About Student Research
Robert McDonald (2002–2006)
Making new proteins that bend DNA
After graduating from the University of Minnesota - Twin Cities, Bob McDonald entered Mayo's M.D./Ph.D. program and undertook a Ph.D. thesis project to extend our understanding of how DNA can be bent by proteins. McDonald worked with purified recombinant proteins based on small, natural yeast DNA binding proteins Gcn4p and Pho4p. These proteins bind DNA as dimers, using recognition of the major grooves of DNA by alpha-helices.
Previous students Julie Soukup and Phil Hardwidge in the laboratory had shown that small proteins of these kinds could be engineered to alter their electric charge in regions adjacent to the DNA contact surface. Such changes have the potential to alter the electrostatic attraction and repulsion forces experienced by the DNA, and to create asymmetric charge neutralization. Bob studied the extent to which these electrostatic changes could induce bending. Bob's work used both conventional electrophoretic gel mobility assays of DNA shape, and the application of fluorescence resonance energy transfer spectroscopy to demonstrate the direction and extent of DNA bending by charged proteins. He also developed methods for investigation of these problems by nuclear magnetic resonance spectroscopy.