Defects in modification of cytoplasmic and mitochondrial transfer RNAs are caused by single nuclear mutations

Many nucleus-encoded mitochondrial enzymes differ in physical and chemical properties from analogous cytoplasmic enzymes, and it is therefore generally assumed that different genes encode analogous mitochondrial and cytoplasmic enzymes. However, our genetic studies show that for at least two different tRNA modifications, mutations in nuclear genes affect cytoplasmic as well as mitochondrial tRNAs. These studies utilize two yeast genes: TRM1 and TRM2. trm1 cells do not have the enzyme activity necessary to methylate guanosine to N²,N²-dimethylguanosine. trm2 is a new mutation that we describe here. trm2 cells are deficient in tRNA(uridine-5)methyltransferase, and hence contain tRNA lacking 5-methyluridine or ribothymidine. Other than lacking 5-methyluridine trm2 cells have no obvious physiological defect. These studies also show that the N²,N²-dimethylguanosine and 5-methyluridine modifications are not added to tRNA in an obligatory order, and that 5-methyluridine is not required for removal of intervening sequences from precursor tRNA.     

HALOGENATED NUCLEIC ACIDS: STRUCTURE AND CONFORMATIONAL STUDIES OF 5-FLUOROCYTIDINE BY X-RAY CRYSTALLOGRAPHY AND NMR SPECTROSCOPY

Abstract

The stereochemistry and the conformational equilibria of 5-fluorocytidine (5FCyd) have been determined by X-ray crystallography and correlated with NMR spectroscopy in the solution state. Crystals of 5FCyd have unit cell dimensions a=9.854(1), b=l5.012(2), c=15.290(2)Å, α=β=γ=90° with two molecules in the asymmetric unit. Both molecules are in the anti-conformation, C3′-endo sugar pucker and a ? (C4′-C5′) of g⁺. The two molecules in the asymmetric unit show slight variation in their bond distances and bond angles but their overall solid state conformation is similar. The NMR results indicate the 5FCyd has an anti-conformation, a mixed sugar pucker of 36% C2′- endo and 64% C3′-endo and an exocyclic furanose conformation (?) of 74%(g⁺), 19%(t) and 7%(g^?).

Certain purine and pyrimidine analogues readily replace the natural bases in nucleic acid if they are present during replication. Halogenated nucleic acids have been known for the past thirty years when for the first time it was found that 5-iodouracil could be incorporated into the nucleic acid of E coli ¹. This provided the basis for the synthesis of 5-fluoro-nucleic acid bases and their use as a chemotherapeutic agent.

The biological properties of 5-halogenated uracil derivatives have been examined in detail. The incorporation of the halogenated base into mRNA could lead to errors in the reading frame which would alter the phenotype without permanent change in DNA genotype^2-4, also, it can substitute for uracil into mRNA and may exert a mutagenic effect⁵ or can occasionally lead to the production of altered protein^6-7. A substitution of uracil by fluorouracil in the mRNA and a preferential pairing of the 5FUra with a guanosine in the tRNA anti-codons can account for the first substitution. This is because 5FU assumes properties similar to cytosine when the base ionizes. This occurs readily for 5FU (pKa = 7.8) due to the electronegative fluorine atom at C5 instead of hydrogen. 5FCyd shows antifungal activity against Saccharomyces cerevisiae and Candida species. It is the drug of choice for systemic infections. In order to obtain a more basic understanding of the potential of such processes, the present study was undertaken as the first step using solid phase study by X-ray crystallography and its structure in solution by NMR spectroscopy⁸.     

Optical properties and viscosity of hyaluronic acid in mixed solvents: Evidence of conformational transition

Circular dichroism, optical rotatory dispersion, and viscosity of hyaluronic acid at various solvents compositions, concentrations, and pH values have been studied. The data show a large change in the molecular properties in organic/water solvents such as ethanol, p-dioxane, or acetonitrile/water at pH ? pK_a. At this pH range of aqueous solution, hyaluronic acid shows a CD minimum near 210 nm whereas in the presence of organic solvent it exhibits a strong negative dichroism (below 200 nm) and a positive band near 226 nm. It undergoes a sharp, cooperative transition with respect to pH and solvent. The observed CD features are assigned to the π-π* and n-π* transitions of the amide and carboxyl chromophores. The ORD results show a gradual blue shift of trough at 220 nm with increasing magnitude of rotation when the organic solvents and hydrogen ion concentrations are increased. A one-term Drude's equation was used to analyze the ORD data, and the result show a variation of dispersion parameters with different solvents in accordance with the observed CD changes. The intrinsic viscosity of hyaluronic acid in mixed solvent at pH 2.6 is lower than that of aqueous solution. All the observed property changes of hyaluronic acid are reversed on addition of foramide in mixed solvents indicating that the hydrogen bonds are involved in this transition. The observed spectroscopic and hydrodynamic features are attributed to a conformational change of hyaluronic acid in a mixed solvent involving intramolecular hydrogen bonding between the acetamido and carboxyl groups. The possible conformational state of hyaluronic acid in solution under various conditions is discussed in terms of the reported helical structure of hyaluronic acid from x-ray diffraction studies.     

