Date of Award

Spring 1-1-2010

Document Type


Degree Name

Master of Science (MS)


Chemistry & Biochemistry

First Advisor

Arthur Pardi

Second Advisor

Robert T. Batey

Third Advisor

Marcelo C. Sousa


Aptamers consist of nucleic acids that are selected from an in vitro library in order to bind a specific target or catalyze a reaction. Many aptamer-ligand structures have been solved in recent years to characterize the molecular mechanisms that explain the high affinity and specificity observed in these interactions. To this end, NMR resonance assignment experiments were performed as a necessary first step to calculating the solution structure of a therapeutically-active RNA aptamer, Macugen, bound to its in vivo target, the heparin binding domain (HBD) of vascular endothelial growth factor 165 (VEGF165). Though the resonance assignment of Macugen is challenging due to its inability to be isotopically-labeled, techniques were employed that take advantage of the unique chemical modifications of this nucleic acid that are not present in traditional, unmodified RNA. Using the information obtained from two-dimensional heteronuclear (19F, 1H) and homonuclear (1H, 1H) experiments, assignments were made for a sizable number of Macugen atoms. The assignments made in this work will be necessary to calculate a solution structure to better understand the molecular mechanisms that give rise to the high affinity and specificity observed in the Macugen-HBD complex.