • Old Biochem 669B stuff, Spring '96.

• Some of my own favorite places.

• Biochemistry research here at the University of Maryland.

• University of Maryland Chem. and Biochem. Department home page. We were now part of the College of Computer, Mathematical and Natural Sciences.

• The Molecular and Cell Biology Program, now morphing into the MOCB Concentration Area in the umbrella BISI graduate program.

• The Bioengineering Program/Department.

• The list of other University of Maryland C+B faculty.

You can reach me at jdkahn@umd.edu

This page is designed using various tools, primarily Dreamweaver and hand-coding.