DNA-Directed DNA Polymerases Evolve From Reverse Transcriptase

Scientists have been debating for decades the origin of life on earth. A number of hypotheses were proposed as to what emerged first RNA or DNA; with most scientists are in favour of the "RNA World" hypothesis. Assuming RNA emerged first, it fellow that the RNA polymerases would've appeared before DNA polymerases. Using recombinant DNA technology and bioinformatics we undertook this study to explore the relationship between RNA polymerases, reverse transcriptase and DNA polymerases. The working hypothesis is that DNA polymerases evolved from reverse transcriptase and the latter evolved from RNA polymerases. If this hypothesis is correct then one would expect to find various ancient DNA polymerases with varying level of reverse transcriptase activity. In the first phase of this research project multiple sequence alignments were made on the protein sequence of 32 prokaryotic DNA-directed DNA polymerases originating from 11 prokaryotic families against 3 viral reverse transcriptase. The data from such alignments was not very conclusive. DNA polymerases with higher level of reverse transcriptase activity were non-confined to ancient organisms, as one would've expected. The second phase of this project was focused on conditions that may alter the DNA polymerase activity. Various reaction conditions, such as temperature, using various ions (Ni2+, Mn2+, Mg2+) were tested. Interestingly, it was found that the DNA polymerase from the Thermos aquatics family can be made to copy RNA into DNA (i.e. reverse transcriptase activity). Thus it was shown that under appropriate conditions (ions and reactions temperatures) reverse transcriptase activity can be induced in DNA polymerase. In the third phase of this study recombinant DNA technology was used to generate a chimeric DNA polymerase; in attempts to identify the region(s) of the polymerase responsible for RNA-directed DNA polymerase activity. The two DNA polymerases employed were the Thermus aquatic us and Thermus thermophiles. As in the second phase various reaction conditions were investigated. Data indicated that the newly engineered chimeric DNA polymerase can be induced to copy RNA into DNA. Thus the intrinsic reverse transcriptase activity found in ancient DNA polymerases was localized into a domain and can be induced via appropriate reaction conditions.

Polynuclear Ni(II) Complexes with Schiff Bases as Bridging Ligands: A Molecular Approach to Nanoscience

The initial employment of N-salicylidene-2-amino-5-chlorobenzoic acid (sacbH2) as bridging/chelating ligand in metal cluster chemistry has provided access to five new polynuclear NiII complexes with large nuclearities, unprecedented metal core topologies, and interesting magnetic properties. The obtained results are presented in two projects. The first project includes the investigation of the general Ni2+/RCO2-/sacbH2 reaction system (where R- = CH3-, But-, ButCH2-) in which the nature of the carboxylic acid was found to be of crucial importance, affecting enormously the nuclearity of the resulting complexes. The second project deals with the study of the general Ni2+/X-/sacbH2 reaction system (where X- = inorganic anions) under basic conditions, yielding new cluster compounds with molecular chain-like structures and ferromagnetic exchange interactions between the metal centers.

The Effects of Magnetic Dilution and Applied Pressure on Several Frustrated Spinels

The effects of magnetic dilution and applied pressure on frustrated spinels GeNi2O4, GeCo2O4, and NiAl2O4 are reported. Dilution was achieved by substitution of Mg2+ in place of magnetically active Co2+ and Ni2+ ions. Large values of the percolation thresholds were found in GeNi(2-x)MgxO4. Specifically, pc1 = 0.74 and pc2 = 0.65 in the sub-networks associated with the triangular and kagome planes, respectively. This anomalous behaviour may be explained by the kagome and triangular planes behaving as coupled networks, also know as a network of networks. In simulations of coupled lattices that form a network of networks, similar anomalous percolation threshold values have been found. In addition, at dilution levels above x=0.30, there is a T^2 dependency in the magnetic heat capacity which may indicate two dimensional spin glass behaviour. Applied pressures in the range of 0 GPa to 1.2 GPa yield a slight decrease in ordering temperature for both the kagome and triangular planes. In GeCo(2-x)MgxO4, the long range magnetic order is more robust with a percolation threshold of pc=0.448. Similar to diluted nickel germanate, at low temperatures, a T^2 magnetic heat capacity contribution is present which indicates a shift from a 3D ordered state to a 2D spin glass state in the presence of increased dilution. Dynamic magnetic susceptibility data indicate a change from canonical spin glass to a cluster glass behaviour. In addition, there is a non-linear increase in ordering temperature with applied pressure in the range P = 0 to 1.0 GPa. A spin glass ground state was observed in Ni(1-x)MgxAl2O4 for (x=0 to 0.375). Analysis of dynamic magnetic susceptibility data yield a characteristic time of tau* = 1.0x10^(-13) s, which is indicative of canonical spin glass behaviour. This is further corroborated by the linear behaviour of the magnetic specific heat contribution. However, the increasing frequency dependence of the freezing temperature suggests a trend towards spin cluster glass formation.

