About Student Research
Nicole Becker (1995–1999)
In vivo footprinting approaches to searching for unusual DNA structures in living mammalian cells
Nicole Becker received her BS degree in biotechnology from St. Cloud State University and came to Mayo Graduate School to study the potential for monitoring the formation of unusual DNA structures within living cells. A number of interesting variations to conventional double-helical DNA structure have been detected in vitro (e.g. triple-helical DNA, Z-form DNA, G-quadruplex DNA) but the in vivo biology of such putative structures remains obscure at best. These structures share the property of having unpaired DNA bases within or adjacent to their location if embedded in B-form DNA. Nicole traveled to the City of Hope National Medical Center to learn from Gerd Pfeiffer techniques for in vivo footprinting by ligation-mediated PCR for application to monitoring DNA structure in vivo. Her work focused on a long homopurine-homopyrimidine element upstream of the murine metallotheionein-I gene in cultured cells. This element forms an unusual triplex structure at low pH in vitro, and is representative of many similar elements that are over-represented in mammalian genomes. Nicole carefully studied the structure of the MT-I homopurine/homopyrimidine element and other promoters where structural polymorphisms had been suggested. Her work detected no unusual DNA structures in vivo at these sites, raising important questions about the prevalence of unusual DNA structures in vivo.