Nucleic acids are virtually omnipresent; they exist in every living being. These macromolecules constitute the most important genetic storage material: the genes. Genes are conserved throughout the evolution of all living beings; they are transmitted from the parents to their offspring. Many interdisciplinary research groups are interested in modifying nucleic acids for use in a wider variety of applications. These modified oligonucleotides are used in many diverse fields, including diagnostics, detection, and therapeutics. In this account, we summarize our research efforts related to modified nucleic acid systems. First, we discuss our syntheses of modified oligonucleotides containing fluorescent tags for use as molecular probes (molecular beacons) to detect single-nucleotide polymorphisim (SNP) in nucleic acids and to distinguish between the B and Z forms of DNA. We also describe our research efforts into oligonucleotides functionalized with steroid derivatives to enhance their cell permeability, and the synthesis of several calix[4]arene-oligonucleotide conjugates possessing the ability to form defined triplexes. In addition, we have performed systematic studies to have an understanding about the functional groups necessary for a given nucleoside to behave as an organo or hydrogelator. The aggregation properties of a number of nucleoside-based phospholipids have been examined in different solvents; some of these derivatives are potential candidates for use as nucleoside-based liposomes. Finally, we also describe our research efforts toward the preparation of isoxazole- and isoxazoline-containing nucleoside derivatives and the determination of their antiviral activities.

Although chiral separation has been one of the main topics of chromatographic practice for over twenty-five years, it still presents many difficulties. In this work, the ultrasonic dependence of chiral resolution was investigated at various temperatures to improve resolution and reduce analysis time. The chiral resolution was performed on recently commercialized two HPLC chiral stationary phases (CSP 1 and CSP 2) with the analogues of racemic N-acylnaphthylethylamines (1a-d) and racemic amino acid derivatives (2a-c, 3a-c) as analytes. The CSP 1 was prepared from a (R)-N-(3,5-dinitrobenzoyl)phenylglycinol and the CSP 2 was prepared from a (S)-N-3,5-(dinitrobenzoyl) leucine. From the comparison of the chromatographic results under sonic condition with those under non-sonic condition, we found that the ultrasound decreased the elution time in chiral chromatography at all temperatures and improved the enantioselectivity at high temperature (45, 50, 60 ${^{\circ}C}$).

Mushroom tyrosinase (MT) structural changes in the presence of $Cu ^{2+}$ and $Ni ^{2+}$ were studied separately. Far-UV CD spectra of the incubated MT with the either of the metal ions indicated reduction of the well-ordered secondary structure of the enzyme. Increasing in the maximum fluorescence emission of anilinonaphthalene-8-sulfonic acid (ANS) was also revealing partial unfolding caused by the conformational changes in the tertiary structure of MT. Thermodynamic studies on the chemical denaturation of MT by dodecyl trimethylammonium bromide (DTAB) showed decrease in the stability of MT in the presence of $Cu ^{2+}$ or $Ni ^{2+}$ using their activation concentrations. Both activities of MT were also assessed in the presence of different concentrations of these ions, separately, with various monophenols and their corresponding diphenols. Kinetic studies revealed that cresolase activity on p-coumaric acid was boosted in the presence of either of the metal ions, but inhibited when phenol, L-tyrosine, or 4-[(4-methylphenyl)azo]-phenol was substrate. Similarly, catecholase activity on caffeic acid was enhanced in the presence of $Cu ^{2+}$ or $Ni ^{2+}$, but inhibited when catechol, L-DOPA, or 4-[(4-methylbenzo)azo]-1,2-benzenediol was substrate. Results of this study suggest that both cations make MT more fragile and less active. However, the effect of the substrate structure on the MT allosteric behavior can not be ignored.

The proposed head-space supercritical fluid extraction (SFE) methodology as an alternative to an existing conventional procedure was explored for the determination of organochlorine compounds in aqueous matrix. In this study, polychlorinated biphenyls (PCBs) and organochlorine pesticides (OCPs) were utilized as target analytes. To enhance the recovery efficiency, the factors such as the $CO _2$ density, the extraction time, and the extraction mode were investigated. Furthermore, the analytical procedures and the results obtained were compared with those provided by the conventional method (the U.S. EPA method 8080). Under the optimized conditions, i.e., a combination of static with dynamic SFE mode at 2,000 psi and 40 ${^{\circ}C}$, the head-space SFE methodology gave equivalent or better to the conventional method in recovery efficiencies with clear advantages such as simple sample treatment and fast analysis time as well as reduced solvent and reagent consumption.