Structural studies on aqueous and hydroalcoholic solutions of a polyene antibiotic: Amphotericin B

Circular dichroism and absorption and light scattering have been used to study the effect of ethyl alcohol on an aqueous solution of Amphotericin B (“Fungizone”), which is an antifungal heptene. In aqueous solution, light-scattering studies show that Amphotericin B exists in an aggregated form. The estimated mass of these aggregates is about 2 × 10⁶ daltons, representing about 2000 molecules. Since the aggregated form is high molecular weight and scattering, the CD involves probably the differential scattering of right and left polarized light. In aqueous solution, Amphotericin B exhibits a strong dissymetric couplet in CD at the wavelength of the absorption maximum (328 nm). This latter maximum presents a blue shift when compared with the normal absorption in polar organic solvents. In hydroalcoholic solutions, for alcohol concentrations below 35%, the molecular weight of the aggregates is unchanged, while the absorption and CD spectra are modified. For alcohol concentrations greater than 35%, the aggregates mass decreases quickly and becomes undetectable at 50% ethyl alcohol concentration. For these solutions, the CD and absorption spectra are practically constant and characteristic of unaggregated Amphotericin B form.     

A circular dichroism study of modified nucleosides

The conformation of 5-methoxycarbonylmethyluridine and 5-methoxycarbonylmethyl-2-thiouridine was studied by means of circular dichroism in various solvents. In order to calculate the accurate spectral parameters of the Cotton effects, the circular dichroism spectra were resolved into component Gaussian functions which simultaneously fit the adsorption spectra. On the basis of circular dichroism and proton magnetic resonance spectra, these nucleosides were found to occur in the β-configuration with the ³E-gg-anti conformation preferred. Due to the fact that the long-wavelength Cotton effect of mcm⁵s²U is not masked by the Cotton effects of the other nucleic acid monomers, the molecular parameters of this band may be useful for the conformational analysis of tRNA segments.     

Intensity fluctuation spectroscopy and transfer RNA conformation. III. Influence of NaCl concentration on the size and shape of the initially salt-free tRNA in solution.

The influence of sodium ion concentration in solution on the initially salt-free conformation of bulk tRNA from baker's yeast has been investigated by means of photon correlation spectroscopy. From the measured values of translational (D^T) and rotational (D^R) diffusion coefficients, the semiaxes of an ellipsoid of revolution, which are hydrodynamically equivalent to the tRNA molecule, were calculated for tRNA solutions in pure H₂O as well as in 0.005, 0.1, 0.5M NaCl and 0.01M MgCl₂ solutions at pH 4.2 and 7.5. These data, combined with our previous studies, suggested a model which describes the formation of an ordered tRNA structure due to increasing NaCl concentrations. Furthermore, we have obtained information concerning intermolecular interactions between tRNA molecules in solution. In low-salt or salt-free tRNA solutions, we detected in the linewidth distribution function an extra-fast component which can be attributed as possibly due to charge fluctuations related to the reaction of ionization of organic bases. In our light-scattering linewidth measurements, we do not see fluctuations of charged and uncharged states directly as concentration fluctuations. Rather, we postulate a modulation of long-range intermolecular electrostatic interactions between the tRNA molecules due to such charge fluctuations. It is this modulation which is related to the fast component of the time correlation function at finite concentrations. A quantitative theory is needed to provide a more definitive explanation of the dynamical behavior of tRNA in salt-free or low-salt solutions.     

