The molecular characteristics that affect the activity of various dirhodium complexes are reported. The importance of the axial position in the action of dirhodium compounds was studied. Three dirhodium complexes with increasing number of accessible axial coordination sites were synthesized and characterized. In cis-[Rh2(u-OAc)2(np)2]2+ (np = 1,8- naphthyridine) both axial sites are available for coordination, whereas for cis-[Rh2(u-OAc)2(np)(pynp)]+2 (pynp = 2-(2-pyridyl)1,8-naphthyridine) and cis-[Rh2(u-OAc)2(pynp)2]+2 the pyridyl arm on the ligand pynp blocks one and two axial sites, respectively. The availability of the axial positions affects the in vitro and in cellulo activity of these complexes demonstrating that open axial coordination sites are necessary for biological activity. The inhibitory activity of derivatives of dirhodium-dppz complexes (dppz = dipyrido[3,2-a:2',3'-c]phenazine) has also been investigated. The dppz derivatives included compounds with electron-withdrawing (Cl, CN, and NO2) as well as electro-donating (MeO and Me) substituents. These compounds inhibit transcription of T7-RNA polymerase by reducing accessible cysteine residues. The activity correlates with the electron withdrawing character of the substituent on the dppz ligand. Density functional theory (DFT) calculations reveal that the lowest unoccupied molecular orbitals (LUMOs) in the series are ligand-based pi* orbitals localized on the phenazine ring. These complexes represent the first family of dirhodium complexes whose inhibitory ability can be tuned by controlling their redox properties. The effect of the presence of diimine ligands in the dirhodium core in both in vitro and in cellulo activity is discussed. The presence of one diimine ligand allows for dual binding, intercalation and covalent, as observed by melting temperature and relative viscosity measurements, as well as electrophoretic mobility shift assay (EMSA). The mono-substituted dirhodium complexes are effective against HeLa and COLO-316 cell lines, with [Rh2(u-O2CCH3)2(n1-O2CCH3)(dppz)]+ being the most effective compound of the series. Results of the comet assay indicate that all of the monosubstituted complexes studied damage nuclear DNA, although in different degrees. The cytotoxic effect of these complexes is not affected by the presence of glutathione. The addition of the second diimine ligand hinders the ability of the complexes to damage DNA. The bis-substituted complexes are also slightly less cytotoxic than their mono-substituted congeners. Thus, the number of equatorial positions occupied by diimine ligands play a critical role in the mechanism of cytotoxicity of dirhodium(II,II) complexes. Finally, the results also demonstrate that improving the internalization of the dirhodium complexes can be achieved by co-incubation with cell penetrating peptides. This work provides a foundation for the preparation of new and more effective dirhodium complexes.

Human telomerase is a ribonucleoprotein complex that adds hexameric TTAGGG repeats to the ends of chromosomes in order to prevent their shortening. Telomerase activity has been evaluated for its diagnostic and prognostic value in cancer since it is observed in most malignancies but not in most normal somatic tissues. In this study telomerase activity was examined in tumor specimens obtained from cervix, endometrium and their non-cancerous regions by an improved telomeric repeat amplification protocol (TRAP) &ndash / silver staining assay. Appearance of characteristic TRAP leader with 6 base pair increments indicate a positive result and was observed in all cancerous and some of the non-cancerous tissues. Telomerase activities of carcinoma tissues and normal counterparts were compared by densitometric analysis after PCR. Significantly higher telomerase activity was observed in cervical carcinoma samples compared to normal adjacent tissue. No significant difference was observed between endometrium carcinomas and normal endometrial tissue in terms of telomerase activity. High telomerase activity in normal endometrium restricts the use of assay for detection of carcinogenesis. However, in cervical tissues an accurate quantification of telomerase activity by TRAP &ndash / silver stain assay may be valuable as a confirmatory assay.

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This thesis is intended as an introductory lab manual on the experimental methods using fluorescence microscopy in modern radiobiology research. It is written for those who are unfamiliar with biology research. It first covers the proper use of laboratory equipment and growth of cell cultures in the lab. Subsequent chapters provide overviews of relevant modern experimental techniques for the quantification of radiation induced DNA damage in cells, and detailed protocols for performing these procedures. Techniques covered include immunostaining with fluorescent antibodies, the comet assay, and plasmid DNA transfections. Results of some straightforward experiments using these techniques are presented.

