Structural effect of synthetic zwitterionic cosolutes on the stability of DNA duplexes

The molecular design of useful cosolutes for polymerase chain reaction (PCR), which is one of the most important techniques in molecular biology, plays a significant role in amplification of highly stable genome sequences because during PCR, strand dissociation sometimes fails due to high melting temperature. Here, we designed and synthesized eight new zwitterionic cosolutes derived from glycine betaine, a destabilizing reagent for GC-rich DNA duplexes, and systematically compared their ability to destabilize DNA duplexes and to amplify genome DNA by PCR. We found that introduction of n-butyl groups rather than methyl groups into the ammonium group reduced the melting temperature of DNA duplexes 11-fold more than what was observed for the scaffold cosolute, glycine betaine, and furthermore, the cosolute can amplify the stable genome sequence by PCR.     

Creation of a thermostable firefly luciferase with pH-insensitive luminescent color

The thermal instability and pH-sensitive spectral property of firefly luciferase have hampered its use as a sensitive multicolor luminescent label or bioluminescent resonance energy transfer donor. With the intention of improving the thermostability of a previously found firefly Hotaria parvula luciferase mutant with minor pH-sensitive spectral change (V368A), further mutation (E356R) was introduced by taking a reportedly stabilized mutant of Photinus pyralis luciferase into account. The double mutant E356R/V368A showed significantly improved thermostability because > 90% activity remained after incubation for 1 h at 45 degrees C, with its specific activity being maintained. Unlike the wild type or V368A, E356R/V368A showed no change in the emission maximum of 568 nm even at pH 6.3, also implying a mutual relationship between thermostability and the proportion of yellow-green luminescent peak under acidic condition.     

Formation of the main gas compounds during thermal analysis and pyrolysis: Betaine and betaine monohydrate

The thermochemical behaviour of betaine and betaine monohydrate was investigated under two degradation conditions. Betaine was heated up to 700°C at 10°C min^–1 in air and nitrogen flows and the evolved gas was analysed with the combined TG-FTRIR system. The evolved gas from betaine pyrolysis at 350 and 400°C was analysed by gas chromatography using mass-selective detection (Py-GC/MSD). In addition, the electron impact mass spectra of betaine and betaine monohydrate were measured.Esterification is one of the most important pyrolytic processes involving beta- ines. Even glycine betaine can change to dimethylglycine methyl ester via intermolecular transalkylation by heating. Trimethylamine, CO₂, and glycine esters were the main degradation products. Small amounts of ester type compounds evolved both in pyrolysis and with TG-FTIR. The monohydrate lost water between 35 and 260°C while the main decomposition took place at 245-360°C. The residual carbon burnt in air to CO₂ up to a temperature 570°C.This revised version was published online in November 2005 with corrections to the Cover Date.     

Effects of Sucrose and Trehalose on Stability,Kinetic Properties,and Thermal Aggregation of Firefly Luciferase

In this study, we used sugars as stabilizing additives to improve the thermostability and to inhibit aggregation of firefly luciferase. The combination of sucrose and trehalose has a strong stabilizing effect on firefly luciferase activity and prevents its thermoinactivation. These additives can also increase optimum temperature. It has been shown that the presence of both sucrose and trehalose can inhibit thermal aggregation of firefly luciferase and decrease bioluminescence decay rate. In order to understand the molecular mechanism of thermostabilization, we investigated the effects of sucrose and trehalose combination on the secondary structure of luciferase by Fourier transform infrared spectroscopy. Minor changes in content of secondary structure of firefly luciferase are observed upon treatment with additives.     

