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At least 757 records · Page 42Linked to original sources
PubMed1988

Sequence-specific endoribonuclease activity of the Tetrahymena ribozyme: enhanced cleavage of certain oligonucleotide substrates that form mismatched ribozyme-substrate complexes.

A shortened form of the self-splicing intervening sequence RNA of Tetrahymena acts as a sequence-specific endoribonuclease. Specificity of cleavage is determined by Watson-Crick base pairing between the active site of the RNA enzyme (ribozyme) and its RNA substrate [Zaug, A. J., Been, M. D., & Cech, T. R. (1986) Nature (London) 324, 429-433]. Surprisingly, single-base changes in the substrate RNA 3 nucleotides preceding the cleavage site, giving a mismatched substrate-ribozyme complex, enhance the rate of cleavage. Mismatched substrates show up to a 100-fold increase in kcat and, in some cases, in kcat/Km. A mismatch introduced by changing a nucleotide in the active site of the ribozyme has a similar effect. Addition of 2.5 M urea or 3.8 M formamide or decreasing the divalent metal ion concentration from 10 to 2 mM reverses the substrate specificity, allowing the ribozyme to discriminate against the mismatched substrate. The effect of urea is to decrease kcat and kcat/Km for cleavage of the mismatched substrate; Km is not significantly affected at 0-2.5 M urea. Thus, progressive destabilization of ribozyme-substrate pairing by mismatches or by addition of a denaturant such as urea first increases the rate of cleavage to an optimum value and then decreases the rate.

Animals↗
PubMed1981

Solvent effects on the kinetics and thermodynamics of stacking in poly(cytidylic acid).

The Raman laser temperature-jump technique has been used to measure the kinetics of the coil to helix reaction of poly(cytidylic acid) [poly(C)] in aqueous cosolvent mixtures. The rate of helix formation has a low activation energy and is proportional to reciprocal solvent viscosity. The observations suggest helix formation is rotationally diffusion controlled. The rate of coil formation in poly(C) has an activation energy of approximately 11 kcal/mol, presumably reflecting the electronic stacking interactions which stabilize the helix. Viscous cosolvents, glycerol or sucrose, slow down the rate of coil formation; acetonitrile and formamide at 5 mol % increase the rate relative to that in water. The polar cosolvents may specifically attack a cytosine stack. The absorbance vs. temperature profiles for poly(C) are analyzed with the one-dimensional Ising model. When only optical data are used, the cooperativity parameter, sigma, and the enthalpy, delta H, cannot be uniquely determined. A method is proposed that allows determination of sigma by combining spectroscopic and calorimetric data. The values of sigma derived for poly(C) are between 0.8 and 1.0, and delta H is about -9 kcal/mol of stack. An alternative method using integration of the excess heat capacity curve and extrapolation to fully stacked and random coil species yields a delta H of -7 kcal/mol of stack.

Acetonitriles↗
PubMed1996

The importance of the helix 2 region for the cis-cleaving and trans-cleaving activities of hepatitis delta virus ribozymes.

The sequence, secondary structure, and size requirements of the helix 2 region (H2) of a cis-acting hepatitis delta virus ribozyme Rz 1 were examined in this study. Mutational analysis was performed, and the cleavage rate of each H2 mutant of Rz 1 was assayed. We found that H2 could be elongated to twice its original size without affecting ribozyme folding while the shortening of H2 by one base pair severely decreased autolytic activity. In addition, the maintenance of the Watson-Crick base-pairing interactions of the last base pair of H2 (A16U58) was not critical for cis-cleavage reaction. Nevertheless, mutants with an AA, an AG, an AC, or a GG pair at the bottom of H2 were less active, and the sequence of the H2/H3 interface might affect the stability of the catalytic core. The negative effects on ribozyme folding, such as the destabilization of H2, the unfavorable sequences at the last base pair of H2 as well as the disruption of the continuity of H2 and H3, could be compensated for by elongating the H2 region of the corresponding mutants. The extension of H2 may alter the conformation of ribozyme molecules; in addition, it stabilized the catalytic core and enhanced the resistance to formamide. Finally, for a trans-acting ribozyme and its substrate that require the formation of H1, H2, and H4 to reconstitute the autocatalytic domain of HDV RNA, the extension of H2 stabilized the substrate/ribozyme complex and speeded up the cleavage rate but hindered the product release process.

