For thesis abstract select View Thesis Title, Contents and Abstract

<p>RNA is the only biological molecule that can function both as a repository of information and as a catalyst. This, together with the ability to self-replicate, led to recognition of RNA as ‘prelude to life’.</p><p>My work highlights some of the important features of RNA as a catalyst, exemplified by RNase P. It addresses questions of evolutionary preservations of residues and structure, involvement of metal ions and finally structure evolution towards minimal catalytically competent RNA motifs.</p><p>RNase P is the only enzyme involved in 5’ end processing of all pre-tRNAs. Until recently, it was believed that the RNA moiety of RNase P is responsible for mediating catalysis only in Bacteria. However, my recent study conclusively demonstrated that eukaryotic RNase P RNA is catalytically competent in vitro in absence of proteins. These findings evidenced evolutionary preservation of RNA-mediated catalysis in RNase P.</p><p>RNase P RNA is a metalloeznyme. In my studies I analyzed the contributions of individual chemical groups at the cleavage site to catalysis. My findings suggested that the 2’OH of N_-1 and the exocyclic amine of G₊₁ are involved in positioning of functionally important metal ions. Additionally, data appointed the function of Pb²⁺ as both structural metal ion and important in generating the nucleophile. My studies further indicate a conformational change upon RNase P RNA -substrate complex formation in keeping with an induced fit mechanism. </p><p>Studying the effects of reducing the ribozyme size upon dissection of bacterial RNase P RNAs, we defined the smallest catalytically competent domain i.e. P15-loop. Derivatives of this autonomous metal ion binding domain, (the smallest being 31nt-s), are able to cleave both whole-length pre-tRNAs as well as hairpin substrates, though with severely reduced rates relative to their parent ribozymes. The study has inferred that partite ES interactions at the cleavage site prove sufficient for catalysis.</p>

RNA is the only biological molecule that can function both as a repository of information and as a catalyst. This, together with the ability to self-replicate, led to recognition of RNA as ‘prelude to life’. My work highlights some of the important features of RNA as a catalyst, exemplified by RNase P. It addresses questions of evolutionary preservations of residues and structure, involvement of metal ions and finally structure evolution towards minimal catalytically competent RNA motifs. RNase P is the only enzyme involved in 5’ end processing of all pre-tRNAs. Until recently, it was believed that the RNA moiety of RNase P is responsible for mediating catalysis only in Bacteria. However, my recent study conclusively demonstrated that eukaryotic RNase P RNA is catalytically competent in vitro in absence of proteins. These findings evidenced evolutionary preservation of RNA-mediated catalysis in RNase P. RNase P RNA is a metalloeznyme. In my studies I analyzed the contributions of individual chemical groups at the cleavage site to catalysis. My findings suggested that the 2’OH of N-1 and the exocyclic amine of G+1 are involved in positioning of functionally important metal ions. Additionally, data appointed the function of Pb2+ as both structural metal ion and important in generating the nucleophile. My studies further indicate a conformational change upon RNase P RNA -substrate complex formation in keeping with an induced fit mechanism. Studying the effects of reducing the ribozyme size upon dissection of bacterial RNase P RNAs, we defined the smallest catalytically competent domain i.e. P15-loop. Derivatives of this autonomous metal ion binding domain, (the smallest being 31nt-s), are able to cleave both whole-length pre-tRNAs as well as hairpin substrates, though with severely reduced rates relative to their parent ribozymes. The study has inferred that partite ES interactions at the cleavage site prove sufficient for catalysis.

Ball State University LibrariesLibrary services and resources for knowledge buildingMasters ThesesThere is no abstract available for this thesis.

Extractants and extraction methodologies play a vital role in many industrial processes, from the concentration of precious metals from ores to the separation of longlived nuclei from radioactive waste as well as the removal of heavy metals from soils and water for remediation. The vast majority of extractants rely on the use of nitrogen, oxygen, sulfur or selenium as Lewis base donor atoms to form coordination complexes with the metal ions of interest. These extractants often make use of the chelate effect and/or the macrocyclic effect in order to form stable complexes. Some of the best known types of chelate extractants include polyaminopolycarboxylic acids (N and O donors), polyamines (N donors), dithiocarbamate (S donors) and aminopolythias (N and S donors). The most extensively investigated types of macrocycles include crown ethers (O donors), thia crowns (S donors), aza crowns (N donors) and thiacrown ethers (S and O donors). A conspicuous omission from the list of donor atoms is phosphorus. It is noted that phosphorus has been employed as a backbone atom in the development of extractants, primarily in phosphonates, phosphates and phosphine oxides. The omission of phosphorus is interesting from two points. First, many of the precious and heavy metal ions of interest (Pd2+, Ag+, Pt2+, Pb2+, Cd2+and Hg2+) can be classified as soft Lewis acids, according to Pearson’s HSAB theory. The relative softness of phosphorus as a Lewis base as compared to oxygen and nitrogen indicates that phosphorus would be a very good donor atom toward these soft metal cations. Secondly, chelating agents containing phosphorus donors form stable complexes with transition metal cations in a variety of oxidation states due to their versatile bonding capability. The !-donor characteristics of the phosphine donor coupled with the ability to " accept from filled or partially filled d orbitals of the metal cations result in strong phosphine-metal bonds.