Luciferin‐Regenerating Enzyme Crystal Structure Is Solved but its Function Is Still Unclear

Contribution of luciferin‐regenerating enzyme (LRE) for in vitro recycling of D‐luciferin has been reported. According to crystal structure of LRE, it is a beta‐propeller protein which is a type of all β‐protein architecture. In this overview, reinvestigation of the luciferase‐based LRE assays and its function is reported. Until now, sequence of LRE genes from four different species of firefly has been reported. In spite of previous reports, T‐LRE (from Lampyris turkestanicus) was cloned and expressed in Escherichia coli as well as Pichia pastoris in a nonsoluble form as inclusion body. According to recent investigations, bioluminescent signal of soluble T‐LRE–luciferase‐coupled assay increased and then reached an equilibrium state in the presence of D‐cysteine. In addition, the results revealed that both D‐ and L‐cysteine in the absence of T‐LRE caused a significant increase in bioluminescence intensity of luciferase over a long time. Based on activity measurements and spectroscopic results, D‐cysteine increased the activity of luciferase due to its redox potential and induction of conformational changes in structure and kinetics properties. In conclusion, in spite of previous reports on the effect of LRE (at least T‐LRE) on luciferase activity, most of the increase in luciferase activity is caused by direct effect of D‐cysteine on structure and activity of firefly luciferase. Moreover, bioinformatics analysis cannot support the presence of LRE in peroxisome of photocytes in firefly lanterns.     

Driving in vitro selection of anti-HIV-1 TAR aptamers by magnesium concentration and temperature

In vitro selection with either DNA or RNA libraries was performed against the TAR RNA element of HIV-1. The role of the selection conditions on the outcome of the selection was evaluated by varying the magnesium concentration and the temperature. The selection stringency was demonstrated to determine i) the affinity of the best identified aptamers for the TAR target, and ii) the type of interaction between the two partners. Selections performed with a DNA library under low (4 degrees C, 10 mM magnesium) and high stringency (23 degrees C, 3 mM magnesium) led to the emergence of "kissing aptamers"; but even if the motif interacting directly with the TAR loop were identical in the two kinds of aptamers, the consensus was extended from eight to thirteen nucleotides when the Mg(2+) concentration was decreased from 10 to 3 mM. Similar kissing aptamers were selected at 23 degrees C and 37 degrees C starting with two different RNA libraries under identical ionic conditions. In addition, selection performed at 37 degrees C yielded a significant proportion of antisense sequences. Only antisense RNAs complementary to the TAR loop competitively inhibited the association of a Tat peptide with TAR.     

Sequence-specific gene silencing in mammalian cells by alkylating pyrrole-imidazole polyamides

Gene silencing was examined by sequence-specific alkylation of DNA by N-methylpyrrole (Py)-N-methylimidazole (Im) hairpin polyamides. Polyamides ImImPyPygammaImImPyLDu86 (A) and ImImPyPygammaImPyPyLDu86 (B) selectively alkylated the coding regions of the renilla and firefly luciferases, respectively, according to the base pair recognition rule of Py-Im polyamides. Two different plasmids, encoding renilla luciferase and firefly luciferase, were used as vectors to examine the effect of alkylation on gene silencing. Transfection of the alkylated luciferase vectors-by polyamide A or B-into HeLa, 293, and NIH3T3 cells demonstrated that these sequence-specific DNA alkylations lead to selective silencing of gene expression. Next, the vectors were cotransfected into HeLa cells and the cells were treated with polyamide A or B. Selective reduction of luciferase activities was caused by both polyamides. On the basis of this sequence-specific alkylation and gene silencing activity, these alkylating Py-Im polyamides thus have potential as antitumor drugs to target specific gene expression in human cells.     

Binding of adenosine to pendant phenylboronate groups of thermoresponsive copolymer: a quantitative study

Binding of adenosine to the thermosensitive copolymer of N-isopropylacrylamide and 3-(acrylamido)aminophenylboronic acid (82:18, Mn = 47,000 g . mol(-1)) was studied by equilibrium dialysis at 22 degrees C and 37 degrees C, in a 0.1 M glycine buffer containing 0.1 M NaCl at pH 9.2. The copolymer exhibited a the phase transition temperature (T(p)) of 26.5 degrees C under the above conditions. At 22 degrees C the binding of adenosine to the water-soluble copolymer was well described by a Langmuir model, accounting for preferential ionisation of the boronate-nucleoside complexes and, therefore, restricted reactivity of the rest of boronates. At saturation, the copolymer contained 38% of its phenylboronic acid groups in the form of complexes, whereas the association constant was 1,400 M(-1). At 37 degrees C no binding of adenosine to thermally precipitated copolymer was found, presumably owing to interaction of the phenylboronates with hydrophobic segments of polyNIPAM. At high loading of the copolymer by the reversibly bound adenosine the T(p) steeply increases with increasing fraction of the phenylboronate-adenosine complexes in the chains. The increase of the T(p) observed above the saturating adenosine concentration (>1 x 10(-3) M, 22 degrees C) very probably testifies to competition of the nucleoside with hydrophobic polyNIPAM segments for binding to the pendant phenylboronates.     

