应用分子梳技术对DNA与组蛋白相互作用的研究

利用分子梳技术对λ DNA和组蛋白的相互作用进行了研究. 通过这种简单有效的方法，我们将λ DNA分子拉伸到26—28 μm，相当于其原长（约162 μm）的16—17倍. 当组蛋白与DNA结合后，DNA分子发生凝聚现象，复合体的拉伸长度明显变短，其峰值分布在10—14 μm之间. DNA 组蛋白复合体的拉伸长度与组蛋白的浓度、与碱基对和荧光染料的比例有显著的关系. 关键词： 分子梳 组蛋白 DNA 荧光显微     

Interaction of quercetin with ovalbumin: Spectroscopic and molecular modeling studies

The binding of quercetin (QCT) to ovalbumin (OVA) in aqueous solution was investigated by molecular spectroscopy and modeling at pH 7.4. The fluorescence, synchronous fluorescence and UV-absorption spectroscopies were employed to study the mode and the mechanism for this interaction. QCT binding is characterized by one high affinity binding site with the association constants of the order of 10⁵. The distance between donor (OVA) and acceptor (QCT) was estimated according to Forster's theory of non-radiation energy transfer. Molecular docking showed that the QCT can bind to the active site of OVA. The binding dynamics was expounded by thermodynamic parameters, molecular modeling and accessible surface area calculation, which entails that hydrophobic interactions, hydrogen bonding and electrostatic forces stabilizes the interaction.     

Chemical kinetic interactions of NO with a multi-component gasoline surrogate: Experiments and modeling

This work reports an experimental and modeling study on the chemical kinetic interactions of NO with a multi-component gasoline surrogate, namely PACE-20, using a twin-piston rapid compression machine at a stochiometric fuel loading with 20% EGR (exhaust gas recirculation) by mass, pressures of 20 and 40 bar, and temperatures from 700 to 930 K. Five NO concentrations are investigated, namely 0, 20, 50, 70 and 150 ppm, where NO addition effects are characterized through changes in PACE-20 ignition reactivity and heat release characteristics. Experiments indicate that within the low-temperature regime, NO promotes low-temperature heat release rate and main ignition reactivity at low addition levels, with saturation or even inhibiting effects observed at >50 ppm NO addition, while within the NTC/intermediate-temperature regime, adding NO only promotes reactivity. A recently updated, detailed chemical kinetic model with chemistry specific to NOx/hydrocarbons interaction incorporated is used to simulate the experiments, and reasonable agreement is obtained. In-depth sensitivity and rate of production analyses are further performed. The results indicate that NO interacts with PACE-20 via two types of interaction: (a) direct interactions between NO and PACE-20 derivatives, primarily through NO+HO₂↔NO₂+OH and RO₂+NO↔RO+NO₂, and (b) indirect interactions between PACE-20 derivatives and NO₂ produced from the direct interactions, primarily through R+NO₂↔RO+NO. The observed NO inhibiting effect at low temperatures and 150 ppm NO addition is attributed to the lack of HO₂ radicals to sustain NO consumption via NO+HO₂↔NO₂+OH, and the take-up of inhibiting pathways via RO₂+NO↔RO+NO₂. The results also indicate that even with the presence of multiple fuel components, NOx/hydrocarbons interactions are highly selective, and are mainly initiated by the interactions between NO and RO₂ radicals from cyclopentane and ethanol, as well as between NO₂ and R radicals from toluene, 1,2,4-trimethylbenzene and 1-hexene. Further studies on these interactive reactions are therefore highly recommended.     

Identification and molecular modeling of new quinolin-2-one thiosemicarbazide scaffold with antimicrobial urease inhibitory activity

Molecular Diversity - A new series of 6-substituted quinolin-2-one thiosemicarbazides 6a–j has been synthesized. The structure of the target compounds was proved by different spectroscopic...     

Ultrasonic and infrared study of molecular interactions in ternary mixtures of 1-naphthol and 2-naphthol with 2-propanone in benzene

The measurements of ultrasonic velocity and density were made for the ternary mixtures of l-naphthol/2-naphthol with 2-propanone in benzene at 20, 30 and 40°C in the mole fraction range of 0.00 to 0.05. Adiabatic compressibility and intermolecular free length have been evaluated using ultrasonic velocity data. The non-linear variation of ultrasonic velocity and allied parameters with mole fraction indicates solute-solute interactions through hydrogen bonding between unlike molecules. Results of ultrasonic velocity and density measurements are further supported by FT-IR spectra. The change in transmittance as well as the shift in the frequency of the representative peak of the OH stretching in FT-IR spectra give inferences about the complex formation.     

Study of molecular antimony: Sb4 and Sb2 in solid neon

Electronic absorption and laser-induced fluorescence spectra of Sb₂ in solid Ne matrix are observed and examined. The Raman spectrum of Sb₄ is also recorded and two of its three ground state vibrational fundamental vibrations are determined.     