Asymmetric synthesis has become an important tool to prepare enantiomerically pure compounds because it avoids the wasteful discarding of the undesired enantiomer. Combinatorial libraries allow for much faster screening for new and better asymmetric catalysts/auxiliaries, but they generate a large number of samples whose enantiomeric excess (ee) cannot be determined rapidly. This bottleneck currently limits the applicability of such approaches. We propose here the use of faster optical techniques for the determination of ee using common instrumentation, such as UV-vis spectrophotometers, and circular dichroism (CD) spectrophotometers. Our methods are easily transitioned to the microwell format commonly used in parallel/combinatorial chemistry endeavors, just by using common microplate readers: this allows for an even more rapid analysis of samples and a seamless integration in a high-throughput workflow. We have shown that enantioselective indicator displacement assays can be developed to determine ee in a high-throughput fashion utilizing either a UV-vis spectrophotometer or a 96-well plate reader. Two chiral receptors and a commercial pH indicator were used to enantioselectively discriminate α-amino acids by monitoring the degree of indicator displacement. The two receptors were able to enantioselectively discriminate 13 of the 17 analyzed α-amino acids and accurately determine ee values of independent test samples with the use of ee calibration curves. Moreover, a sample of valine was synthesized through an asymmetric reaction, whose ee was then determined with our assay and compared to chiral HPLC and 1H NMR chiral shift reagent analysis, with excellent correlation. An artificial neural network was also successfully employed in the analyses, as an alternative to ee calibration curves. Both techniques consistently produced results accurate enough for preliminary determination of ee in a rapid manner, allowing for high throughput screening (HTS) of asymmetric reactions. The use of circular dichroism spectroscopy with chiral BINAP was also explored to enantioselectively discriminate α-chiral ketones. The ketones were derivatized with pyridyl hydrazines to produce hydrazones, which were then bound to enantiomerically pure [Cu(I)(BINAP)]+, forming diastereomeric complexes with differential steric interactions leading to different degrees of twist in the BINAP moiety and characteristic signatures in the CD spectrum, as a function of sample ee. / text

Determining the presence of an analyte of interest, and finding the enantiomeric purity of chiral molecules are challenging tasks. This work in molecular recognition is carried out routinely by many different researchers, including both academic as well as industrial research groups. The following dissertation presents original research directed toward two different areas of interest to the molecular recognition community: enantioselective sensing in solution, and sensing at a defined interfacial environment. This work begins with a review of the non-chromatographic ways that the enantiomeric purity of chiral carboxylic acids is determined, presented in Chapter 1. Carboxylic acids are important functional groups, both for organic synthesis as well as pharmaceutical drug development. Chapter 2 presents efforts that have been made to rapidly assess both the enantiomeric purity and identity of chiral carboxylic acids, utilizing the technique of exciton-coupled circular dichroism (ECCD). A twist is imparted on a complex, and can be correlated with the absolute configuration of the stereocenter. The enantiomeric composition can be rapidly determined. After creating the assay, the focus of the work shifted toward applying this system to new classes of analytes. Chapter 3 covers chemo- and enantioselective differentiation of [mathematical symbol]-amino acids, and continues to discuss the expansion to [mathematical symbol]-homoamino acids. Then a synthetic substrates was tested, and a series of reactions screened to determine if any enantioselectivity had been imparted by a Baeyer-Villiger oxidation. Finally, the enantiomeric composition of a biaryl atropisomer, a compound lacking a stereocenter, was determined. The signal produced from this assay is at a relatively short wavelength, and efforts were undertaken to push this signal to longer wavelength. Chapter 4 is a compendium of the lessons that were learned upon attempting to create a self-assembled sensing system. The final chapter details work that was done in collaboration with Professor Katsuhiko Ariga at the National Institute of Materials Science in Tsukuba, Japan. In this chapter, an indicator displacement assay was carried out for the first time at the air-water interface. This contribution opens the door for sensing to be carried out at defined regions, rather than free in bulk solution. / text

