Author ORCID Identifier


Date of Award


Degree Type


Degree Name

Doctor of Philosophy (PhD)



First Advisor

W. David Wilson

Second Advisor

Markus W. Germann

Third Advisor

Gregory Poon


The broad range of diseases controlled by transcription factors (TFs) and their potential abilities to modulate gene expression have led to an emerging interest in the development of small molecules that target TF-DNA complexes. Still, there is only a limited number of types of designed small molecules that show strong and sequence-specific binding to DNA along with good cellular uptake properties for therapeutic use. Most of the successful nuclear stains or therapeutic agents that bind non-covalently in the minor groove of DNA are AT specific. Synthesis of novel compounds to better target the mixed AT/GC base pair (bp) sequences with a broad range of applications like targeting TF is a daunting task.

Our novel heterocyclic cation, DB2277, contains the aza-benzimidazole group (aza-BI) that specifically recognizes the single GC bp interspersed between AT bp sequences in the minor groove of DNA. NMR spectroscopy revealed the presence of major and minor binding species in the DB2277 complex with AAAGTTT type of DNA. NMR exchange dynamics have shown that the exchange between major and minor species is much faster than the compound’s dissociation from the complex, as determined using surface plasmon resonance (SPR). To understand the molecular basis of recognition of mixed bp sequences and to acquire ideas to design new sequence-specific compounds, structural information of the DB2277-DNA complex is essential. Experimental structure of the unique and selective binding orientation of DB2277 with “AAGATA” binding site of DNA has been obtained using high-resolution NMR and molecular dynamics (MD) simulations, which suggests the involvement of two specific and strong H-bonds in recognition of the central GC bp. Extended MD calculations have shown dynamic water-mediated H-bond contacts between amidine of DB2277 and the bases at the floor of the minor groove and 180° rotations of the phenyl linked to a flexible linker (OCH2) in a bound compound for the first time. Therefore, designing additional compounds with the ability to recognize a vast array of biologically important DNA sequences is essential for extending the use of new heterocyclic compounds in therapeutic applications in the future.