Base Sequence↗
PubMedDate not supplied

Characteristics of a mesoporous silicate immobilized trypsin bioreactor in organic media.

Mesoporous silicates (MPS) materials are attractive materials for immobilizing proteins/enzymes because of their well ordered structures, large surface areas (up to 1000 m(2) g(-1)), narrow pore size distributions, large pore diameters, and pore volumes. MPS with average pore diameters ranging from 28 to 300 Angstroms were prepared using cationic and nonionic surfactants. The influence of water content, pH, storage, and thermal treatment on the activity of trypsin immobilized onto MPS was investigated. In a range of solvents, the amidolytic activity of immobilized trypsin was higher than that of the lyophilized preparation. Significant increases in k(cat)/K(M) occurred in propanol, ethanol, methanol, and formamide of 90, 62, 45 and 26, respectively. The observed increases were primarily a result of substantial increases in k(cat).

Alcohols↗
PubMed2005

Vacuum ultraviolet (VUV) photodecomposition of urea isolated in cryogenic matrix: first detection of isourea.

Vacuum ultraviolet (VUV) irradiation at wavelengths of lambda > 160 nm of urea-h4 (NH2CONH2) and urea-d4 (ND2COND2) has been monitored by Fourier transform infrared spectroscopy in argon and xenon matrixes. Several primary photoproducts, such as HNCO:NH3 (isocyanic acid:ammonia), CO:N2H4 (carbon monoxide:hydrazine) molecular complexes, and isourea (H2N(OH)C=NH), which is reported for the first time, were characterized. The assignment of complexes was achieved by co-depositing the pairs of respective species, whereas the isourea identification was based on the comparison between the experimental and theoretical (B3LYP) infrared spectra. Isourea is found in the argon matrix in its most stable (s-Z)-(E) configuration. It is an intermediate in the VUV decomposition process; its dehydration leads to the NH2CN:H2O complex. In the xenon matrix, the photochemistry of urea yields the HNCO:NH3 complex as a major product, whereas the CO:N2H4 complex is observed in trace amounts. The observed differences between the argon and xenon matrixes suggest the crossing between S1 and T1 potential surfaces of urea to be responsible for the formation of the HNCO:NH3 complex. A comparison is also performed with other carboxamides, such as formamide (HCONH2) or acetamide (CH3CONH2).

Acetamides↗
PubMed2005

Solvation properties of N-substituted cis and trans amides are not identical: significant enthalpy and entropy changes are revealed by the use of variable temperature 1H NMR in aqueous and chloroform solutions and ab initio calculations.

The cis/trans conformational equilibrium of N-methyl formamide (NMF) and the sterically hindered tert-butylformamide (TBF) was investigated by the use of variable temperature gradient 1H NMR in aqueous solution and in the low dielectric constant and solvation ability solvent CDCl3 and various levels of first principles calculations. The trans isomer of NMF in aqueous solution is enthalpically favored relative to the cis (deltaH(o) = -5.79 +/- 0.18 kJ mol(-1)) with entropy differences at 298 K (298 x deltaS(o) = -0.23 +/- 0.17 kJ mol(-1)) playing a minor role. The experimental value of the enthalpy difference strongly decreases (deltaH(o) = -1.72 +/- 0.06 kJ mol(-1)), and the contribution of entropy at 298 K (298 x deltaS(o) = -1.87 +/- 0.06 kJ mol(-1)) increases in the case of the sterically hindered tert-butylformamide. The trans isomer of NMF in CDCl3 solution is enthalpically favored relative to the cis (deltaH(o) = -3.71 +/- 0.17 kJ mol(-1)) with entropy differences at 298 K (298 x deltaS(o) = 1.02 +/- 0.19 kJ mol(-1)) playing a minor role. In the sterically hindered tert-butylformamide, the trans isomer is enthalpically disfavored (deltaH(o) = 1.60 +/- 0.09 kJ mol(-1)) but is entropically favored (298 x deltaS(o) = 1.71 +/- 0.10 kJ mol(-1)). The results are compared with literature data of model peptides. It is concluded that, in amide bonds at 298 K and in the absence of strongly stabilizing sequence-specific inter-residue interactions involving side chains, the free energy difference of the cis/trans isomers and both the enthalpy and entropy contributions are strongly dependent on the N-alkyl substitution and the solvent. The significant decreasing enthalpic benefit of the trans isomer in CDCl3 compared to that in H2O, in the case of NMF and TBF, is partially offset by an adverse entropy contribution. This is in agreement with the general phenomenon of enthalpy versus entropy compensation. B3LY/6-311++G** and MP2/6-311++G** quantum chemical calculations confirm the stability orders of isomers and the deltaG decrease in going from water to CHCl3 as solvent. However, the absolute calculated values, especially for TBF, deviate significantly from the experimental values. Consideration of the solvent effects via the PCM approach on NMF x H2O and TBF x H2O supermolecules improves the agreement with the experimental results for TBF isomers, but not for NMF.

