Investigation of the NIR cyanine dye MHI-36 shows binding affinity to charged amino acids. This cyanine dye showed aggregation and dimer formation at higher dye concentration (2.0x10-3 M) induced by lysine. When dye concentration decreased to 1.0x10-4M no strong aggregate formation was viewed. Dye shows strong binding and selectivity properties towards charged amino acids lysine and arginine, compared to neutral leucine. It’s believed the positively charged presence was able to break and disrupt the conjugated π- π bonds at lower dye concentration. Computational work showed intramolecular aggregation of the phenyl groups on the dye. These aggregates are believed to create electron rich environment suitable for lysine interaction.

Of the seven existing classes of serotonin receptors, the 5-HT7 receptors (5-HT7Rs) are the most recently discovered. Abundance of 5-HT7 in the central nervous system is suggestive of the receptor’s role in several physiological and pathophysiological functions. Existing research has afforded a number of compounds exhibiting specific affinity to the receptor. These selective ligands can provide structural information about the receptor and can serve as the foundation for pharmacological profiling . This thesis describes the synthesis of substituted pyrimidines and pyridines for affinity to the 5-HT7 receptor. Organometallic species are the cornerstone for sev-eral of the synthetic pathways.

Water is the most common solvent for most biological reactions, therefore it is vital that we fully understand water and all its properties. The complex hydrogen bonding network that water forms can influence protein-protein and protein-substrate interactions and can slow protein conformational shifts. Here, I examine an important property of water known as energetic roughness. The network of interactions between individual water molecules affect the energy landscape of proteins by altering the underlying energetic roughness. I have attributed this roughness to the making and breaking of hydrogen bonds as the network of hydrogen bonds constantly adopts new conformations. Through a novel computational approach I have analyzed five prominent water models and have determined their inherent roughness to be between 0.43 and 0.62 kcal/mol.

Diamidines are compounds with antiparasitic properties that target the minor groove of DNA. The mechanism of action of these compounds is unknown, but topological changes to DNA structure are a possibility. In this study, we have developed a polyacrylamide gel based screening method to determine topological effects of diamidines on four target sequences: AAAAA, TTTAA, AAATT, and ATATA. The changes caused are sequence dependent, but generally the effect on AAAAA and AAATT is the same while the effect on TTTAA and ATATA is the same. A few compounds show interesting sequence dependent topological effects in the polyacrylamide screening method that could be caused by the compound forming a dimer. Mass spectrometry is used to determine the stoichiometry of DNA-compound complexes. Once compounds show topological effects in the screening method, a bent fragment of kinetoplast DNA is isolated to determine if the same effects occur with DNA from a parasite.

The development of novel selective 5-HT6 and 5-HT7 receptor antagonists is an ever-growing area of interest among medicinal chemists. The potential of developing a therapeutic agent useful as an antipsychotic or antidepressant, as well as the possibility to develop a drug for Alzheimer’s disease and obesity has led to an increase in synthesis of possible lead compounds. The synthesis of unfused biheteroaryl derivatives is described within. The derivatives have been evaluated for binding affinity at 5-HT2A, 5-HT6 and 5-HT7 receptors. The most potent 5-HT6 receptor antagonists include a benzene ring, a hydrophobic group and a protonated nitrogen atom. The most potent and selective compound synthesized is 1-[3-butyl-5-(thienyl)phenyl]-4-methylpiperazine. The binding site of the 5-HT7 receptor is similar to that of the 5-HT6 receptor and the most selective and potent 5-HT7 receptor antagonist also contains a potonated nitrogen atom and a hydrophobic group. The difference in selectivity between the 5-HT6 and 5-HT7 receptor antagonists is the aromatic ring. The most potent 5-HT7 receptor antagonist synthesized contains a pyridine ring instead of benzene, as in the 5-HT6 receptor antagonist. The most potent and selective 5-HT7 receptor antagonist is 1-[4-(3-furyl)-6-methylpyridin-2-yl]-4-methylpiperazine. The need to increase selectivity for both 5-HT6 and 5-HT7 receptors has led to the synthesis of flexible-chain linked derivatives and the results are described within.