The cyanide ligand has frequently been used to prepare clusters with novel magnetic properties due to its ability to provide an efficient pathway for superexchange between metal centers that are bound in an end-to-end fashion. One of the common synthetic approaches in this chemistry is to design suitable cyanide containing precursors and then to react such building blocks with metal complexes consisting of accessible sites. The triphos ligand (triphos: 1,1,1-tris(diphenylphosphinomethyl)ethane) has been employed in this vein to prepare metal complexes, one of which is a five coordinate paramagnetic complex (S = 1/2) with a square pyramidal metal center, [CoII(triphos)(CN)2]. A family of molecular squares, [{MIICl2}2{CoII(triphos)(CN)2}2] (M= Mn (2), Fe (3), Co (4), Ni (5), and Zn (6)), has been synthesized by the reaction of CoII(triphos)(CN)2 and MCl2 (M= Mn, Co, Ni, Zn) or Fe4Cl8(THF)6 in CH2Cl2/EtOH mixture. A series of cyanide-bridged trinuclear complexes, {[Co(triphos)(CN)2]2 [M(MeOH)4]}(ClO4)2 ( M = Mn (7), Fe (8), Co (9), and Ni (10)) and tetranuclear complexes, {[Co(triphos)(CN)2]2[M(MeOH)4]2}(ClO4)4 ([Co2M2] M = Mn (11) and Ni (12)) have been synthesized in a similar fashion by the reaction of CoII(triphos)(CN)2 and M(ClO4)2.6H2O (M= Mn, Fe, Co, Ni) in methanol. The trinuclear compounds (7-9), and tetranuclear complexes (2-6, 11, 12), are characterized by antiferromagnetic coupling between metal centers while magnetic behavior of 10 indicates the presence of ferromagnetic interactions between the paramagnetic metal centers. Interactions between magnetic orbitals of Co(II) and M(II) ions were also investigated by means of the density functional theoretical (DFT) calculations. Another triphos containing building block, [(triphos)Re(CN)3] anion (13), has been employed to prepare derivatives of a cubic SMM cluster with four octahedral Re(II) ions and four tetrahedral Mn(II) sites bridging through cyanide ligand. The reactions of Re(II) precursor with MnI2 and solvated Mn(II) ions resulting in derivatives of Re4Mn4 cube with different ligands attached to the Mn center other than the chloride atom were reported. Our efforts on linking these cubes using organo cyanide ligands such as dicyanamide (dca) and 7,7,8,8-tetracyanoquinodimethane (TCNQ) to form extended networks were also discussed.

Research in the fields of molecular conductors and magnets over the past four decades has involved collaborative efforts of chemists and physicists whose common goal is to design useful materials composed of molecular building blocks. Of particular interest are materials whose properties can be tuned by electronic or steric changes in the molecular sub-units. The research on TCNQ derivatives described in this thesis was inspired by the observation that, although a vast amount of research has been directed at understanding binary M(TCNQ•-) materials, analogous compounds based on substituted TCNQ acceptors are surprisingly scarce. Single crystals of a new structure type for the M+(TCNQ)•- binary family were isolated from reactions of two dihalogenated TCNQ derivatives with Cu(I) ions, namely Cu(TCNQX2) (X = Cl, Br). The new 3-D compound Cu(TCNQCl2) exhibits the highest conductivity of the M+(TCNQ)•- series to date, despite the greater separation of TCNQCl2 units as compared to other derivatives. Compounds of lower dimensionality were also obtained, namely the 2-D Cu(TCNQBr2)(CH3CN) and 1-D Cu(TCNQI2)(CH3CN)2 phases. Several 2p-3d heterospin molecular magnets were also synthesized. For example a “magnetic sponge” material based on a 2-D hexagonal framework of composition {[Mn2(TCNQF4)(CH3OH)7.5(H2O)0.5]-(TCNQF4)2•7.5CH3OH}∞, as well as molecular magnets based on first row metal ions and TCNQF4 ligands of composition MII(TCNQF4)-•(TCNQF42-)0.5(CH3CN) (M = Mn, Co) were prepared. In addition, unprecedented isostructural 2-D frameworks based on combinations of first row metal ions with TCNQBr2 radicals of composition [M(TCNQBr2)2(H2O)2]∞ (M = Mn, Zn) were synthesized. Lanthanide chemistry is also described in this dissertation. A series of mononuclear Ln-TCNQF4 heterospin complexes of composition {MIII[TCNQF4]2[H2O]x}(TCNQF4)(3H2O) (M = La, Pr, Nd, Sm, Eu, Gd, Dy, Ho, Er and Yb) was also obtained which exhibit remarkable properties. In this family of compounds there exists an unprecedented subtle interplay between single molecule magnetic behavior and phonon bottleneck effect behavior for the Tb analogue. Magnetic ordering was observed for the Sm analogue. A homologous series of 1-D materials based on alternating lanthanide ions and hexacyanometallates of formula {[Ln(tptz)(H2O)4Fe(CN)6]•8H2O}∞ (Ln = Pr, Nd, Sm, Eu, Gd, Tb) was obtained and a detailed magnetic study provided incontrovertible evidence that the SmIII-[FeIII(CN)6]3- compound exhibits ferromagnetic and not antiferromagnetic coupling as had been reported for related 1-D chains.