Conformations of Complexes Derived from the Interactions of Two Stereoisomeric Bay-Region 5-Methylchrysene Diol Epoxides with DNA

Abstract

The reaction mechanisms of two isomeric bay-region diol epoxides of 5-methylchrysene (trans-1,2-dihydroxy-anti/-3,4-epoxy-1,2,3,4-tetrahydro-5-methylchrysene (DE-I) and trans-7,8-dihydroxy-anti-9,10-epoxy-7,8,9,10-tetrahydro-5-methylchrysene (DE-II) with double-stranded DNA in aqueous solutions were studied utilizing kinetic flow dichroism and fluorescence techniques. As in the case of the previously studied benzo(a)pyrene-7,8-diol-9,10-oxide isomers (BaPDE), both DE-I and DE-II rapidly form intercalation-type complexes (association constants K = 2700 and 1500 M^?1 respectively in a neutral 5mM phosphate solution). The physically bound diol epoxide molecules react on time scales of minutes to form predominantly tetraols; a greater fraction (6±1%) of DE-I than of DE-II (2–3%) molecules react with the DNA to form covalent products. The DE-II isomer is characterized by a greater reactivity than DE-I, and the rates of reaction are markedly accelerated in the presence of DNA in both cases. The linear dichroism spectra of the covalent adducts reveal that the conformations of both types of adducts are similar, with the long axes of the phenanthrenyl chromophores tilted, on the average, at angles of 38-52° with respect to the average orientations of the transition moments (at 260 nm) of the DNA bases. The conformations of the covalently bound DE-I and DE-II molecules resemble those observed in the case of the highly tumorigenic (+) enantiomer of anti-BaPDE. The differences in the biological properties of these and other polycyclic aromatic diol epoxides are discussed in terms of their reactivities with DNA and the conformations of the adducts formed.     

Identification of bacteriophage T4-specific precursor tRNA by using a host mutant defective in the methylation of tRNA.

A mutant of Escherichia coli K-12 that is defective in the synthesis of 5-methyluridine (ribothymidine) in tRNA was used to identify precursors to phage T4-specific tRNA. The precursor molecules, isolated by gel filtration, were more than twice the size of tRNA. This method is suitable for isolation of rather large amounts of such precursor molecules.     

Kinetics of hydrolysis to tetraols and binding of benzo(a)pyrene-7,8-dihydrodiol-9,10-oxide and its tetraol derivatives to DNA. Conformation of adducts

When the major reactive metabolite of benzo(a)pyrene, $\text{trans}$ -7,8-dihydroxy - $\text{anti}$-9,10-epoxy -7,8,9,10-tetrahydrobenzo(a)pyrene ($\text{anti}$-BPDE) is incubated with DNA in aqueous solution at 25°C, both covalent binding and hydrolysis of $\text{anti}$-BPDE to its tetraols occur. Using fluorescence and absorption spectroscopy it is shown that hydrolysis of $\text{anti}$-BPDE is markedly accelerated by DNA. In the presence of 5A₂₆₀ units of DNA per ml in cacodylate buffer solution, at an initial concentration of DNA phosphate/$\text{anti}$-BPDE ratio of 100, both the extent of covalent binding to DNA ( < 7% of the total $\text{anti}$-BPDE initially present) and hydrolysis of $\text{anti}$-BPDE reach their maximum levels within less than five minutes after mixing. Absorption and electric linear dichroism spectra indicate that the tetraols bind non-covalently to DNA by an intercalation mechanism, whereas the covalent product displays the characteristics of an externally bound complex.     

Formation of Inclusion Complexes of Cycldextrin with Ethanol under Anhydrous Conditions

Complex formation of poorly water soluble organic compounds with cyclodextrin (CD) is quite difficult in an aqueous cyclodextrin system. Formation of the inclusion complex of d-limonene, phenyl ethanol, acetophenone, or menthol was investigated in a slurry form of α-, β-, or γ-CD in organic solvents or alcohol under anhydrous conditions. Ethanol and methanol were found to be good solvents for this method. The use of ethanol as the solvent was investigated in greater detail. There existed an optimal amount of ethanol for the maximum inclusion of d-limonene as the guest compound. However, an excess of ethanol inhibited the inclusion. An adsorption model of alcohol on CD, analogous to the substrate inhibition model of enzyme kinetics, could correlate the inclusion ratio with the amount of alcohol added to CD.     

