Date of Award


Document Type


Degree Name

Doctor of Philosophy (PhD)

Legacy Department



Arya, Dev P

Committee Member

Newby-Spano , Meredith

Committee Member

Dieter , Karl

Committee Member

Christensen , Kenneth

Committee Member

Pennington , Bill


This manuscript reflects our most recent advancements in the recognition of nucleic acids. Chapter one focuses on previously established methods in nucleic acid recognition. Nucleic acid targeting by small molecules affords a unique way to potentially inhibit biological functions, which is different from targeting enzyme and protein bio-macromolecules. We seek to further develop an aminoglycoside approach to targeting nucleic acids. Since aminoglycosides were first introduced, over 60 years ago, as treatment for tuberculosis, natural product discovery and demands for therapeutically more effective aminoglycosides, with lowered toxicity, have dominated the landscape of aminoglycoside research. More recently, our group has established neomycin as a major groove binding ligand capable of binding nucleic acids outside of their traditional target, the A-site of 16S rRNA in the 20S subunit of ribosomal RNA. These non-A-site structures shared a common motif, A-form conformation within the helix.
To this end, chapter two of this manuscript focuses on advancements in targeting DNA:RNA hybrids. DNA:RNA hybrids are viable therapeutic targets as they appear in a number of biological processes: transcription, reverse transcription, DNA replication, mitochondrial DNA replication and telomerase activity. Surprisingly, the number of ligands which target DNA:RNA hybrids is fewer than ten! We report the development of a novel neomycin-methidium chloride conjugate capable of targeting DNA:RNA hybrids with selectivity as well as high affinity.
Chapters three and four introduce our most recent advancements in targeting DNA. Prior work by our group suggested conjugation of neomycin to a minor groove binding ligand can be used as a method of targeting the DNA duplex. Although these dual recognition conjugates demonstrated the ability to stabilize the duplex, improvements in affinity remained. A departure from previous work, we focus on targeting GC-rich DNA, over AT-rich DNA; as reports suggest GC-rich DNA is capable of displaying A-form characteristics. When designing our minor groove binding ligand, we utilized DNA minor groove-polyamide, pairing rules established by Dervan. Subsequent conjugation to neomycin to polyamides comprised of N¬-methylimidazole and N-methylpyrrole afforded us a library of polyamide conjugates. In chapter three, we focus on the development and bioanalytical studies of tetramer polyamide - neomycin conjugates. Chapter four discusses our most recent advancements in the development of hairpin polyamide - neomycin conjugates which were designed to target GC-rich DNA.