Identification of accessible sites in targeted RNAs is a major limitation to the effectiveness of antisense oligonucleotides. A class of antisense oligodeoxynucleotides, known as the “10-23” DNA enzyme or DNAzyme, which is a small catalytic DNA, has been shown to efficiently cleave target RNA at purine-pyrimidine junctions in vitro. We have designed a strategy to identify accessible cleavage sites in the target RNA, which is hepatitis C virus nonstructural gene 3 (HCV NS3) RNA that encodes viral helicase and protease, from a pool of random DNAzyme library. A pool of DNAzymes of 58 nucleotides-length that possess randomized annealing arms, catalytic core sequence, and fixed 5'/3'-end flanking sequences was designed and screened for their ability to cleave the target RNA. The screening procedure, which includes binding of DNAzyme pool to the target RNA under inactive condition, selection and amplification of active DNAzymes, incubation of the selected DNAzymes with the target RNA, and target site identification on sequencing gels, identified 16 potential cleavage sites in the target RNA. Corresponding DNAzymes were constructed for the selected target sites and were tested for RNA-cleavage in terms of kinetics and accessibility. These selected DNAzymes were effective in cleaving the target RNA in the presence of $Mg^{2+}$. This strategy can be applicable to identify accessible sites in any target RNA for antisense oligonucleotides-based gene inactivation methods.

Carnosine, homocarnosine and anserine might act as anti-oxidants and free radical scavengers in vivo. In the present study, the protective effects of carnosine and related compounds on the $H_2O_2$-mediated cytochrome c modification were studied. Carnosine, homocarnosine and anserine significantly inhibited the oligomerization of cytchrome c induced by $H_2O_2$. All three compounds also inhibited the formation of carbonyl compound and dityrosine during the incubation of cytochrome c with $H_2O_2$. These compounds effectively inhibited the peroxidase activity in the cytchrome c treated with $H_2O_2$. The results suggested that carnosine, homocarnosine, and anserine might protect cytochrome c against $H_2O_2$-mediated oxidative damage through a free radical scavenging.

The new MPV-type reagents, B-acetoxydiisopinocampheylborane ($Ipc _2$BOAc) and B-trifluoroacetoxydiisopinocampheylborane $(Ipc _2BO _2CCF _3)$, have been prepared and their reducing characteristics in the reduction of carbonyl compound have been examined in order to find out a new reducing system with unique applicability in organic synthesis. In general, the reactivity of $Ipc _2BO _2CCF _3$ appears to be stronger than that of $Ipc _2$BOAc, presumably due to the acidity increase by the electron-withdrawing fluorine-substituent. Both reagents show an excellent selectivity in 1,2-reduction of $\alpha,\beta$-unsaturatedcarbonyl compounds and in competitive reduction between structurally different carbonyl compounds. In addition, $Ipc _2BO _2CCF _3$ shows interesting features in the stereoreduction of cyclic ketones.

A new approach to fabricate an enzyme electrode was described based on the immobilization of horseradish peroxidase (HRP) on dithiobis-N-succinimidyl propionate (DTSP) self-assembled monolayer (SAM) formed on gold-nanoparticles (Au-NPs) which were electrochemically deposited onto glassy carbon electrode (GCE) surface. The overall surface area and average size of Au-NPs could be controlled by varying deposition time and were examined by Field Emission-Scanning Electron Microscope (FE-SEM). The $O_2$ reduction capability of the surface demonstrated that Au-NPs were thermodynamically stable enough to stay on GCE surface. The immobilized HRP electrode based on Au-NPs/GCE presented faster, more stable and sensitive amperometric response in the reduction of hydrogen peroxide than a HRP immobilized on DTSP/gold plate electrode not containing Au-NPs. The effects of operating potential, mediator concentration, and pH of buffer electrolyte solution on the performance of the HRP biosensor were investigated. In the optimized experimental conditions, the HRP immobilized GCE incorporating smaller-sized Au-NPs showed higher electrocatalytic activity due to the high surface area to volume ratio of Au-NPs in the biosensor. The HRP electrode showed a linear response to $H_2O_2$ in the concentration range of 1.4 $\mu$M-3.1 mM. The apparent Michaelis-Menten constant ($K _M\; ^{app}$) determined for the immobilized HRP electrodes showed a trend to be decreased by decreasing size of Au-NPs electrodeposited onto GCE.