Yeast tRNAAsp-Aspartyl-tRNA Synthetase Complex: Low Resolution Crystal Structure

Abstract

Yeast aspartyl-tRNA synthetase, a dimer of molecular weight 125000, and two molecules of its cognate tRNA (M_r = 24160) cocrystallize in the cubic space group 1432 (a = 354 Å). The crystal structure was solved to low resolution using neutron and X-ray diffraction data. Neutron single crystal diffraction data were collected in five solvents differing by their D₂O content in order to use the contrast variation method to distinguish between the protein and tRNA The synthetase was first located at 40 Å resolution using the 65% D₂O neutron data (tRNA matched). tRNA molecules were found at 20 Å resolution using both neutron and X-ray data. The resulting model was refined against 10 Å resolution X-ray data, using density modification and least-squares refinement of the tRNA positions. The crystal structure, solved without a priori phase knowledge, was confirmed later by isomorphous replacement. The molecular model of the complex is in good agreement with results obtained in solution by probing the protected part of the tRNA by chemical reagents.     

Myoglobin-catalyzed epoxidation of styrene in organic solvents accelerated by bioimprinting

Myoglobin imprinted in aqueous solution with ligands binding to its heme iron, followed by lyophilization, catalyzed the epoxidation of styrene with H₂O₂or tert-butyl hydroperoxide in organic solvents much faster than the non-imprinted protein under otherwise the same conditions.     

Effect of organic solvents on the properties of the complexes of DNA with proflavine and similar compounds

In order to obtain information on the binding forces involved in the formation of the complex proflavine–DNA by the stronger process I, the stability of the complexes was investigated in the presence of various organic solvents, methanol, ethanol, n-propanol, isopropanol, formamide, dimethyl sulfoxide, p-dioxane, glycerol, and ethylene glycol. Quantitative data on binding in terms of K/n and r were obtained by means of absorption and fluorescence spectra, as well as by a thermal denaturation technique. All organic solvents used decrease the binding ability of the dye. The effectiveness of the solvents increases with their hydrocarbon content, but can hardly be related to their dielectric constant. The complex formation is effectively suppressed by organic solvent concentrations, in which DNA still preserves its double-helical conformation. These results demonstrate the importance of hydrophobic forces in the formation of the complex proflavine–DNA in aqueous solution. The similarity in spectroscopic properties of proflavine bound to DNA by process I and the same dye dissolved in an organic solvent make it possible to interpret the observed red shift of the long-wavelength absorption peak as being due to the interaction of the dye molecules with the less polar environment. The same behavior was found for other dyes capable of intercalation like purified trypaflavine, phenosafranine and ethidium bromide. However, intercalation is not a necessary condition, as it was shown in the case of pinacyanol, which binds only at the surface of DNA.     

Amphiphilic molecular gels from ω-aminoalkylated l-glutamic acid derivatives with unique chiroptical properties

Self-assembling amphiphiles with unique chiroptical properties were derived from l-glutamic acid through ω-aminoalkylation and double long-chain alkylation. These amphiphiles can disperse in various solvents ranging from water to n-hexane. TEM and SEM observations indicate that the improvement in dispersity is induced by the formation of tubular and/or fibrillar aggregates with nanosized diameters, which makes these amphiphiles similar to aqueous lipid membrane systems. Spectroscopic observations, such as UV–visible and CD spectroscopies indicate that the aggregates are constructed on the basis of S- and R-chirally ordered structures through interamide interactions in water and organic media, respectively, and that these chiroptical properties can be controlled thermotropically and lyotropically. It is also reported that the chiral assemblies provide specific binding sites for achiral molecules and then induce chirality for the bonded molecules. Further, the applicability of the amphiphiles to template polymerization is discussed.     

A New Synthesis of Hepialone [(R)-2-Ethyl-6-methyl-2,3-dihydro-4H-pyran-4-one], the Principal Component from Male Sex Scales of the Ghost Moth,Hepialus californicus B

Microorganisms that produce 5-methyluridine (ribothymidine) directly from purine nucleosides and thymine were screened from our stock cultures. Of the 400 strains tested, Erwinia carotovora AJ- 2992 was found to possess the most potent ability as to production of 5-methyluridine from guanosine and thymine. In the presence of intact cells of Er. carotovora AJ-2992 as the enzyme source, 222 mm 5-methyluridine was produced from 300 mm guanosine and 300 mm thymine at 60°C on 48 hr incubation. The enzymatic production of 5-methyluridine by Er. carotovora AJ-2992 was found to involve the following two successive reactions via ribose-1-phosphate as an intermediate: phosphorolysis of purine nucleosides to ribose-1-phosphate and purine bases by purine nucleoside phosphorylase, followed by condensation of ribose-1-phosphate and thymine into 5-methyluridine by pyrimidine nucleoside phosphorylase.     

