Date of Award


Document Type


Degree Name



Chemistry and Biochemistry

First Advisor

Byron W. Purse, Ph.D.

Second Advisor

Andrei Kutateladze

Third Advisor

Gareth Eaton

Fourth Advisor

Martin Margittai

Fifth Advisor

Scott Barbee


Nucleosides, Enzymatic DNA synthesis, Fluorescent probes


A brief history of nucleosides and their photophysics provides the background information for the discussion of synthesis, photophysics and incorporation of fluorescent nucleotide analogs during enzymatic DNA synthesis. Through the use of nucleoside starting material, it is possible to synthesize a number of modified nucleotides for use as fluorescent probes in biochemical research. Synthetic endeavors into the synthesis of these and related molecules from nucleobase starting materials are also presented. The synthesis of these molecules involved re-development of the synthetic routes to broaden substrate scope by overcoming the changed reactivity resulting from the presence of additional functionality.

While many highly useful fluorescent probes exist today, there remains to be filled significant gaps in performance. Brighter probes, probes that emit at various wavelengths while maintaining fluorescence when present in folded biomolecules (proteins, nucleic acids), and probes that work together as a nucleic acid FRET pairs are still needed.

In the work described in this thesis, a series of cytidine analogs that are closely related have been synthesized and investigated to elucidate trends in effects on photophysical properties by the electronic character and position of substituents. The location of substitution as well as the surrounding environment has an influence on how the introduction of new functionality affects the photophysical properties of the chromophore. Tricyclic cytosine skeletons have been substituted to produce analogs that are brighter, and more or less sensitive to their environment.

These substitutions affect not only the photophysical properties of the compound but also the tautomeric equilibrium between cytosine and tyrosine-like hydrogen bonding patterns. This equilibrium between hydrogen positions controls the base pairing properties of the compound and how it is treated by cellular machinery during incorporation in nascent nucleic acids. Incorporation studies reveal that the substitution affects the incorporation efficiency for templates containing different hydrogen bonding partners.

Publication Statement

Copyright is held by the author. User is responsible for all copyright compliance.


Received from ProQuest

Rights holder

Brittney Rodgers

File size

278 p.

File format