A Chloride Ion-Selective Potentiometric Sensor Based on a Polymeric Schiff Base Complex

This paper describes the fabrication of an ion-selective electrode in which a polymeric Schiff base complex of cobalt(II) is used as the ionophore.The main advantage of the electrode is that it is mechanically stable upto 3 months..The electrode shows a linear response in the range of 2.5 × 10-5-0.5 × 10-1 mol dm-3. The response time of the electrode is 30 s.The pH range at which the electrode works is 3.8 to 6.8. The electrode was found to be selective towards chloride ion in the presence of ions like Na+, Ca2+, Mn2+, ,Fe3+, Co2+, Ni2+, Cu2+, Zn2+, CH3COO-, NO3-, SO42- ,Br- and NO2-.

Development of Macrocyclics based Electrochemical Sensors

Electroanalytical techniques represent a class of powerful and versatile analytical method which is based on the electrical properties of a solution of the analyte when it is made part of an electrochemical cell. They offer high sensitivity, accuracy, precision and a large linear dynamic range. The cost of instrumentation is relatively low compared to other instrumental methods of analysis. Many solid state electrochemical sensors have been commercialised nowadays. Potentiometry is a very simple electroanalytical technique with extraordinary analytical capabilities. Since valinomycin was introduced as an ionophore for K+, Ion Selective Electrodes have become one of the best studied and understood analytical devices. It can be used for the determination of substances ranging from simple inorganic ions to complex organic molecules. It is a very attractive option owing to the wide range of applications and ease of the use of the instruments employed. They also possess the advantages of short response time, high selectivity and very low detection limits. Moreover, analysis by these electrodes is non-destructive and adaptable to small sample volumes. It has become a standard technique for medical researchers, biologists, geologists and environmental specialists. This thesis presents the synthesis and characterisation of five ionophores. Based on these ionophores, nine potentiometric sensors are fabricated for the determination of ions such as Pb2+, Mn2+, Ni2+, Cu2+ and Sal- ion (Salicylate ion). The electrochemical characterisation and analytical application studies of the developed sensors are also described. The thesis is divided into eight chapters

Systematic studies on 3d-3d and 3d-4f multimetallic complexes with interesting magnetic and/or luminescent properties

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Inhibition of human mesangial cell proliferation by targeting T-Type calcium channels

Background: Aberrant glomerular mesangial cell (MC) proliferation is a common finding in renal diseases. T-type calcium channels (T-CaCN) play an important role in the proliferation of a number of cell types, including vascular smooth muscle cells. The hypothesis that T-CaCN may play a role in the proliferation of human MC was investigated. Methods: The presence of T-CaCN in primary cultures of human MC was examined using voltage clamping and by RT-PCR. The effect of calcium channel inhibitors, and of siRNA directed against the Cav3.2 T-CaCN isoform, on MC proliferation was assessed using the microculture tetrazolium assay and nuclear BrdU incorporation. Results: Human MC express only the Cav3.2 T-CaCN isoform. Co-incubation of MC with a T-CaCN inhibitor (mibefradil, TH1177 or Ni2+) results in a concentration-dependent attenuation of proliferation. This effect cannot be attributed to direct drug-induced cytotoxicity or apoptosis and is not seen with verapamil, an L-type channel blocker. Transfection of MC with siRNA results in knockdown of T-CaCN Cav3.2 mRNA and a clear attenuation of MC proliferation. Conclusions: These results demonstrate for the first time an important role for T-CaCN in human MC proliferation. This could potentially lead to a novel therapy in the treatment of proliferative renal diseases.

