Study of interactions between actinomycin D and oligonucleotides by microchip electrophoresis and ESI-MS

In the present study, the interactions between actinomycin D (ActD) and single stranded DNA (ssDNA) 5′-CGTAACCAACTGCAACGT-3′ and a duplex stranded DNA (dsDNA) with this sequence were investigated by microchip-based non-gel sieving electrophoresis and electrospray ionization mass spectrometry (ESI-MS). The ssDNA was designed according to the conserved regions of open reading frame 1b (replicase 1B) following the Tor 2 SARS genome sequence of 15611-15593. The binding constants of the interactions between ActD and ssDNA/dsDNA were (8.3 ± 0.32) × 10⁶ M⁻¹ (ssDNA) and (2.8 ± 0.02) × 10⁵ M⁻¹ (dsDNA), respectively, calculated from microchip electrophoresis via Scatchard plot. The binding stoichiometries were 1:1 (single/1ActD molecule) and 1:2 (duplex/2ActD molecules) calculated from microchip electrophoresis, and the results were further verified by ESI-MS. The results obtained by these two methods indicated that ActD bound much more tightly to ssDNA used in this work than dsDNA. Furthermore, this is shown that the microchip-based non-gel sieving electrophoresis method is a rapid, highly sensitive and convenient method for the studies of interactions between DNA and small molecule drugs.     

The apparent molar heat capacities and volumes of aqueous NaCl from 0.01 to 3 mol kg−1 in the temperature range 274.65 to 318.15 K

The heat capacities per unit volume of aqueous solutions of NaCl were measured with a flow microcalorimeter. The molality and temperature range covered were 0.01 to 3 mol kg^?1 and 274.65 to 318.15 K. The derived apparent molar heat capacities C₂, φ, when extrapolated to infinite dilution, give standard partial molar heat capacities C₂^o which are in excellent agreement with those of Criss and Cobble. The excess apparent molar heat capacities (C₂, φ - C₂^o) can be used to predict the temperature dependence of (H₂, φ - H₂^o), the excess apparent molar enthalpy. The calculated values of ΔH₂, φ agree within experimental uncertainty with the integral enthalpies of dilution of Ensor and Anderson and of Messikomer and Wood up to 323.15 K. Above this temperature significant differences are observed. The densities of the solutions were also remeasured in the same range of temperature and molality with a flow densimeter, and the derived apparent molar volumes agree with the literature values.     

Thermochemistry of aqueous solutions of nucleic acid bases and their alkylated derivatives

Enthalpy of solution, ΔH _sol ^o , enthalpy of sublimation, ΔH _subl ^o , apparent partial molar volume and heat capacities,V ₂ ^o andC _p,2 ^o were determined for aqueous solutions of thirty alkylated derivatives of uracyl and adenine, eight derivatives of cytosine and guanine. Calculated accessible surface areas and molar volumes are presented, too. The values of enthalpy of solution, enthalpy of sublimation can be useful in the studies on the nature of interaction between these compounds and water molecules. Apparent partial molar volume and heat capacity give a new aspect on hydrophob properties of the examined nucleic acid base derivatives.     

Thermodynamic characterization of proflavine–DNA binding through microcalorimetric studies

The interaction of an important acridine dye, proflavine hydrochloride, with double stranded DNA was investigated using isothermal titration calorimetry and differential scanning calorimetry. The equilibrium constant for the binding reaction was calculated to be (1.60 ± 0.04) · 10⁵ · M⁻¹ at T = 298.15 K. The binding of proflavine hydrochloride to DNA was favored by both negative enthalpy and positive entropy contributions to the Gibbs energy. The equilibrium constant for the binding reaction decreased with increasing temperature. The standard molar enthalpy change became increasingly negative while the standard molar entropy change became less positive with rise in temperature. However, the standard molar Gibbs free energy change varied marginally suggesting the occurrence of enthalpy–entropy compensation phenomenon. The binding reaction was dominated by non-polyelectrolytic forces which remained virtually unchanged at all the salt concentrations studied. The binding also significantly increased the thermal stability of DNA against thermal denaturation.     