The positions of $PbI _2$ molecule synthesized into the molecular-dimensioned cavities of $\mid K_6 (Pb _4I_2)(PbI_2) _{0.67}-(H_2O)_2\mid [Si _{12}Al _{12}O _{48}]$-LTA have been determined. A single crystal of $\mid Pb _6\mid [Si _{12}Al _{12}O _{48}]$-LTA, prepared by the dynamic ion-exchange of $\mid Na _{12}\mid [Si _{12}Al _{12}O _{48}]$-LTA with aqueous 0.05 M $Pb _(NO _3)_2$ and washed with deionized water, was placed in a stream of flowing aqueous 0.05 M KI at 294 K for three days. The resulting crystal structure of the product $( \mid K_6 (Pb _4I_2)(PbI_2) _{0.67}(H_2O)_2\mid [Si _{12}Al _{12}O _{48}]$-LTA, a = 12.353(1) $\AA$) was determined at 294 K by single-crystal X-ray diffraction in the space group Pm3 m. It was refined with all measured reflections to the final error index $R_1$ = 0.062 for 623 reflections which $F_o$ > 4$\sigma$($F_o$). 4.67 $Pb ^{2+}$ and six $K^+$ ions per unit cell are found at three crystallographically distinct positions: 3.67 $Pb ^{2+}$ and three $K^+$ ions on the 3-fold axes opposite six-rings in the large cavity, three $K^+$ ions off the plane of the eight-rings, and the remaining one $Pb ^{2+}$ ion lies opposite four-ring in the large cavity. 0.67 $Pb ^{2+}$ ions and 1.34 $I^-$ ions per unit cell are found in the sodalite units, indicating the formation of a $PbI _2$ molecule in 67% of the sodalite units. Each $PbI _2$ (Pb-I = 3.392(7) $\AA$) is held in place by the coordination of its one $Pb ^{2+}$ ion to the zeolite framework (a $Pb ^{2+}$ cation is 0.74 $\AA$ from a six-ring oxygens) and by the coordination of its two $I^-$ ions to $K^+$ ions through six-rings (I-K = 3.63(4) $\AA$). Two additional $I^-$ ions per unit cell are found opposite a four-ring in the large cavity and form $Pb _2K_2I^{5+}$ and $Pb _2K_2I^{3+}$ moieties, respectively, and two water molecules per unit cell are also found on the 3-fold axes in the large cavity.

Chromium(III) complexes, cis-[Cr([14]-decane)$(HOC _6H _4COO) _2$]$ClO _4$ I and cis-[Cr([14]-decane)(OH) $(OC _6H _4NO _2)$]$ClO _4{\cdot}H _2O$ II ([14]-decane = rac-5,5,7,12,12,14-hexamethyl-1,4,8,11-teraazacyclotetradecane) are synthesized and structurally characterized by a combination of elemental analysis, conductivity, IR and VIS spectroscopy, and X-ray crystallography. The complexes crystallizes in the monoclinic space groups, $C2 _1$/a in I and $P2 _1$/n in II. Analysis of the crystal structure of complex I reveals that central chromium(III) ion has a distorted octahedral coordination environment and two hydrogensalicylato ligands are unidentate to the chromium(III) ion via the carboxyl groups in the cis-position. For monomeric complex I the hydrogensalicylato coordination geometry is as follows: Cr-O(average) = 1.984(3) $\AA$;Cr-N range = 2.105(3)-2.141(4) $\AA$;C(24)-O(4) = 1.286(5) $\AA$;N(2)-Cr-N(4) (equatorial position) = 96.97(15)${^{\circ}}$; N(1)-Cr-N(3) (axial position) = 168.27(15)${^{\circ}}$; O(1)-Cr-O(4) = 85.70(13)${^{\circ}}$. The crystal structure of II has indicated that chromium(III) ion is six-coordinated by four secondary amines of the macrocycle, hydroxide anion and nitrophenolate anion.