Algorithms↗
PubMed2006

Effects of hydrogen bonding on the ring stretching modes of pyridine.

The effects of hydrogen bonding on the ring stretching modes (both ring breathing and triangle) of pyridine are experimentally investigated using noisy light based coherent Raman scattering spectroscopy. Three systems, pyridine/formamide, pyridine/water, and pyridine/acetic acid, provide varying degrees of strength for the diluent-pyridine hydrogen bond complex. Formamide forms a relatively weaker hydrogen bond, while acetic acid essentially fully transfers a proton to pyridine. Both dilution studies and temperature studies are performed on the three systems. Together, these provide a broad context in which a very simple model for the electronic behavior of pyridine is formulated. This model is based on a molecular orbital picture and electrostatic arguments, and it well explains the observed experimental results. Additionally, a new mechanism for the line broadening of the ring breathing mode for the pyridine-water hydrogen bonded complex is proposed.

Acetic Acid↗
PubMedDate not supplied

N-alkylformamides are metabolized to N-alkylcarbamoylating species by hepatic microsomes from rodents and humans.

Hepatotoxic formamides such as N-methylformamide (NMF) and N,N-dimethylformamide (DMF) are metabolized in vivo to N-acetyl-S-(N-methylcarbamoyl)cysteine via oxidation at the formyl carbon, which yields a reactive intermediate. The hypothesis was tested that this biotransformation route can be studied in vitro with hepatic fractions. NMF was incubated with microsomes or cytosol obtained from BALB/c mice, and metabolically generated N-methyl-carbamoylating species were analyzed after derivatization with ethanol in base to furnish ethyl N-methylcarbamate. Generation of metabolite was catalyzed by microsomes, but not by cytosol. Detection of the N-methylcarbamoylating species was dependent on the presence in the incubation mixture of NMF, viable microsomes, NADPH, and a thiol-containing agent such as glutathione. Metabolite formation was inhibited by SKF 525-A (3 mM) and abolished when the incubation atmosphere consisted of an air/carbon monoxide mixture (1:1) instead of air. Metabolism was not induced by pretreatment of mice with phenobarbital or beta-naphthoflavone. N-Ethylformamide and the DMF metabolite N-(hydroxymethyl)-N-methylformamide, but not DMF, were metabolized by microsomes to the N-alkylcarbamoylating metabolite at a measurable rate. NMF metabolism was also observed with liver microsomes from Sprague-Dawley rats or from humans. In the case of rat microsomes the rate of metabolism was half of that measured with murine microsomes. The results suggest that (i) the metabolic toxification of NMF can be studied in hepatic microsomes and (ii) the oxidation of the formyl moiety in N-alkylformamides is catalyzed by cytochrome P-450.

Animals↗
PubMed2002

Synthesis of oligonucleotides and thermal stability of duplexes containing the beta-C-nucleoside analogue of Fapy*dG.