In this work, interference and coherence phenomena, appearing in atomic and molecular ensembles interacting with coherent light sources, as electromagnetically induced transparency (EIT), coherent population trapping (CPT), and slow group velocity of light are investigated. The goal of the project is to make the steps towards various applications of these phenomena, first, by studying them in solid media (which are the most advantageous for applications), second, by suggesting some novel applications such as CPT-based plasma diagnostics, and realization of new types of solid-state lasers (based on suppression of excited-state absorption via EIT). The third goal of the project is extension of coherence and interference effects well-known in optics to the gamma-ray range of frequencies and, correspondingly, from atomic to nuclear transitions. A particular technique of chirped pulse compression applied to M??ossbauer transitions is considered and the possibility of compression of M??ossbauer radiation into ultrashort gamma-ray pulses is analyzed. The theoretical treatment of the interference and coherence effects is based on the semiclassical description of atom-light interaction, which is sufficient for correct analysis of the phenomena considered here. Coherent media are considered in two-, three-, and four-level approximations while their interaction with light is studied both analytically and numerically using the Maxwell-Bloch set of equations.

This dissertation focuses on the spectroscopic and thermodynamic characterization of the unusual metal-RNA cluster found in the P5abc subdomain of the Tetrahymena group I intron. The P5abc subdomain is a part of the P4-P6 domain found in the Tetrahymena thermophila group I intron selfsplicing RNA. From both X-ray crystal structures of the P4-P6 domain, a remarkable cluster of Mg2+ or Mn2+ ions was found in the P5abc subdomain (Cate et al. 1996; Juneau et al. 2001). It is believed that the metal ion core in the P5abc subdomain stabilizes the active conformation of the RNA (Cate et al. 1996). An understanding of the role of these metal ions in facilitating the correct structure of the P5abc subdomain provides insight into how metal ions help overcome the folding barriers of complex RNA structures. Under solution conditions, the properties of this uncommon metal ion core and its influence on the truncated P5abc subdomain structure have been investigated. Both EPR spectroscopy and thermal denaturation experiments have been employed to search for a spectroscopic signature of metal ion core formation and also determine the thermodynamic contribution of the metal ion core on the stability of the folded P5abc structure. A spectroscopic signature of metal ion core formation was assigned for the P5abc subdomain by EPR microwave power saturation studies. Power saturation studies of the P5abc subdomain, P4-P6 domain and corresponding mutants reveal that the addition of 5 equivalents of Mn2+ are required for the wild type P5abc subdomain to form the metal ion core under solution conditions in 0.1 M NaCl. Results from both domain and subdomain microwave power saturation studies suggest that this technique can be applied for detecting clustering of Mn2+ ions in other RNA structures. The thermodynamic consequence of this metal ion core was probed by thermal denaturation techniques including UV-Vis spectroscopy and differential scanning calorimetry (DSC). DSC experiments were utilized to directly determine the thermodynamic contribution of the metal ion core. This value was determined to be an average of &#8710;&#8710;G of -5.3 kcal/mol and is consistent with &#8710;&#8710;G values obtained for other RNA tertiary structures.

Fluorescence microscopy is a powerful analytical tool for visualizing biological processes at the subcellular level. In this regard, 1,3,5-triarylpyrazoline based fluorescent probes which act as "turn-on" probes, have been extensively researched. These probes achieve their fluorescence "turn-on" response by inhibition of fluorescence quenching by acceptor-excited photoinduced electron transfer upon binding of an analyte. It has been recently shown that some fluorescent probes used in biological research form colloids composed of nanoparticles, due to their hydrophobic character. This hydrophobic character can also lead to partitioning of the probe into cellular membranes. Colloid formation and membrane partitioning may affect the probes' photophysical properties such as absorption and emission wavelength and quantum yields. Recently, a series of 1,3,5-triarylpyrazolines synthesized in our group by M. T. Morgan, showed no formation of aggregates in aqueous buffer. Surprisingly, these probes increased their fluorescence intensity in the presence of liposomes. The photoinduced electron transfer process is greatly affected by the polarity of the medium in which the probe is used. In this study, the effect of membrane proximity on the photoinduced electron transfer process for pyrazoline based "turn-on" probes has been investigated. A series of water soluble 1,3,5-triarylpyrazolines have been synthesized in which a N,N-dialkylaniline moiety acts as an electron donor and a proton acceptor and an alkylated sulfonamide moiety acts as a molecular anchor for interaction with neutral and anionic liposomes.