USD Chemistry and Biochemistry  
   
 
Research

Synthesis, and study of non-natural DNA nucleosides and studies of ligand:DNA interactions by NMR .

In collaboration with Dr. Tammy Dwyer, we are studying the effect that replacement of Watson-Crick base pairs with non-hydrogen bonding isosteres has on the structure of DNA duplexes and on their ability to recognize and bind drug molecules.   In our early work, using 2-D NMR techniques, we have determined the structure of a duplex containing a central G-C base pair and compared it to a G-T wobble base pair and a G-F base pair. We have learned that the G-F base pair behaves somewhat like a hybrid with the G-side of the duplex retaining characteristics of a typical Watson-Crick base pair while the F containing strand has features of a wobble base pair. These results may have implications in the study of mismatch DNA repair.

Pfaff, D. A.; Clarke, K. M.; Parr, T. A.; Cole, J. M.; Geierstanger, B. H.; Tahmassebi, D. C.; Dwyer, T. J., Journal of the American Chemical Society, (2008), DOI: 10.1021/ja7103608.
 
Utilizing a novel fluorophore-quencher pair to monitor protein motion
In collaboration with Dr. David Millar at TSRI, we are studying the motion of the Klenow fragment of DNA polymerase when it recognizes and then incorporates nucleotides. The figure on the left overlays the “open” form of Klenow when it “samples” available nucleotides to position opposite the template strand. The O-helix colored green in the “open” form moves closer to the DNA in the “closed” form (blue) when it has bound the correct incoming nucleotide. We are studying the motion of the O-helix by positioning a quencher along the O-helix and a novel fluorescent nucleoside in the DNA primer:template.
 
Synthesis and study of supramolecular host molecules
A family of supramolecular host complexes, which vary by the nature of the amino acid spacer group, have been synthesized. The alanine complex is shown on the left. The host molecule contains an organic template, amino acids as spacer molecules, and is closed by the addition of Fe(II) which complexes with the bipyridine ligands. These complexes exhibit strong diastereoselectivity in their formation which depends both on the nature of the amino acid spacer and the solvent. Studies continue to help predict this selectivity and to study how the selectivity in formation may be related to selectivity in complex interaction with suitable chiral guests.