Date of Award

Fall 12-14-2018

Document Type


Degree Name

Master of Science in Chemistry (MSChem)



First Advisor

Dr. Irene Zegar

Second Advisor

Dr. James McAfee

Third Advisor

Dr. Khamis Siam

Fourth Advisor

Dr. Christine Brodsky


The systematic evolution of ligands by exponential enrichment (SELEX) is a powerful method for the development of high affinity RNA ligands toward and infinite array of target molecules. SELEX is based upon the generation of a randomized population of RNA or DNA molecules followed by a target molecule that selects high affinity ligands from the randomized population followed by the subsequent amplification of the selected molecules. The procedure of selection and amplification is typically carried out through multiple cycles to insure that the identified ligands exhibits the highest affinity toward the target. The procedure is very time- consuming often taking months to complete, as well as being costly. Another drawback is that every surface that the randomized RNA molecules come in contact with becomes a potential target. Therefore, numerous artefactual ligands are often the product of the procedure. To enhance the efficiency and to reduce the problems associated with controlling surface selection problems we are investigating the efficacy of using a computer generated SELEX procedure. To accomplish this we have generated a library of 5,000 randomized RNA molecules and used comparative modeling to determine the structure of about 1000 of these sequences. SELEX has been used to identify high affinity RNA ligands for the RNA binding domain of the heterogeneous nuclear ribonucleoprotein C (hnRNP C). To test our system, we included one of these RNA aptamers identified from this study, in our library of randomized molecules, and demonstrated that our computational method could select the high affinity ligand from the random population.


final version

Included in

Biochemistry Commons


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