Date of Award

Spring 5-28-2017

Document Type

Undergraduate Honors Thesis

Degree Name

Bachelor of Arts in Biochemistry


Chemistry & Biochemistry


Dr. Tammy Dwyer, PhD


DNA is the genetic blueprint responsible for the traits of living organisms. The "genetic alphabet" consists of four molecules called nucleobases, represented by the letters A, T, G, and C strung together in a "strand." A DNA duplex consists of two "strands" held together such that A is across from T and G across from C, referred to A-T and G-C "base pairs". Recently, the genetic alphabet or code has been expanded by synthetic biologists in an effort to unveil new insights to the machinery of DNA replication, and potentially develop new medicines to cure diseases like HIV. The new unnatural base pair 5SICS-NaM is the first to be stably replicated by a semi-synthetic E. Coli organism. This project investigates the structure of a novel DNA duplex containing two 5SICS-NaM pairs arranged side-by-side using a technique called NMR spectroscopy. Thus far, NMR chemical shift assignments for this duplex have been largely completed which provide some information as to the structural configuration of the base pairs. Preliminary results indicate that one of the two adjacent 5SICS-NaM pairs is situated within the duplex, whereas the other may have the 5SICS base pushed out of the duplex with its paired NaM base stacked quite normally. Further analysis of the data should allow us to propose a more precise structure of the DNA duplex as well as provide insight into the versatility of DNA replication machinery to recognize altered DNA structures.

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