College of Science and Health Theses and Dissertations

Date of Award

Spring 6-14-2013

Degree Type


Degree Name

Master of Science (MS)



First Advisor

Catherine Southern, Ph.D.

Second Advisor

Richard Niedziela, Ph.D.

Third Advisor

Caitlin Karver, Ph.D.


Ensemble and single molecule methods were used to study model systems of 11 base pair and 16 base pair oligonucleotides. From these experiments it was possible to determine the best ensemble analysis method to use, in conjunction with single molecule experiments, to investigate the structure of lgG in solution. To study the interactions within the antigen-binding fragments (Fab), the binding sites were labeled with a FRET pair. Single molecule fluorescence measurements on the antibody indicate minimal FRET occurring between the dye pair suggesting the distance is too large to be measured using single molecule FRET. Ensemble and single molecule FRET were also used to investigate proposed conformational changes that occur within the crystallizable fragment (Fe) region of the antibody when the oligosaccharides are removed. Ensemble measurements were indistinguishable for the lgG samples. The single molecule FRET histogram shows a narrow, 16% efficiency of energy transfer for the glycosylated lgG and a broad distribution with a center at 53% for the aglycosylated lgG. This suggests the absence of oligosaccharide molecules facilitates a greater flexibility within the Fe region of the antibody.

Included in

Chemistry Commons