A new firefly luciferase with bimodal spectrum: identification of structural determinants of spectral pH-sensitivity in firefly luciferases

Fireflies emit flashes in the green-yellow region of the spectrum for the purpose of sexual attraction. The bioluminescence color is determined by the luciferases. It is well known that the in vitro bioluminescence color of firefly luciferases can be shifted toward the red by lower pH and higher temperature; for this reason they are classified as pH-sensitive luciferases. However, the mechanism and structural origin of pH sensitivity in fireflies remains unknown. Here we report the cloning of a new luciferase from the Brazilian twilight active firefly Macrolampis sp2, which displays an unusual bimodal spectrum. The recombinant luciferase displays a sensitive spectrum with the peak at 569 nm and a shoulder in the red region. Comparison of the bioluminescence spectra of Macrolampis, Photinus and Cratomorphus firefly luciferases shows that the distinct colors are determined by the ratio between green and red emitters under luciferase influence. Comparison of Macrolampis luciferase with the highly similar North American Photinus pyralis luciferase (91%) showed few substitutions potentially involved with the higher spectral sensitivity in Macrolampis luciferase. Site-directed mutagenesis showed that the natural substitution E354N determines the appearance of the shoulder in the red region of Macrolampis luciferase bioluminescence spectrum, helping to identify important interactions and residues involved in the pH-sensing mechanism in firefly luciferases.     

Luciferins, bioluminescent substances

The bioluminescence of the American firefly Photinus is due to the reaction of 2-(6-hydroxybenzothiazol-2-yl)-Δ²-1,3-thiazoline-4-carboxylic acid (“firefly luciferin”) with the enzyme luciferase in the presence of ATP and magnesium ion. In the crustacean Cypridina, on the other hand, the bioluminescence is due to the reaction of a luciferase with 8-(3-guanidinopropyl)-6-indol-3-yl-2-(1-methylpropyl)-3,7-dihydroimidazo[1,2-a]-pyrazin-3-one (“Cypridina luciferin”). The luciferin in Latia is 1,3,3-trimethyl-2-(4-formyloxy-3-methyl-3-butenyl)-1-cyclohexene and that in Renilla is a tryptamine derivative that has not yet been accurately identified; the luciferins of other luminescent organisms are not yet known. A review is given of the investigations which have been carried out on the above luciferins and the course of the luciferin-luciferase reaction is examined. Numerous spectral data obtained during the examination of these compounds are included in the text.     

Dynamic viscoelastic properties of spread monostearin monolayer in the presence of glycine

The monostearin monolayer at the air-aqueous interface is more expanded in presence of glycine and at higher temperature from both the surface pressure-area per molecule (pi-A) isotherms and static elasticity-surface pressure (E(s)-pi) curves. The dilational viscoelastic properties of monostearin monolayer spread on the subphase of glycine solution have been determined by the dynamic oscillation method and discussed as a function of surface pressure, temperature, and frequency. At the frequency of 50 mHz, the monostearin monolayer on pure water shows negative dilational viscosity and is viscoelastic at some surface pressures, while the monostearin monolayer in the presence of glycine is nearly elastic over a wide range of surface pressure, especially at 25 degrees C. Both positive and negative loss angle tangent can be deduced as a function of surface pressure. The negative dilational viscosity can be attributed to the phase transitions induced by the propagation of the surface waves during the dynamic oscillation. It can be convinced that the interactions between monostearin and glycine play an important role in the formation and rheological behavior of the monolayer. On the other hand, temperature has effect on the dilational elasticity and the dilational viscosity of the monostearin monolayer in different extents. Furthermore, at the surface pressure of 20 mN/m, the monostearin monolayer on the glycine solution at 18 degrees C is essentially elastic at lower frequency (<100 MHz) and shows viscoelastic behavior at higher frequency. These phenomena should be associated with the complicated monolayer structure and structural reorganization due to the interactions between monostearin and glycine in presence of glycine.     