A method has been described for the chemical speciation, preconcentration and determination of Cr(III) and Cr(VI) species in filtered tannery waste waters by flame atomic absorption spectrometry using ion-exchange resins. Amberlite IR-120($H^+$) strongly acidic cation exchanger and Amberlite IRA-410($CI ^-$) strongly basic anion exchanger resins were used for the separation and preconcentration of Cr(III) and Cr(VI) species, respectively. Optimum condition for preconcentration and speciation was obtained by testing pH of sample and eluent, flow rates of sample and eluent, amount of resins, volume of sample and eluents, and effect of foreign ions. The recommended method has been successfully applied for the preconcentration and determination of chromium species in the dissolved phase of waste water samples collected from a tannery waste water treatment plant in Kayseri, Turkey. The detection limits achieved were 0.73 $\mu$g/L for Cr(III) and 0.81 $\mu$g/L for Cr(VI). Recovery studies showed 99% for Cr(III) and 98% for Cr(VI), for samples spiked with single species.

Escherichia coli RNase P is a ribonucleoprotein composed of M1 RNA and C5 protein. Previously, analysis of RNA aptamers selected for C5 protein from a synthetic RNA library showed that C5 protein could bind various RNA molecules as an RNA binding protein. In this study, we searched cellular RNA motifs that could be recognized by C5 protein by a genomic SELEX approach. We found various C5 protein-binding RNA motifs derived from E. coli genomic sequences. Our results suggest that C5 protein interacts with various cellular RNA species in addition to M1 RNA.

The synthesis of a new series of 1 $\beta$-methylcarbapenems having 5-(1,2-disubstituted ethyl)pyrrolidine moiety are described. Their in vitro antibacterial activities against both Gram-positive and Gram-negative bacteria were tested and the effect of substituents on the pyrrolidine ring was investigated. Among them, compound (IIIc) having 1-methoxyimino-2-hydroxyethyl moiety showed the most potent antibacterial activity.

$S_2O$-donor macrocyclic isomers incorporating a xylyl group in o- ($L^1$), m- ($L^2$) and p-positions ($L^3$) extract no metal ions except silver(I) from aqueous to chloroform phase. And the magnitudes of %Ex for silver(I) are in the order of $L^1$ > $L^2$ > $L^3$. Taking this result into account, $L^1$-$L^3$ were utilized as membrane active components to prepare potentiometric silver(I)-selective electrodes. The proposed macrocycles-based electrodes E1 ($L^1$), E2 ($L^2$) and E3 ($L^3$) exhibited comparable results which show considerable selectivity toward silver(I) over alkali, alkali earth and other transition metal ions. Comparative NMR study on $L^1$-$L^3$ and their complexes with silver(I) in solution was also accomplished. In addition, a unique sandwich-type complex $[Ag(L^1)_2]CIO_4$ was prepared from the assembly reaction of $L^1$ with $AgClO_4$ and structurally characterized by an X-ray diffraction analysis.

The heterogeneous association behaviour of various concentration binary mixtures of mono alkyl ethers of ethylene glycol with ethyl alcohol were investigated by dielectric measurement in benzene solutions over the entire concentration range at 25 ${^{\circ}C}$. The values of static dielectric constant $\epsilon_0$ of the mixtures were measured at 1 MHz using a four terminal dielectric liquid test fixture and precision LCR meter. The high frequency limiting dielectric constant $\epsilon_\infty$ values were determined by measurement of refractive index $n_D$ ($\epsilon_\infty\;=\;n_D\;^2$). The measured values of $\epsilon_0$ and $\epsilon_\infty$ were used to evaluate the values of excess dielectric constant $\epsilon^E$, effective Kirkwood correlation factor $g^{eff}$ and corrective correlation factor $g_f$ of the binary polar mixtures to obtain qualitative and quantitative information about the H-bond complex formation. The non-linear behaviour of the observed $\epsilon_0$ values of the polar molecules and their mixtures in benzene solvent confirms the variation in the associated structures with change in polar mixture constituents concentration and also by dilution in non-polar solvents. Appearance of the maximum in $\epsilon^E$ values at different concentration of the polar mixtures suggest the formation of stable adduct complex, which depends on the molecular size of the mono alkyl ethers of ethylene glycol. Further, the observed $\epsilon^E$ < 0 also confirms the heterogeneous H-bond complex formation reduces the effective number of dipoles in these polar binary mixtures. In benzene solutions these polar molecules shows the maximum reduce in effective number of dipoles at 50 percent dilutions. But ethyl alcohol rich binary polar mixtures in benzene solvent show the maximum reduce in effective number of dipoles in benzene rich solutions.