Dissolution properties of N-guanylurea dinitramide (GUDN) in dimethyl sulfoxide and N-methyl pyrrolidone

The enthalpies of dissolution of N-guanylurea dinitramide (GUDN) in dimethyl sulfoxide (DMSO) and N-methyl-2-pyrrolidone (NMP) were measured using an RD496-2000 Calvet microcalorimeter at 298.15 K under atmospheric pressure, respectively. Empirical formulae for the calculation of the enthalpy of dissolution (Δ_diss H), relative partial molar enthalpy (Δ_diss H _partial), and relative apparent molar enthalpy (Δ_diss H _apparent) were obtained from the experimental data of the dissolution processes of GUDN in DMSO and NMP. Furthermore, the corresponding kinetic equations describing the two dissolution processes were dα/dt = 10^?3.39(1 ? α)^0.70 for the dissolution of GUDN in DMSO, and dα/dt = 10^?4.06(1 ? α)^1.11 for the dissolution of GUDN in NMP.     

Synthesis and characterization of functional l-lactic acid/citric acid oligomer

Oligomers of l-lactic acid and citric acid (PLCA) were synthesized by reacting lactic acid with citric acid in the presence of stannous chloride. The chemical compositions of these multicarboxylated oligomers were verified by FT-IR and ¹H-NMR spectroscopy. The thermal characteristics of the oligomers, such as glass transition temperature T_g, melting temperature T_m and melting enthalpy, were confirmed by DSC. The crystallinity of the oligomers were determined by DSC and WXRD. Meanwhile, the acid-base surface characteristics of PLCA have been determined by contact angle. The results implicated that these oligomers may be used to entrap the cospecies on PLLA surface in tissue engineering.     

Volumetric and compressibility behaviour of ionic liquid, 1-n-butyl-3-methylimidazolium hexafluorophosphate and tetrabutylammonium hexafluorophosphate in organic solvents at T = 298.15 K

Density and speed of sound measurements have been made on the systems containing the ionic liquid 1-n-butyl-3-methylimidazolium hexafluorophosphate ([BMIM][PF₆]) and some organic solvents having a wide range of dielectric constants. Similar studies have been carried out for tetrabutylammonium hexafluorophosphate ([TBA][PF₆]), which has common anion ([PF₆]⁻) with the studied ionic liquid. For the systems investigated, the apparent molar volumes and apparent molar isentropic compressibilities were determined and fitted to the Redlich–Mayer and the Pitzer equations from which the corresponding limiting values were obtained. These limiting values were used to obtain some information about ion–solvent interactions. Furthermore, using the ionic limiting apparent volume values for [TBA]⁺ from the literature and limiting apparent molar volume for the ionic liquid and [TBA][PF₆] obtained in this work, the ionic limiting apparent molar volume values for the cation [BMIM]⁺ in different organic solvents were also estimated.     

Interactions of Peptides and Lysozyme with Aqueous Tetraethylammonium Bromide at 298.15 K

The apparent molar volumes, V _{ø, 2}, of gly-leu, gly-gly-leu and the partial specific volume ν^° of hen-egg-white lysozyme have been determined in aqueous of TEAB solutions by density measurements at 298.15 K. These data have been used to calculate the infinite dilution apparent molar volumes V _2,m ^o for the peptides in aqueous TEAB solutions and the standard partial molar volumes of transfer Δ_tr V _2,m ^o of the peptides from water to aqueous TEAB solutions. The results on Δ_tr V _2,m ^o of peptides from water to aqueous TEAB solutions have been interpreted in terms of ion-ion, ion-polar, hydrophilic-hydrophilic and hydrophobic-hydrophobic group interactions. In order to supplement this information, enthalpies of transfer of aqueous peptides from water to TEAB solution have been determined at 298.15 K using a VP-ITC titration calorimeter. The data on partial molar volumes and enthalpies of transfer have been discussed in light of various interactions operating in the ternary system of peptides, water and TEAB. The partial specific volume of transfer of lysozyme from water to aqueous TEAB solutions also indicates the predominance of hydrophobic interactions.     