Study of interaction of butyl p-hydroxybenzoate with human serum albumin by molecular modeling and multi-spectroscopic method

Study of the interaction between butyl p-hydroxybenzoate (butoben) and human serum albumin (HSA) has been performed by molecular modeling and multi-spectroscopic method. The interaction mechanism was predicted through molecular modeling first, then the binding parameters were confirmed using a series of spectroscopic methods, including fluorescence spectroscopy, UV-visible absorbance spectroscopy, circular dichroism (CD) spectroscopy and Fourier transform infrared (FT-IR) spectroscopy. The thermodynamic parameters of the reaction, standard enthalpy ΔH⁰ and entropy ΔS⁰, have been calculated to be −29.52 kJ mol⁻¹ and −24.23 J mol⁻¹ K⁻¹, respectively, according to the Van’t Hoff equation, which suggests the van der Waals force and hydrogen bonds are the predominant intermolecular forces in stabilizing the butoben-HSA complex. Results obtained by spectroscopic methods are consistent with that of the molecular modeling study. In addition, alteration of secondary structure of HSA in the presence of butoben was evaluated using the data obtained from UV-visible absorbance, CD and FT-IR spectroscopies.     

Microwave l-type resonance transitions of the v4 = 1 state in PF3: Detailed interactions and molecular structure

Observation of the direct l-type resonance transitions in the microwave spectrum of the v₄ = 1 state of PF₃ has been extended to J = 36. The w-type interaction, (Δl = 0, ΔK = 6), has been found from measurements on the “forbidden” Stark trasitions in the $\text{K}\text{= 3}$ series. Also in this series a close accidental degeneracy was found between J = 30, $\text{K}\text{= 3}$ and 0, leading to new zero-field “forbidden” transitions through the r-type interaction (Δl = 2, ΔK = ?1) and to the determination of the C rotational constant. Nine spectroscopic parameters were determined using 140 observed frequencies including two “forbidden” trasitions. After suitable correction the B and C constants were used to determine the r₀, r_z, and r_e structures for PF₃. The equilibrium structure is estimated to be P-F = 1.561 ± 0.001 Å and ∠FPF = 97.7 ± 0.2°.     

Femtosecond laser interactions with dielectric materials: insights of a detailed modeling of electronic excitation and relaxation processes

Electronic excitation–relaxation processes induced by ultra-short laser pulses are studied numerically for dielectric targets. A detailed kinetic approach is used in the calculations accounting for the absence of equilibrium in the electronic subsystem. Such processes as electron–photon–phonon, electron–phonon and electron–electron scatterings are considered in the model. In addition, both laser field ionization ranging from multi-photon to tunneling one, and electron impact (avalanche) ionization processes are included in the model. The calculation results provide electron energy distribution. Based on the time-evolution of the energy distribution function, we estimate the electron thermalization time as a function of laser parameters. The effect of the density of conduction band electrons on this time is examined. By using the average electron energy, a new criterion is proposed based on determined damage threshold in agreement with recent experiments (Sanner et al. in Appl. Phys. Lett. 96:071111, 2010).     

Study of magnetic interactions of the Fe2+ ions and the protons of crystallization water in FeSO4.n H2O hydrates

The paper deals with a study of interactions of protons in crystallization water of paramagnetic hydrates FeSO₄.n H₂O (wheren=1, 4, 5 and 7). The interaction of protons and paramagnetic ions Fe²⁺ and the nuclear dipole-dipole interaction of protons have been studied by means of the parameters expressing the dependence of the second moment of the proton nuclear magnetic resonance (NMR) spectrum on the external magnetic field, by means of the volume magnetic susceptibilities and the relaxation timesT ₁ of the investigated series of hydrates.We are grateful to Prof. Dr. hab. Z.Pajak, director of Department of Radiospectroscopy IF UAM in Poznan, and to his coworkers Dr. J.Kapturczak, Dr. K.Jurga, Dr. S.Glowinkowski and Mgr. F.Brych for facilitating our measurements mentioned in the paper as well as for a valuable discussion.     

Interaction of human serum albumin with N-(4-ethoxyphenyl)-N′-(4-antipyrinyl) thiourea using spectroscopies and molecular modeling method

The interaction between N-(4-ethoxyphenyl)-N′-(4-antipyrinyl) thiourea (EPAT) and human serum albumin (HSA) was studied by fluorescence spectroscopy in combination with UV absorption spectroscopy. The intrinsic fluorescence of human serum albumin was quenched by EPAT through a static quenching procedure. The binding constants of EPAT with HSA were estimated according to the fluorescence quenching results at different temperatures. The binding distance was obtained and the binding force was suggested to be mainly hydrophobic force, which was in accordance with the study of molecular model. The effect of common ions on the binding constants was also investigated. A new fluorescence spectroscopy assay of the proteins is presented, and results were very satisfactory.     