The formamidopyrimidine lesions (Fapy.dA, Fapy.dG) are formed in significant amounts when DNA is exposed to oxidative stress. These lesions are unusual in that they readily epimerize in solution. The distribution of configurational isomers in DNA is unknown. Nonepimerizable, nonhydrolyzable analogues are useful probes for investigating the configuration of Fapy lesions in DNA and as potential enzyme inhibitors. The beta-C-nucleoside of Fapy.dG has been prepared and introduced sight-specifically into oligonucleotides via its respective beta-cyanoethyl phosphoramidite. The phosphoramidite was prepared via a Wittig reaction between a protected form of deoxyribose and a suitably functionalized pyrimidine. The pyrimidine contained methyl and 2-propyl groups at the O4 and O2 positions, respectively, to differentiate between them following C-nucleoside formation. The formamide was derived from a nitro group at C5. The phosphoramidite coupled in 80% yield via a single 15-min coupling using tetrazole as activator. Oligonucleotides as long as 36 nucleotides were prepared and characterized by ESI-MS.

DNA Damage↗
PubMed1997

Specific induction of the hsr omega locus of Drosophila melanogaster by amides.

We report here that 3-aminobenzamide and other amides, such as formamide, acetamide and nicotinamide, specifically induce a high rate of transcription at the 93D puff (the hsr omega heat shock gene) in polytene chromosomes of Drosophila melanogaster. Other chemicals, such as benzamide, colchicine, thiamphenicol and paracetamol, that are already known to specifically induce transcription at the hsr omega locus are also identified as amides. In view of the specific induction of the 93D puff by different amides and other data that demonstrate hsr omega transcription in response to benzamide and colchicine etc. to be independent of its heat shock induction, it appears likely that amides induce this locus through distinct regulatory elements that we propose to designate amide response elements (AREs).

Acetamides↗
PubMed2005

Angle resolved ion scattering spectroscopy at surfaces of pure liquids: topography and orientation of molecules.

The topography of a liquid surface has not been the subject of experimental research because of a lack of experimental methods. The hereby outlined investigation shows how the topography of a liquid surface can be classified through the angular mode of neutral impact collision ion scattering spectroscopy. It further shows how concentration depth profiles with a high depth resolution are gained. These can be used as the basis to determine quantitatively the orientation of molecules. The substances investigated are the polar solvents formamide and benzyl alcohol.

Benzyl Alcohol↗
PubMed1972

Molecular hybridization of ribonucleic acid with a large excess of deoxyribonucleic acid.

When RNA is annealed in solution with a sufficiently large excess of DNA, the kinetics of DNA-RNA hybridization are relatively simple. Methods are described for following the course of both DNA renaturation and DNA-RNA hybridization in this system. To explore the characteristics of the reaction a series of model systems was used. Each one utilized DNA (sheared to constant size) from a bacterium or bacteriophage and homologous cRNA, i.e. RNA synthesized in vitro on a template of the same DNA. Temperature optima were determined for the hybridization of Escherichia coli nucleic acids in 2xSSC and 3xSSC-50% formamide buffers, and of Proteus mirabilis nucleic acids in 2xSSC buffer. Rate-constants for DNA-RNA hybridization were measured by two methods. These gave somewhat different results, but in all cases the rate-constant of DNA-RNA hybridization was clearly less than that of DNA renaturation. Thus hybridization is a slower reaction than DNA renaturation. Nevertheless, in some cases, with a high concentration of DNA and a long annealing time, 90-95% of the added RNA became resistant to ribonuclease. Experiments are described which show that it is possible to deduce the analytical complexity of DNA with reasonable accuracy from its hybridization with complementary RNA. Similarly, it is possible to estimate the reiteration frequency of multiple DNA sequences (such as ribosomal DNA) from the hybridization of the total DNA with RNA complementary to the multiple sequences. The effect on the system of various DNA/RNA ratios from 100 to 1 is described.

Coliphages↗
PubMed1974

Microbial metabolism of the pyridine ring. The metabolism of pyridine-3,4-diol (3,4-dihydroxypyridine) by Agrobacterium sp.