Microcalorimetry and spectroscopic studies on the binding of dye janus green blue to deoxyribonucleic acid

The interaction of the phenazinium dye janus green blue (JGB) with deoxyribonucleic acid was investigated using isothermal titration calorimetry and thermal melting experiments. The calorimetric data were supplemented by spectroscopic studies. Calorimetry results suggested the binding affinity of the dye to DNA to be of the order of 10⁵ M^?1. The binding was predominantly entropy driven with a small negative favorable enthalpy contribution to the standard molar Gibbs energy change. The binding became weaker as the temperature and salt concentration was raised. The temperature dependence of the standard molar enthalpy changes yielded negative values of standard molar heat capacity change for the complexation revealing substantial hydrophobic contribution in the DNA binding. An enthalpy–entropy compensation behavior was also observed in the system. The salt dependence of the binding yielded the release of 0.69 number of cations on binding of each dye molecule. The non-polyelectrolytic contribution was found to be the predominant force in the binding interaction. Thermal melting studies revealed that the DNA helix was stabilized against denaturation by the dye. The binding was also characterized by absorbance, resonance light scattering and circular dichroism spectral measurements. The binding constants from the spectral results were close to those obtained from the calorimetric data. The energetic aspects of the interaction of the dye JGB to double-stranded DNA are supported by strong binding revealed from the spectral data.     

Volumetric, viscometric and refractive index behavior of some α-amino acids in aqueous tetrapropylammonium bromide at different temperatures

Densities, ρ, viscosities, η, and refractive indices, n _D, of glycine (Gly), DL-alanine (Ala), DL-valine (Val) (0.05, 0.10, 0.15, 0.20, 0.25 mol kg^?1), and L-leucine (Leu) (0.02, 0.05, 0.10 mol kg^?1) in water and in 0.20 mol kg^?1 aqueous tetrapropylammonium bromide (TPAB) have been measured at 298.15, 303.15, 308.15, and 313.15 K. The density data have been utilized to calculate apparent molar volumes, ?_v, partial molar volumes at infinite dilution, ?_v°, and partial molar volumes of transfer, ? _v°(tr) of amino acids. The viscosity data have been analyzed by means of Jones-Dole equation to obtain Falkenhagen coefficient, A, and Jones-Dole coefficient, B, free energy of activation of viscous flow per mole of solvent, Δµ₁°*, and solute, Δµ₂°*, and enthalpy, ΔH*, and entropy of activation, ΔS*, of viscous flow. The refractive index data have been used to calculate molar refractivity, R _D, of amino acids in aqueous tetrapropylammonium bromide solutions. It has been observed that ?_v°, B-coefficient and Δµ₂°* vary linearly with increasing number of carbon atoms in the alkyl chain of amino acids, and they were split to get contributions from the zwitterionic end groups (NH₃ ⁺, COO^-) and methylene group (CH₂) of the amino acids. The behavior of these parameters has been used to investigate the solute-solute and solute-solvent interactions as well as the effect of tetrapropylammonium cation (C₃H₇)₄N⁺ on these interactions.     

Structure and molecular interactions in {ethanol + (propan-1-ol/propan-2-ol)} mixtures at 303.15 K

In view of industrial importance of binary {ethyl alcohol + (propan-1-ol/propan-2-ol)} mixtures, the densities (ρ) and refractive indices (n _D ) of these alkanols mixtures were measured for different compositions at 303.15 K. Molar volumes (V _m) and excess molar volumes (V ^E) of these binary mixtures were calculated from experimental density data of pure solvents and solvents mixtures. The measured refractive index and density data was used to calculate specific refractions (R _D ), molar refractions (R _M) and apparent molar refractions (R _{φ, i} ) of binary mixtures. From mole fraction dependence of apparent molar refractions, the limiting apparent molar refractions (R _{φ, i} ^○ ) of propan-1-ol and propan-2-ol have been determined. The graphical values of R _{φ, i} ^○ for propan-1-ol and propan-2-ol were found to be 9.5664 and 7.405 cm³ mol^?1 respectively. Structural changes, geometrical fittings and molecular interactions in binary mixtures of these alkanols have been discussed.     