A rapid flotation methodology for zinc(II) separation and enrichment from human biofluids is established. At pH 6.0 and ambient temperature, using oleic acid (HOL) as a foaming reagent, zinc(II) was separated with phenanthraquinone monophenyl thiosemicarbazone (PPT) as a new flotation collector for Zn(II). The floated red colored 1 : 2 Zn(II)-PPT complex was measured spectrophotometrically at 526 nm with a molar absorptivity of $1.83 \;{\times}\; 10^5\; L$ mol $L ^{-1}\;cm ^{-1}$. Beer's law was obeyed over a concentration range 0.05-1.0 mg $L ^{-1}$ in the aqueous as well as in the scum layers. The proposed preconcentration flotation methodology was applied to determine Zn(II) in human biofluids. Application was, also, extended to determine Zn(II) in pharmaceutical samples and natural water samples spiked with known amounts of Zn(II) with a preconcentration factor of 100 and a detection limit of 10 ng m$L ^{-1}$. The method was verified by comparison of the spectrophotometric results with flame atomic absorption spectrometric (AAS) measurements. Moreover a postulation for the mechanism of flotation is proposed.

Nucleophilic addition reactions of p-substitutedbenzylamines $(XC _6H_4CH _2NH _2)$ to $\alpha$-phenyl-$\beta$-thiophenyl-acrylonitriles ($YC _4SH _2CH=C(CN)C_6H_4$Y') have been studied in acetonitrile at 25.0, 30.0, and 35.0 ${^{\circ}C}$. The reactions take place in single step in which the $C_\beta$ -N bond formation and proton transfer to $C_\alpha$ of $\alpha$-phenyl-$\beta$-thiophenylacrylonitriles occur concurrently with four-membered cyclic transition structure. These mechanistic conclusions are drawn based on (i) the large negative $\rho$x and large positive $\rho$Y' values and also large magnitude of $\rho$X, (ii) the negative sign and large magnitude of the cross-interaction constants ($\rho$XY), (iii) the normal kinetic isotope effects ($k_H/k_D$ > 1.0), and (iv) relatively low $\Delta H ^\neq$ and large negative $\Delta S ^\neq$ values.

Synthesis of cholic acid-based tripodal receptor (1) and its high chloride ion affinity in comparison with that of chenodeoxycholic acid (2) and lithocholic acid-based receptor (3) was achieved. Anion binding affinities of the receptors were evaluated $by\;^1H$ NMR and ITC titrations. Tripodal receptor 1 showed a selective affinity for $CI ^-$ over $Br ^-$, $I^-$, $H_2 PO _4\;^-$, and $CH _3 CO_2\;^-$. The selectivity of 1 for $CI ^-$ is about 3 times that of $Br ^-$, and 17 times that for $H_2 PO_4\;^-$.

Research on tripodal complexes has grown in recent decades and has been subject of numerous reports.1-11 The reasons for this interest include their relevance to model functions of metalloenzymes1-3 and their potential applications in catalysis.13-17 The ligand system used most in this category has been tren, the tripodal tetraamine N(CH2CH2NH2)3, and its derivatives.4 The bz3tren is a versatile tetradentate ligand, known to form stable complexes not only with transition metals5-11 including Cu2+, Zn2+ and Co2+ but also anion species.12 However, only few results on the d10 metal complexes with bz3tren have been reported by us10 and others.6,7 As a part of on going efforts, we therefore focus our attention to extend other d10 system that includes heavy metal ions.

The compound B(C6F5)3 and its variations have been widely employed as alkyl carbanion abstracting reagents to produce metallocene cations for olefin polymerization.1-3 Weakly coordinating anions containing boron can greatly improve the activity of metallocene catalysts used in industrial olefin polymerization4 and thus group IV and V metallocene complexes of the organohydroborate anions have been intensively investigated.5 Recently, many organohydroborate metallocene complexes have been reported by Shore and co-workers.6-8 A common structural feature of those complexes is the three-center two electron M-H-B bond, like that observed in transition metal tetrahydroborate complexes but the reactivity and fluxional behavior of organohydroborate complexes are unlike those of the tetrahydroborate analogues.6 Although many of those metallocenes have been synthesized, few complexes could be used in the olefin polymerization and then this laboratory has been involved in the chemistry of the cyclic organohydroborate anions, and their group IV metallocene derivatives for the catalyst.9 Described here is recent work that led to the preparation of a novel cyclic organohydroborate hafnocene complex (h5-C5H5)2Hf ？(μ-H)2BC8H14 ,Cl. The hafnocene complex contains the three-center two electron bond Hf-H-B10 in which the hydride abstraction for olefin polymerization may occur.