1. Pyridine-3,4-diol (3,4-dihydroxypyridine, 3-hydroxypyrid-4-one), an intermediate in 4-hydroxypyridine metabolism by an Agrobacterium sp (N.C.I.B. 10413), was converted by extracts into 1mol of pyruvate, 2mol of formate and 1mol of NH(3) at pH7.0. 2. Formate, but not the alternative likely product formamide, was further oxidized fivefold faster by 4-hydroxypyridine-grown washed cells than by similar organisms grown on succinate. 3. The oxidation of pyridine-3,4-diol by crude extracts at pH8.5 required 1mol of O(2)/mol of substrate, produced 1mol of acid and led to the formation of formate and a new compound with an extinction maximum of 285nm (Compound I). This step was believed to be mediated by a new labile dioxygenase (t((1/2))=4h at pH7.0, 4 degrees C) cleaving the pyridine ring between C-2 and C-3. 4. Many of the properties of this pyridine-3,4-diol dioxygenase paralleled those of the extradiol (;meta') oxygenases of aromatic-ring cleavage. The extreme lability of the enzyme has so far precluded extensive purification. 5. Compound I showed changes in the u.v.-absorption spectrum with pH but after acidification it was converted into a new product, 3-formylpyruvate, with an extinction maximum now at 279nm. 6. Both Compound I and 3-formylpyruvate were metabolized by extracts but at very different rates. The slower rate of metabolism of Compound I was nevertheless consistent with that of pyridine-3,4-diol metabolism. 7. On acidification Compound I released about 0.65mol of NH(3) and has been identified as 3-formiminopyruvate. 8. 3-Formylpyruvate was hydrolysed to formate and pyruvate (K(m) 2mum) by an acylpyruvate hydrolase active against several other dioxo homologues. The activity of this enzyme was much lower in extracts of succinate-grown cells.

Ammonia↗
PubMed2003

The nuclear actin-related protein Act3p/Arp4p of Saccharomyces cerevisiae is involved in transcription regulation of stress genes.

A mutational analysis of the essential nuclear actin-related protein of Saccharomyces cerevisiae, Act3p/Arp4p, was performed. The five residues chosen for substitution were amino acids conserved between actin and Act3p/Arp4p, the tertiary structure of which most probably resembles that of actin. Two thermosensitive (ts) mutants, a single and a double point mutant, and one lethal double point mutant were obtained. Both ts mutants were formamide-sensitive which supports a structural relatedness of Act3p/Arp4p to actin; they were also hypersensitive against hydroxyurea and ultraviolet irradiation pointing to a possible role of Act3p/Arp4p in DNA replication and repair. Their 'suppressor of Ty' (SPT) phenotype, observed with another ts mutant of Act3p/Arp4p before, suggested involvement of Act3p/Arp4p in transcription regulation. Accordingly, genome-wide expression profiling revealed misregulated transcription in a ts mutant of a number of genes, among which increased expression of various stress-responsive genes (many of them requiring Msn2p/Msn4p for induction) was the most salient result. This provides an explanation for the mutant's enhanced resistance to severe thermal and oxidative stress. Thus, Act3p/Arp4p takes an important part in the repression of stress-induced genes under non-stress conditions.

Actins↗
PubMed2002

Substrate-regulated cyanide hydratase (chy) gene expression in Fusarium solani: the potential of a transcription-based assay for monitoring the biotransformation of cyanide complexes.

The fungus Fusarium solani detoxifies cyanide through induction of the cyanide hydratase gene activity (chy) in the presence of either KCN or the metal-complexed cyanides, K2Ni(CN)4 or K4Fe(CN)6, at pH 7.0 and 4.0 respectively. Sequence analysis of the chy gene identified primers for reverse transcriptase-polymerase chain reaction (RT-PCR)-directed analysis of mRNA transcripts, which demonstrated that activity correlated to the substrate-specific induction of gene expression. chy transcription was initiated 30-60 min after exposure of F. solani cultures to cyanide complexes. Maximum expression was detected within 4.5 h, after which chy mRNA synthesis declined below the limits of detection within 26 h. A lag period of approximately 2 h, following initial transcription, was recorded before cyanide complexes were converted to formamide. mRNA transcripts of chy were not detected in the absence of cyanide or cyanide complexes. The presence of introns within the gene resulted in a difference in size of 100 bp for DNA compared with mRNA of the corresponding 5' region. This size difference facilitated PCR detection of gene and transcript respectively. Comparisons of the predicted amino acid sequence of the F. solani chy gene and those of Gloeocerospora sorghi, Fusarium lateritium and Leptosphaeria maculans demonstrate that cyanide hydratase genes are highly conserved and of a similar evolutionary origin. These data predict that the functional assay described here to monitor the induction of chy gene expression and, potentially, cyanide degradation would be applicable to a variety of polluted environments.