EFFECT OF GROWTH TEMPERATURE ON LIPID COMPOSITION and ULTRAVIOLET SENSITIVITY OF HUMAN CELLS

Human skin fibroblasts were incubated at either 25 or 37 degrees C before UV irradiation. Cells incubated at 25 degrees C were more resistant to near UV radiation than cells grown at 37 degrees C, but cells grown at the lower temperature were more sensitive to 254 nm radiation. Fatty acid analysis of membranes of cells showed that cells incubated at the lower temperature contained significantly higher amounts of linoleic acid (18:2) and linolenic acid (18:3) than cells incubated at 37 degrees C. To determine if this difference in fatty acid content of the membranes was responsible for the UV survival characteristics of cells incubated at different temperatures, cells were enriched with either linoleate or linolenate during a 37 degrees C incubation period. Gas chromatography revealed that cells incorporated the supplied fatty acid. Fatty acid enriched cells were then irradiated with near UV, and survival characteristics were compared to those obtained with cells grown at the lower incubation temperature. The results suggest that the different proportion of fatty acid content of the cells is not the cause of different UV sensitivities of cells grown at 25 degrees C compared to cells grown at 37 degrees C.     

Biodegradable microspheres containing poly(epsilon-caprolactone)-Pluronic block copolymers for temperature-responsive release of proteins

Temperature-responsive microspheres were fabricated for the purpose of releasing protein in responsive to surrounding temperature changes. Temperature-responsive polymer, Pluronic was synthesized into block copolymers of poly(epsilon-caprolactone)-Pluronic with two different chain lengths of poly(epsilon-caprolactone). Microspheres loaded with proteins were prepared by a W/O/W emulsion method. The surface morphology was examined by scanning electron microscopy, showing that microspheres with diblock copolymers had porous structures due to hydrophilicity of Pluronic blocks. After incubating the microsphere at 37 degrees C for 7 days, temperature-responsive protein release was monitored with alternating temperature changes between 20 and 37 degrees C. The protein release was attenuated when the microsphere was incubated at 20 degrees C but the release rate was recovered at 37 degrees C, confirming variable release rate according to the temperature changes. The variable release rate of protein was dependent on the length of poly(epsilon-caprolactone) blocks attached to Pluronic.     

Temperature selectivity effects in reversed-phase liquid chromatography due to conformation differences between helical and non-helical peptides

In order to characterize the effect of temperature on the retention behaviour and selectivity of separation of polypeptides and proteins in reversed-phase high-performance liquid chromatography (RP-HPLC), the chromatographic properties of four series of peptides, with different peptide conformations, have been studied as a function of temperature (5-80 degrees C). The secondary structure of model peptides was based on either the amphipathic alpha-helical peptide sequence Ac-EAEKAAKEX(D/L)EKAAKEAEK-amide, (position X being in the centre of the hydrophobic face of the alpha-helix), or the random coil peptide sequence Ac-X(D/L)LGAKGAGVG-amide, where position X is substituted by the 19 L- or D-amino acids and glycine. We have shown that the helical peptide analogues exhibited a greater effect of varying temperature on elution behaviour compared to the random coil peptide analogues, due to the unfolding of alpha-helical structure with the increase of temperature during RP-HPLC. In addition, temperature generally produced different effects on the separations of peptides with different L- or D-amino acid substitutions within the groups of helical or non-helical peptides. The results demonstrate that variations in temperature can be used to effect significant changes in selectivity among the peptide analogues despite their very high degree of sequence homology. Our results also suggest that a temperature-based approach to RP-HPLC can be used to distinguish varying amino acid substitutions at the same site of the peptide sequence. We believe that the peptide mixtures presented here provide a good model for studying temperature effects on selectivity due to conformational differences of peptides, both for the rational development of peptide separation optimization protocols and a probe to distinguish between peptide conformations.     