Bok/Mtd (Bcl-2-related ovarian killer/Matador) is considered a pro-apoptotic member of the Bcl-2 family. Though identified in 1997, little is known about its biological role. We have previously demonstrated that Bok mRNA is upregulated following E2F1 over-expression. In the current work, we demonstrate that Bok RNA is low in quiescent cells and rises upon serum stimulation. To determine the mechanism underlying this regulation, we cloned and characterized the mouse Bok promoter. We find that the mouse promoter contains a conserved E2F binding site (-43 to -49) and that a Bok promoter-driven luciferase reporter is activated by serum stimulation dependent on this site. Chromatin immunoprecipitation assays demonstrate that endogenous E2F1 and E2F3 associate with the Bok promoter in vivo. Surprisingly, we find that H1299 cells can stably express high levels of exogenous Bok. However, these cells are highly sensitive to chemotherapeutic drug treatment. Taken together these results demonstrate that Bok represents a cell cycle-regulated pro-apoptotic member of the Bcl-2 family, which may predispose growing cells to chemotherapeutic treatment.

Ferrochelatase catalyzes the terminal step of heme biosynthesis by inserting ferrous iron into protoporphyrin IX. The current study is aimed at understanding the structural basis of porphyrin binding and distortion in ferrochelatase-catalyzed reaction by functional analysis of a highly conserved active site loop motif. The loop was shown to contact bound porphyrin based on crystallographic and molecular modelling observations, and its role in murine ferrochelatase was assessed by random mutagenesis and steady-state kinetic analysis. To overcome the limitations of conventional kinetic assay methods for ferrochelatase, a continuous assay was developed by monitoring porphyrin fluorescence decrease using natural substrates ferrous iron and protoporphyrin IX under anaerobic conditions. For wild-type murine ferrochelatase, the assay yielded KmPPIX of 1.4 uÌ?M, KmFe2+ of 1.9 uÌ?M and kcat of 4.0 min-1 at 30 °C. The results of random mutagenesis indicated that all the loop re sidues spanning Q248-L257 tolerated functional substitutions. While Q248, S249, G252, W256 and L257 possessed high informational content, the other five positions contained low informational content. Selected active loop variants exhibited kcat comparable to or higher than that of wild-type enzyme, while KmPPIX was increased in most variants. The kcat/KmPPIX remained largely unchanged, with the exception of a 10-fold reduction in variant K250M/V251L/W256Y. Molecular modeling of the active loop variants suggested that loop mutations resulted in alterations of the active site architecture. Distortion of porphyrin substrate, a crucial step in ferrochelatase-catalyzed metal chelation, was examined using resonance Raman spectroscopy. The results revealed that both wild-type enzyme and loop variants induced saddling of substrate protoporphyrin. Further, loop mutations generally interfered with porphyrin saddling, with the least deformation observed in variant K250M/V251L/W256Y.N-alkyl porphyrins are potent competitive inhibitors of mammalian ferrochelatase. The present study showed that while N-methyl protoporphyrin strongly inhibited the wild-type enzyme with an inhibition constant in the nanomolar range, it was less effective in inhibiting variants P255R and P255G. These results suggest that inhibitor binding may be associated with a protein conformational change mediated by P255. Wild-type ferrochelatase is a homodimeric [2Fe-2S] cluster-containing protein. Variants S249A/K250Q/V251C and S249A/K250R/G252W were found to retain enzymatic activity in the absence of FeS cluster and form active, higher order oligomers. These observations raise the possibility that FeS cluster and homodimeric organization are not essential to ferrochelatase catalysis.

Studies on a series of polymethine cyanine dyes and analogs (1-24) show that certain near-infrared cyanines are capable of damaging DNA in the absence of light and external reducing agents. Experimental results imply that in this DNA thermal cleavage, the cyanine reduces Cu(II) to Cu(I) which reacts with O2 to generate the reactive oxygen species (ROS) O2∙- and ∙OH. The formation of these ROS is also thought to be responsible for the irreversible bleaching of the dyes in aqueous solutions. A correlation between structural features and DNA thermal cleavage activity as well as dye bleaching is suggested. Long polymethine chains appear to confer instability to cyanines in aqueous solutions and further contribute to undesired thermal DNA cleavage. These drawbacks can be overcome by introducing an electron-withdrawing group to the polymethine bridge of the cyanine dye.