Amino Acid Sequence↗
PubMed2005

Intermolecular electrostatic energies using density fitting.

A method is presented to calculate the electron-electron and nuclear-electron intermolecular Coulomb interaction energy between two molecules by separately fitting the unperturbed molecular electron density of each monomer. This method is based on the variational Coulomb fitting method which relies on the expansion of the ab initio molecular electron density in site-centered auxiliary basis sets. By expanding the electron density of each monomer in this way the integral expressions for the intermolecular electrostatic calculations are simplified, lowering the operation count as well as the memory usage. Furthermore, this method allows the calculation of intermolecular Coulomb interactions with any level of theory from which a one-electron density matrix can be obtained. Our implementation is initially tested by calculating molecular properties with the density fitting method using three different auxiliary basis sets and comparing them to results obtained from ab initio calculations. These properties include dipoles for a series of molecules, as well as the molecular electrostatic potential and electric field for water. Subsequently, the intermolecular electrostatic energy is tested by calculating ten stationary points on the water dimer potential-energy surface. Results are presented for electron densities obtained at four different levels of theory using two different basis sets, fitted with three auxiliary basis sets. Additionally, a one-dimensional electrostatic energy surface scan is performed for four different systems (H2O dimer, Mg2+-H2O, Cu+-H2O, and n-methyl-formamide dimer). Our results show a very good agreement with ab initio calculations for all properties as well as interaction energies.

Computer Simulation↗
PubMed1971

Further characterization of the cellular DNA hybridizing with the RNA of Rous sarcoma virus.

Both 70S and 4S RNAs of Rous sarcoma virus (RSV) contain nucleotide sequences homologous to those in cellular DNA. Preparations of these RNAs were found to include some adventitious cellular sRNA. Nevertheless, both 70S and 4S RSV-RNAs were found by competition techniques to contain sequences distinct from those in cellular ribosomal RNA and 4S RNA. Competition experiments also reveal substantial homology between 70S and 4SRSV-RNA. In hybridization experiments performed in formamide at low temperatures, the melting profiles of hybrids between 70S RSV-RNA and cellular DNA, and 4S RSV-RNA and cellular DNA, are essentially superimposable. It is suggested that there are at least two origins of 4S RSV-RNA in RSV-RNA preparations: degradation of 70S RSV-RNA and inclusion of adventitious cellular 4S RNA. The possibility of a specific viral 4S RNA is not excluded.

Avian Sarcoma Viruses↗
PubMed1972

RNA-linked nascent DNA fragments in Escherichia coli.

Nucleic acid that is extracted from E. coli labeled by a brief pulse of [(3)H]dT and depatured by treatment with heat, formamide, or formaldehyde bands in a region with a density higher than that of single-stranded E. coli DNA in a Cs(2)SO(4) equilibrium density gradient. If treated with alkali or RNase, it then exhibits the density of single-stranded DNA. These results suggest the presence of a short strand of RNA covalently linked to the nascent DNA. Evidence for the presence of covalently linked RNA-DNA molecules is also obtained by pulse labeling with [(3)H]U. Analyses of nascent nucleic acids from cells pulse labeled for various times, and of the molecules with different sizes, support the hypothesis that the short DNA fragments are formed by extension of even shorter RNA chains, which are synthesized on the parental DNA strands and are removed before ligation of the DNA fragments. The synthesis of the RNA segment of the RNA-DNA molecule is much less sensitive to rifampicin than is the synthesis of bulk RNA.

Carbon Isotopes↗