Ultrasound-assisted surface treatment of ZrO2 with BSA and incorporating in PVC to improve the properties of the obtained nanocomposites: Fabrication and characterization

This paper describes the preparation of poly(vinyl chloride) (PVC) nanocomposites (NCs) reinforced with modified zirconia (ZrO₂) nanoparticles (NPs). The ZrO₂ NPs were defined as efficient filler for PVC NCs. For achieving the best dispersion and improvement of properties, the surface of ZrO₂ NPs was modified by Bovine Serum Albumin (BSA). Carboxylic acids and amines are important functional groups of BSA which handle the grafting BSA on the surface of ZrO₂ NPs. The PVC/ZrO₂-BSA NCs were fabricated by incorporation of various amounts of the ZrO₂-BSA NPs (3, 6 and 9 wt%) into PVC matrix. All the above processes were accomplished by ultrasonication as a green and environmentally-friendly method. Also, the magnetic and mechanical stirrer was used for the preparation of samples but the results are not suitable and the aggregation was observed which indicated the use of ultrasonic irradiation is the best method for the preparation of NC. The products were characterized by Fourier transform infrared spectroscopy, Transmission electron microscopy, Field emission scanning electron microscopy, X-ray diffraction, Thermogravimetric analysis, Ultraviolet–visible spectroscopy, photoluminescence spectroscopy, energy dispersive X-ray spectroscopy, wettability, and mechanical tests. The achieved PVC/ZrO₂-BSA NCs showed high thermal stability, good mechanical, optical and wettability properties compared to the pure PVC. In addition, among the obtained NCs, the PVC/ZrO₂-BSA NC 6 wt% showed the best improvement.     

Sono-photocatalytic degradation of 2-chlorophenol in water: kinetic and energetic comparison with other techniques.

The degradation of 2-chlorophenol in water was kinetically investigated using the following different techniques, employed either separately or simultaneously, always with the same experimental set-up: light irradiation (315-400 nm), sonication, photocatalysis with different types of TiO2, photocatalysis with sonication. The influence of the reaction volume and of different gas mixtures, containing Ar and O2, as well as O2/O3, was also investigated. Finally, an energetic comparison among these different techniques was performed, focused on an industrial application of some of them.     

Lithium/Silver-Doped Cu_2ZnSnS_4 with Tunable Band Gaps and Phase Structures: a First-Principles Study

Doping is an effective approach for improving the photovoltaic performance of Cu_2 ZnSnS_4(CZTS). The doping by substitution of Cu atoms in CZTS with Li and Ag atoms is investigated using density functional theory. The results show that the band gaps of Li_(2 x)Cu_(2(1-x))ZnSnS_4 and Ag_(2 x)Cu_(2(1-x))ZnSnS4 can be tuned in the ranges of 1.30-3.43 and 1.30-1.63 eV, respectively. The calculation also reveals a phase transition from kesterite to wurtzite-kesterite for Li_(2 x)Cu_(2(1-x))ZnSnS_4 as x is larger than 0.9. The tunable band gaps of Li_(2 x)Cu_(2(1-x))ZnSnS_4 and Ag_(2 x)Cu_(2(1-x)) ZnSnS_4 make them beneficial for achieving band-gap-graded solar cells.     

Comparisons of some molecular properties calculated with basis sets of Slater-type orbitals and floating spherical gaussian orbitals for BH3, BH4 -, B2H6, B4H4, C2H2, C2H4, C2H6, CH4, and C3H4

Some one-electron molecular properties are calculated for BH₃, BH₄ ^-, B₂H₆, B₄H₄, CH₄, C₂H₂, C₂H₄, C₂H₆, and C₃H₄. The wave functions used are constructed from minimal basis sets of STO's and FSGO's. The results obtained from the latter wave functions show that the good agreement with the STO values of the molecular energy is not always maintained with one-electron properties.     

Nondestructive room-temperature adsorption of 2,4,6-tri(2'-thienyl)-1,3,5-triazine on a Si-B interface: high-resolution STM imaging and molecular modeling

Organic nanostructures on semiconductors are currently investigated but the surfaces are known to interact strongly with molecules. To reduce the molecule-surface interaction, we used the Si(111)-B square root 3 x square root 3R30 degrees . Deposition of isolated 2,4,6-tri(2'-thienyl)-1,3,5-triazine, was achieved at room temperature without modification of their pi skeleton. This fascinating arrangement, observed by STM, has been validated by full density functional theory computations onto the entire system. The theoretical results give a clear explanation for the specific adsorption sites of molecules on the substrate.     

Phase transitions in a metal–organic coordination polymer: [Zn2(C8H4O4)2(C6H12N2)] with guest molecules. Thermal effects and molecular mobility

Thermal effects of a series of [Zn₂(C₈H₄O₄)₂(C₆H₁₂N₂)] porous compound with the guest molecules located in the pores were studied using differential scanning calorimetry combined with solid-state ¹H nuclear magnetic resonance spectroscopy. The intercalation of the molecules was shown to produce various thermal anomalies and phase transitions, which were characterized and analyzed.