More than one-third of all Magnetic Resonance Imaging (MRI) scans employ image-enhancing contrast agents to increase the differential signal intensity between diseased and normal tissue. Because current clinical contrast agents exhibit low relaxivity (mM-1 s-1), low dose efficiency, and rapid secretion, we have designed a group of protein-based MRI contrast agents with multiple gadolinium binding sites. In this study, the developed purification method for Class ProCA-3 agents allows for a quick and cost-effective way to abstract up to 109 mg of pure, soluble protein from a 1L E. Coli cell pellet devoid of DNA or RNA “contamination” for extensive animal studies. Circular dichroism far-UV spectra ensure the metal stability of the agents, revealing maintenance of their native α-helical structure in the presence and absence of metal ions. Furthermore, substantial evidence supports the high dose efficiency of these agents, exhibiting up to five folds higher relaxivity than their analogous commercial competitors.

KCN-1 is known to reduce tumor growth 6-fold in mice implanted with LN229 glioma cells. Although this inhibitor is effective, the mechanism of action for KCN-1 is not well understood. Based on preliminary studies, KCN-1 reduces tumor growth by disrupting the HIF 1 (hypoxia-induced factor-1) pathway. The binding target of KCN-1 needs to be investigated in order to develop KCN-1 or its analogs for therapeutic applications. In this research, a molecule was designed and synthesized for the identification of the binding target of KCN-1. Specifically, this molecule contains the inhibitor (KCN-1), a photocleavable linker, beads, and the affinity label (L DOPA). When UV light shines on the linker, the trans-alkene isomerizes to cis-alkene and undergoes intramolecular ring-closing reaction, which helps cleave the immobilized bead from the linker. The immobilized bead is used to separate the binding fragment attached to the photocleavable linker from the solution after enzyme digestion. The affinity label (L-DOPA) reacts with a nucleophile from the binding target and creates a covalent bond. If the design is successful, this method is able to analyze the mass of the peptide sequence and determine the binding target of KCN-1.

Within this study, the focus will be on oligoglycines. Numerous studies pertaining to the mobility and conformations of oligoglycines have been completed, as this is a driving force for the study. The oligopeptide is modeled using a “coarse-grained” model created in the Allison lab at Georgia State University [Xin,Y.,et. al, J. Phys. Chem. B 2006, 110, 1038-1045], which will be briefly explained within this paper. Oligoglycines will be studied in a few different systems, as the overall charge on the peptide and system will affect its mobility. The conclusion drawn is that the peptide adopts three different conformations based on the temperature of the system and length of the peptide; random conformation at high temperatures, and compact conformations at low temperature. Oligoglycines of length three to five amino acids adopts a cyclic conformation at low temperatures. [Allison, S., et al., J. Sep. Sci. 2010, 33, 2430- 2438.]

Part One. X-ray crystallography has benefited from the synthetic introduction of selenium to different positions within nucleic acids by easing the solving of the phase problem. Interestingly, its addition to the 2' position of the ribose ring also significantly enhances crystal formation. This phenomenon was investigated to describe the effect of selenium-based and other 2' modifications to the ribose ring of nucleosides in solution, as well as the incorporation of the selenium-modified nucleotides into a helical structure. This work correlates the difference in conformation propensity between the selenium containing nucleosides and oligomers towards a rationale behind the enhanced crystal forming behavior. Part Two. Recombinant protein production is a critical tool in laboratories and industries, and inducing extracellular transport of these products to the culture medium shows potential for improving cases where the yields are not sufficient in quality or quantity. This review incorporates current practices and systems with future perspectives.

There is a high demand for quadruplex-specific compounds that not only bind preferentially to quadruplex DNA over duplex DNA, but also bind to one quadruplex motif over other motifs. Quadruplex structures are recognized as common occurrences in cancer cells, and if a compound could stabilize this structure, it may serve as an effective anti-cancer treatment with minimal side effects. In this study, cyanine dyes’ interactions with DNA were analyzed with fluorescence titrations, UV-Vis thermal studies, circular dichroism titrations, and surface plasmon resonance (SPR) analysis. With these techniques, binding affinity, DNA stabilization, and conformational shifts were analyzed to determine if cyanine dyes could act as quadruplex-specific binding compounds for possible cancer treatments.