Firefly Luciferase‐based Fusion Proteins and their Applications in Bioanalysis

Firefly luciferase is widely used in molecular biology and bioanalytical systems as a reporter molecule due to the high quantum yield of the bioluminescence, availability of stable mutant forms of the enzyme with prescribed spectral characteristics and abundance of bacterial expression systems suitable for production of recombinant proteins in limitless quantities. In this review, we described fusion proteins of luciferase with biotin‐binding domain and streptavidin, with proteins A and G, antibodies, with DNA‐ and RNA‐binding proteins, as well as fusion proteins designed for BRET systems. The firefly luciferase‐based fusion proteins are represented as an effective tool for the development of different bioanalytical systems such as (1) systems in which luciferase is attached to the surface of the target and the bioluminescence signal is detected from the specific complexes formed; (2) BRET‐based systems, in which the specific interaction induces changes in the bioluminescence spectrum; and (3) systems that use modified or split luciferases, in which the luciferase activity changes under the action of the analyte. All these systems have wide application in biochemical analysis of physiologically important compounds, for the detection of pathogenic bacteria and viruses, for evaluation of protein–protein interactions, assaying of metabolites involved in cell communication and cell signaling.     

New poly(d-glucaramidoamine)s induce DNA nanoparticle formation and efficient gene delivery into mammalian cells

In this report, four new poly(d-glucaramidoamine)s (1-4) have been designed to lower the toxicity of conventional polymeric nucleic acid delivery vehicles by incorporating a carbohydrate comonomer within a polyethylenimine (PEI)-like backbone. Polymers 1-4 were synthesized via polycondensation of esterified d-glucaric acid and four different amine-containing comonomers [diethylenetriamine (1), triethylenetetramine (2), tetraethylenepentamine (3), and pentaethylenehexamine (4)] in methanol. Viscometry and NMR studies suggest that the polymers are mostly linear (for 1-4, the alpha value in the Mark-Houwink-Sakurada equation = 0.6-0.7), thus indicating that polymerization occurs predominantly through the primary amines with a low degree of branching off the secondary amines. Results of gel electrophoresis shift assays show that polymers 1-4 bind pDNA at N/P ratios of 5, 3, 2, and 2, respectively. Also, dynamic light scattering and TEM experiments indicate that 1-4 compact DNA into nanoparticles (polyplexes) between 140 and 440 nm at an N/P ratio of 30. Furthermore, polyplexes formed with 1-4 deliver pDNA (plasmid DNA) containing the firefly luciferase reporter gene to BHK-21 cells in a nontoxic and highly efficient manner (as determined by luciferase gene expression). In particular, polymer 4 reveals very high delivery efficiency (equivalent to linear PEI). This result may be due in part to the "proton sponge" hypothesis proposed by Behr et al. Polymers containing amines that are protonated in the endosomal pH range (between about 7.4-5.0) reveal enhanced gene delivery profiles.     

Partial Molar Volume,Ionization, Viscosity and Structure of Glycine Betaine in Aqueous Solutions

Densities, partial molar volumes, and viscosities of aqueous solutions of betaine have been measured at 5, 10, 15, 20, 25, 30, 37, and 45 °C over the concentration range 0.05 to 5.0 mol⋅L⁻¹. The partial molar volumes show that betaine exists partly as a monohydrate and partly in its anhydrous form. The proportion of the anhydrous form increases with increasing temperature. Also, an associated form of betaine appears in concentrated betaine solutions, possibly with water as a bridging group. The significance of the viscosity B-coefficient is discussed. The signs of B _st, the increment of the viscosity B-coefficients arising from structural changes of water, are negative and the signs of dB/dT, the temperature derivative of B, are positive. These results show that betaine is a water structure breaker especially at lower temperatures, and this effect decreases to insignificance at higher temperatures. The ionization equilibria of betaine were investigated in aqueous 0.5 mol⋅L⁻¹ and 1.0 mol⋅L⁻¹ NaNO₃ at 5, 15, 25, and 37 °C by a potentiometric method. Using the least-square computer program SUPERQUAD, the complex forms are deduced to be betanium BH, bis(betanium) BHB, and bis(betaine) B₂ or bis(betaine)hydrate BH₂OB.