The role of voltage gated T-type Ca2+ channel isoforms in mediating "capacitative" Ca2+ entry in cancer cells

The mechanism by which Ca2+ enters electrically non-excitable cells is unclear. The sensitivity of the Ca2+ entry pathway in electrically non-excitable cells to inhibition by extracellular Ni2+ was used to direct the synthesis of a library of simple, novel compounds. These novel compounds inhibit Ca2+ entry into and, consequently, proliferation of several cancer cell lines. They showed stereoselective inhibition of proliferation and Ca2+ influx with identical stereoselective inhibition of heterologously expressed Cav3.2 isoform of T-type Ca2+ channels. Proliferation of human embryonic kidney (HEK)293 cells transfected with the Cav3.2 Ca2+ channel was also blocked. Cancer cell lines sensitive to our compounds express message for the Cav3.2 T-type Ca2+ channel isoform, its delta25B splice variant, or both, while a cell line resistant to our compounds does not. These observations raise the possibility that clinically useful drugs can be designed based upon the ability to block these Ca2+ channels.

Metal complexes of a tetraazacyclophane: solution and molecular modelling studies

An alternative synthetic approach to yield the compound 2,3,5,6,8,9,11,14-octahydrobenzo[1][ 1,4,7,10]tetraazacyclotetradecine (bz[14]N-4) is presented. The protonation constants of bz[14]N-4 and the stability constants of its complexes with Ni2+, Cu2+, Zn2+, Cd2+, Pb2+ were determined in H2O at 25degreesC with ionic strength 0.10 mol dm(-3) in KNO3 and they were compared with structurally related macrocycles cyclam (1,4,8,11-tetraazacyclotetradecane) and cyclen (1,4,7,10-tetraazacyclododecane). These studies indicate that only 1 : 1 ( M : L) species are formed in solution, and the ligand exhibits a high affinity for larger ions such as Cd2+ and Pb2+. The X-ray study of [bz[14]N4H3](3+) shows that an inclusion compound with a chloride counter-anion is formed through NH...Cl hydrogen bonds. Spectroscopic data in solution ( electronic and NMR spectra) showed that the macrocycle adopts a planar arrangement upon metal complexation. Molecular mechanics calculations reveal that in spite of the presence of the benzene ring in the macrocyclic framework this ligand can encapsulate metal ions with different stereo-electronic sizes in square planar arrangements. Our results indicate that the presence of the benzene ring in the backbone of the bz[14]N-4 confers a coordination behaviour intermediate between that of cyclam and cyclen.

Metal complexes of a dipyridine octaazamacrocycle: stability constants, structural and modelling studies

Two 28-membered octaazamacrocycles, [28]py(2)N(6) and Me-2[28]py(2)N(6), have been synthesized. The protonation constants of the N-methyl. derivative and the stability constants of its complexes with Ni2+, Cu2+, Zn2+, Cd2+, and Pb2+ were determined at 25degreesC in 0.10 mol dm(-3) KNO3. The high overall basicity of Me-2[28]py(2)N(6) is ascribed to the weaker repulsion between protonated contiguous charged ammonium sites separated by propyl chains. These studies together with NMR, UV-vis and EPR spectroscopies indicated the presence of mono- and di-nuclear species, The single crystal structure of the complex [Ni-2([28]py(2)N(6))(H2O)(4)]Cl-4.3H(2)O was determined, and showed each nickel centre in a distorted octahedral co-ordination environment. The nickel centres are held within the macrocycle at a large distance of 6.991(g) Angstrom from each other. The formation of mononuclear complexes was evaluated theoretically via molecular mechanics (MM) and molecular dynamics (MD) calculations and showed that these large macrocycles have sufficient flexibility to encapsulate metal ions with different stereo-electronic sizes. Structures for small and large metal ions are proposed.

Bis[1,1 '-N,N '-(2-picolyl)aminomethyl]ferrocene as a redox sensor for transition metal ions