Synthesis of 1-(2,3-Dideoxy-β-d-glycero-pent-2-enofuranosyl)thymine (d4T; Stavudine) from 5-Methyluridine

Abstract

A practical synthetic method of d4T (3) from 5-methyluridine (2a) was developed. The Marumoto-Mansuri method was modified using 2′,3′-O-methoxy-ethylidene-5-methyluridine (10) as an intermediate to afford 1-(3,5-di-O-acetyl-2-bromo-2-deoxy-β-D-ribofuranosyl)thymine (6a) in high yield with less formation of by-products. The reaction mechanism was also discussed.

     

The viscosity behavior and conformations of low-molecular-weight poly-γ-benzyl-L-glutamate in various solvents

Reduced viscosity and infrared spectra of low-molecular-weight poly-γ-benzyl-L -glutamate (which was prepared by polymerization of the N-carboxyanhydride with n-hexylamine initiation at [A]/[I] 3, 4, and 8) have been measured in various organic solvents. Infrared spectra indicate that the polypeptide molecules consist of a series of residues of two forms, the solvated σ-form and the hydrogen-bonded β-form, and relative abundance of the two forms depends on solvent species and polypeptide concentration. An approximate method is developed for estimating the content of β-structure from a single spectrum of dissolved polypeptide. The reduced viscosity of some solutions is scarcely dependent in polypeptide concentration, in which a single conformation is predominantly kept over the concentration range. In the other solutions the reduced viscosity displays a strong concentration dependence or some anomalous behavior. The observed viscosity behavior has been attributed to the changes in size and shape of aggregates, which are determined by the number of hydrogen bonds in the aggregate. This unusual behavior is exhibited by solutions of the polypeptides which have a moderate content of β-structure at a finite concentration. Both the content of β-structure and the extent of association increase in the following solvents, ranked in order of effectiveness: dimethylformamide, trifluoroethanol < trimethyl phosphate < chloroform < dioxane < ethylene dichloride < ethylene dibromide. Infrared spectra suggest that the conformation of the polypeptide in dichloroacetic acid differs from either the σ- or the β-conformation.     

Diamide model for the optical activity of collagen and polyproline I and II

A diamide, N-acetyl-L -proline-N,N-dimethylamide (AcProDMA), in water solution has optical rotatory dispersion (ORD) and circular dichroism (CD) spectra very similar to those of poly-L -proline II and the fibrous protein collagen. In contrast, AcProDMA in cyclohexane solution has optical activity resembling that of poly-L -proline I. Conformational analysis shows that AcProDMA is confined by steric constraints to either of two narrow regions of conformational space. The trans isomer of AcProDMA assumes conformations near those of polyproline II and collagen nearest neighbors, while cis-AcProDMA assumes conformations near that of polyproline I nearest neighbors. Nuclear magnetic resonance (NMR) experiments show that an equilibrium mixture of the cis and trans isomers of AcProDMA is present in solution. The trans isomer predominates in aqueous solution, but the equilibrium shifts to favor the cis isomer in nonpolar organic solvents such as cyclohexane. Analysis of the ORD spectra in terms of two basic spectra reveals a solvent dependent isomerization which parallels that observed by NMR. The optical activity of the pure isomers of AcProDMA can be derived from the ORD, CD and NMR data. A comparison of component cotton effects confirms the similarity in optical activity of trans-AcProDMA, polyproline II, and collagen on the one hand, and of cis-AcProDMA and Polyproline I on the other.     

Enzyme Catalysed Synthesis in Ambient Temperature Ionic Liquids

The activity of three different lipases, a glycosidase and a protease in ionic liquids has been studied. Ambient temperature ionic liquids are a new class of solvents that are nonvolatile and nonflammable and thus an interesting alternative to classical organic solvents. Monitoring the synthesis of a simple ester, all lipases were found to exhibit both excellent activity and stability in the non-polar ionic liquid 1-butyl-3-methylimidazohum hexaflurophosphate ([bmin][PF₆], 1). Furthermore, β-galactosidase from E. coli and the Subtilisin protease Savinase^TM were both found to exhibit a hydrolytic activity in a 50% aqueous solution of the water-miscible ionic liquid 1-butyl-3-methyhmidazoUum tetra-fluoroborate ([bmin][BF₄], 2) comparable to the activity observed in 50% aqueous solutions of ethanol and acetonitrile.