DNA Research at UAF

Shown below is a typical bent DNA-protein complex, the E. coli CAP-DNA complex. The structure was determined by G. Parkinson, et al. (file 1ber from the Protein Data Bank). The bending is achieved in part by neutralizing the negative charges of the sugar phosphates on one side of the DNA double helix by specific interactions with positively charged amino acid sidechains of the CAP protein.

Students in J. Keller's lab are studying interactions of the DgdR protein with its cognate site. This is a member of the large LysR family of prokaryotic transcriptional regulators. This research involves various experimental approaches including expression and purification of the protein, in vitro footprinting of the protein-DNA complex, physical characterization of the affinity and shape of the complex using gel mobility shift assays.

Bert Boyer and his students are focusing on several proteins involved in control of thermogenesis. They use Arctic ground squirrels, which hibernate and undergo periodic re-warming, to study the molecular mechanisms responsible for thermogenesis. They have cloned and sequenced some related genes, and have done in vivo DNA footprinting to identify regulatory protein binding sites.
 

Show +-charged sidechains (Lys=blue, His=green, Arg=dark green)

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