Date of Award


Document Type

Honors Thesis

Degree Name

Bachelor of Science



Advisor/Committee Chair

Sweta Vangaveti

Committee Member

Alan Chen


In the recent years, there has been a growing demand for the development of antibiotic treatments as bacterial infections have acquired defense mechanisms to commonly used antibiotics, such as penicillin. During the growth of bacterial cells, resistant mutants are able to survive antibiotic treatment and continue proliferation. Thus, creating a resistant bacterial cell population that can no longer be targeted through antibiotic treatment. Due to the recent need of new approaches, there has been an explosion of research in developing techniques that combat bacterial resistance. Both bacteriophage-RNA aptamer binding and modifications in bacterial tRNA show potential to be exploited for antibiotic development. However, further development is needed as obtaining purified bacteriophages is currently a rather difficult process. Another approach currently being investigated are using RNA aptamers, obtained through SELEX, for binding to the bacteriophage. Additionally, modifications of uridine at the 34th wobble position in bacterial tRNA has also been shown to be a promising method to combat antibiotic resistance as these modifications have been linked to the stress pathways in bacteria. In this project, we use all-atom molecular dynamics simulations (MDS) to find the binding sites of various RNA aptamers and both parameterize and model 8 uridine modifications to characterize andheir base-pairing specificities.

Included in

Chemistry Commons