The compound bis[1,1'-N,N'-(2-picolyl) aminomethyl] ferrocene, L-1, was synthesized. The protonation constants of this ligand and the stability constants of its complexes with Ni2+, Cu2+, Zn2+, Cd2+ and Pb2+ were determined in aqueous solution by potentiometric methods at 25degreesC and at ionic strength 0.10 mol dm(-3) in KNO3. The compound L-1 forms only 1:1 (M:L) complexes with Pb2+ and Cd2+ while with Ni2+ and Cu2+ species of 2:1 ratio were also found. The complexing behaviour of L-1 is regulated by the constraint imposed by the ferrocene in its backbone, leading to lower values of stability constants for complexes of the divalent first row transition metals when compared with related ligands. However, the differences in stability are smaller for the larger metal ions. The structure of the copper complex with L-1 was determined by single-crystal X-ray diffraction and shows that a species of 2:2 ratio is formed. The two copper centres display distorted octahedral geometries and are linked through the two L1 bridges at a long distance of 8.781(10) Angstrom. The electrochemical behaviour of L-1 was studied in the presence of Ni2+, Cu2+, Zn2+, Cd2+ and Pb2+, showing that upon complexation the ferrocene-ferrocenium half-wave potential shifts anodically in relation to that of the free ligand. The maximum electrochemical shift (DeltaE(1/2)) of 268 mV was found in the presence of Pb2+, followed by Cu2+ (218 mV), Ni2+ (152 mV), Zn2+ (111 mV) and Cd2+ (110 mV). Moreover, L-1 is able to electrochemically and selectively sense Cu2+ in the presence of a large excess of the other transition metal cations studied.

Bis- and tris-(3-aminopropyl) derivatives of 14-membered tetraazamacrocycles containing pyridine: synthesis, protonation and complexation studies

New N-(3-aminopropyl) (L-1, L-2) and (2-cyanoethyl) (L-3, L-4) derivatives of a 14-membered tetraazamacrocycle containing pyridine have been synthesized. The protonation constants of L-1 and L-2 and the stability constants of their complexes with Ni2+, Cu2+, Zn2+ and Cd2+ metal ions were determined in aqueous solutions by potentiometry, at 298.2 K and ionic strength 0.10 mol dm(-3) in KNO3. Both compounds have high overall basicity due to the presence of the aminopropyl arms. Their copper(II) complexes exhibit very high stability constants, which sharply decrease for the complexes of the other studied metal ions, as usually happens with polyamine ligands. Mono- and dinuclear complexes are formed with L-2 as well as with L-1, but the latter exhibits mononuclear complexes with slightly higher K-ML values while the dinuclear complexes of L-2 are thermodynamically more stable. The presence of these species in solution was supported by UV-VIS-NIR and EPR spectroscopic data. The single crystal structures of [Cu(H2L2)(ClO4)](3+) and [(CoLCl)-Cl-3](+) revealed that the metal centres are surrounded by the four nitrogen atoms of the macrocycle and one monodentate ligand, adopting distorted square pyramidal geometries. In the [(CoLCl)-Cl-3](+) complex, the macrocycle adopts a folded arrangement with the nitrogen atom opposite to the pyridine at the axial position while in the [Cu(H2L2)(ClO4)](3+) complex, the macrocycle adopts a planar conformation with the three aminopropyl arms located at the same side of the macrocyclic plane.

Bis- and tris-(methylphosphonic) acid derivatives of a 14-membered tetraazamacrocycle containing pyridine: synthesis, protonation and complexation studies

Two N-methylphosphonic acid derivatives of a 14-membered tetraazamacrocycle containing pyridine have been synthesized, H4L1 and H6L2. The protonation constants of these compounds and the stability constants of complexes of both ligands with Ni2+, Cu2+ and Zn2+ were determined by potentiometric methods at 298 K and ionic strength 0.10 mol dm(-3) in NMe4NO3. The high overall basicity of both compounds is ascribed to the presence of the phosphonate arms. H-1 and P-31 NMR spectroscopic titrations were performed to elucidate the sequence of protonation, which were complemented by conformational analysis studies. The complexes of these ligands have stability constants of the order of or higher than those formed with ligands having the same macrocyclic backbone but acetate arms. At pH = 7 the highest pM values were found for solutions containing the compound with three acetate groups, followed immediately by those of H6L2, however, as expected, the increasing pH favours the complexes of ligands containing phosphonate groups. The single-crystal structure of Na-2[Cu(HL1)]NO3.8H(2)O has shown that the coordination geometry around the copper atom is a distorted square pyramid. Three nitrogen atoms of the macrocyclic backbone and one oxygen atom from one methylphosphonate arm define the basal plane, and the apical coordination is accomplished via the nitrogen atom trans to the pyridine ring of the macrocycle. To achieve this geometric arrangement, the macrocycle adopts a folded conformation. This structure seems consistent with Uv-vis-NIR spectroscopy for the Ni2+ and the Cu2+ complexes and with the EPR for the latter.

Ditopic hexaazamacrocycles containing pyridine: synthesis, protonation and complexation studies

Structural studies of metal complexes of five ditopic hexaazamacrocycles containing two pyridine rings ([n] py(2)N(4) n = 18, 20, 22, 24 and 26) have been carried out. The synthesis of macrocycles [22]- to [26]- py(2)N(4) are also reported. The protonation constants of the last three compounds and the stability constants of their complexes with Ni2+, Cu2+, Zn2+, and Pb2+ were determined at 25 degreesC in 0.10 mol dm(-3) KNO3 in aqueous solution. Our results with [22] py(2)N(4) show significant differences from those described previously, while [24] py(2)N(4) has not been studied before and [ 26] py2N4 is a new compound. Mononuclear and dinuclear complexes of the divalent metal ions studied with [ 22]- to [26]- py(2)N(4) were found in solution. The stability constants for the ML complexes of the three ligands follow the Irving - Williams order: NiL2+ < CuL2+ >> ZnL2+ > PbL2+, however for the dinuclear complexes the values for Pb2+ complexes are higher than the corresponding values for the Ni2+ and the Zn2+ complexes. The X-ray single crystal structures of the supramolecular aggregates [Cu-2([20] py(2)N(4))(H2O)(4)][Cu(H2O)(6)](SO4)(3) . 3H(2)O ( 1) and [Cu-2([20] py(2)N(4))(CH3CN)(4)][Ni([20] py(2)N(4))](2)(ClO4)(8) . H2O (2), which are composed of homodinuclear [Cu-2([20] py(2)N(4)])(H2O)(4)](4+) ( 1a) and [Cu-2([20] py(2)N(4)])(CH3CN))(4)](4+) (2a), and mononuclear species, [Cu(H2O)(6)](2+) (1b) and [Ni([20] py(2)N(4))](2+) ( 2b), respectively, assembled by an extensive network of hydrogen bonds, are also reported. In both homodinuclear complexes the copper centres are located at the end of the macrocycle and display distorted square pyramidal coordination environments with the basal plane defined by three consecutive nitrogen donors and one solvent molecule, water in 1a and acetonitrile in 2a. The macrocycle adopts a concertina-type conformation leading to the formation of macrocyclic cavities with the two copper centres separated by intramolecular distances of 5.526(1) and 5.508(7) Angstrom in 1a and 2a, respectively. The mononuclear complex [Ni([20] py(2)N(4)])](2+) displays a distorted octahedral co-ordination environment with the macrocycle wrapping the metal centre in a helical shape. EPR spectroscopy of the copper complexes indicated the presence of mono- and dinuclear species.

Dioxadiaza- and trioxadiaza-macrocycles containing one dibenzofuran unit selective for cadmium

The binding properties of dioxadiaza-([17](DBF) N2O2) and trioxadiaza- ([22](DBF)N2O3), macrocyclic ligands containing a rigid dibenzofuran group ( DBF), to metal cations and structural studies of their metal complexes have been carried out. The protonation constants of these two ligands and the stability constants of their complexes with Ca2+, Ba2+, and Mn2+, Co2+, Ni2+, Cu2+, Zn2+ and Cd2+, were determined at 298.2 K in methanol-water ( 1 : 1, v/v), and at ionic strength 0.10 mol dm(-3) in KNO3. The values of the protonation constants of both ligands are similar, indicating that no cavity size effect is observed. Only mononuclear complexes of these ligands with the divalent metal ions studied were found, and their stability constants are lower than expected, especially for the complexes of the macrocycle with smaller cavity size. However, the Cd2+ complex with [ 17]( DBF) N2O2 exhibits the highest value of stability constant for the whole series of metal ions studied, indicating that this ligand reveals a remarkable selectivity for cadmium(II) in the presence of all the metal ions studied, except copper( II), indicating that this ligand reveals a remarkable selectivity for cadmium( II) in the presence of the mentioned metal ions. The crystal structures of H-2[17](DBF)N2O32+ (diprotonated form of the ligand) and of its cadmium complex were determined by X-ray diffraction. The Cd2+ ion fits exactly inside the macrocyclic cavity exhibiting coordination number eight by coordination to all the donor atoms of the ligand, and additionally to two oxygen atoms from one nitrate anion and one oxygen atom from a water molecule. The nickel( II) and copper( II) complexes with the two ligands were further studied by UV-vis-NIR and the copper( II) complexes also by EPR spectroscopic techniques in solution indicating square-pyramidal structures and suggesting that only one nitrogen and oxygen donors of the ligands are bound to the metal. However an additional weak interaction of the second nitrogen cannot be ruled out.