Determination of specific heat capacity and standard molar combustion enthalpy of taurine by DSC

Using XRY-1C calorimeter, the standard molar enthalpy of taurine was determined to be ?2546.2?kJ?mol^?1 . The reliability of the instrument used was tested by using naphthalene as reference material; and through comparing the molar combustion enthalpy of naphthalene measured with its standard value found in literature, the absolute error and relative error were found to be 4.53?kJ?mol^?1 and 0.09%, respectively. The melting point and melting enthalpy of taurine were determined by Differential Scanning Calorimetry (DSC), which was found to be 588.45?K and ?22.197?kJ?mol^?1, respectively. Moreover, using the DSC method, the specific heat capacities C _p of taurine was measured and the relationship between C _p and temperature was established. The thermodynamic basic data obtained are available for the exploiting new synthesis method, engineering design and industry production of taurine.     

Electrochemical strategy for sensing DNA methylation and DNA methyltransferase activity

The present work demonstrates a novel signal-off electrochemical method for the determination of DNA methylation and the assay of methyltransferase activity using the electroactive complex [Ru(NH₃)₆]³⁺ (RuHex) as a signal transducer. The assay exploits the electrostatic interactions between RuHex and DNA strands. Thiolated single strand DNA1 was firstly self-assembled on a gold electrode via Au–S bonding, followed by hybridization with single strand DNA2 to form double strand DNA containing specific recognition sequence of DNA adenine methylation MTase and methylation-responsive restriction endonuclease Dpn I. The double strand DNA may adsorb lots of electrochemical species ([Ru(NH₃)₆]³⁺) via the electrostatic interaction, thus resulting in a high electrochemical signal. In the presence of DNA adenine methylation methyltransferase and S-adenosyl-l-methionine, the formed double strand DNA was methylated by DNA adenine methylation methyltransferase, then the double strand DNA can be cleaved by methylation-responsive restriction endonuclease Dpn I, leading to the dissociation of a large amount of signaling probes from the electrode. As a result, the adsorption amount of RuHex reduced, resulting in a decrease in electrochemical signal. Thus, a sensitive electrochemical method for detection of DNA methylation is proposed. The proposed method yielded a linear response to concentration of Dam MTase ranging from 0.25 to 10 U mL⁻¹ with a detection limit of 0.18 U mL⁻¹ (S/N = 3), which might promise this method as a good candidate for monitoring DNA methylation in the future.     

Thermochemistry of the dissolution of DL-α-alanyl-DL-norleucine in aqueous solutions of amides at 298.15 K

Enthalpies of the dissolution of DL-α-alanyl-DL-norleucine are determined by calorimetry in aqueous solutions of formamide (FA), N-methylformamide (MFA), N,N-dimethylformamide (DMF), and N,N-dimethylacetamide (DMA) at a concentration of amides of x ₂ = 0–0.4 molar parts and T = 298.15 K. Standard values of enthalpies of dissolution Δ_sol H ^o and Δ_tr H ^o of DL-α-alanyl-DL-norleucine transfer from water to binary solvent are calculated, along with the enthalpy coefficients of pair interactions h _xy of DL-α-alanyl-DL-norleucine with amide molecules. The effect of the composition of water-organic mixtures and the structure of amides on the enthalpy characteristics of dissolution and transition of DL-α-alanyl-DL-norleucine is considered. Quantitative estimates of the contributions to energy from DL-α-alanyl-DL-norleucine-amides pair interactions determined by the polarity, polarizability, and electron acceptor and electron donor ability of organic cosolvents are given using the Kamlet-Taft correlation equation.     

Apparent molar heat capacities and apparent molar volumes of Pr(ClO4)3(aq), Gd(ClO4)3(aq), Ho(ClO4)3(aq), and Tm(ClO4)3(aq) at T=(288.15, 298.15, 313.15, and 328.15) K and p=0.1 MPa

Acidified aqueous solutions of Pr(ClO₄)₃(aq), Gd(ClO₄)₃(aq), Ho(ClO₄)₃(aq), and Tm(ClO₄)₃(aq) were prepared from the corresponding oxides by dissolution in dilute perchloric acid. Once characterized with respect to trivalent metal cation and acid content, the relative densities of the solutions were measured at T=(288.15, 298.15, 313.15, and 328.15) K and p=0.1 MPa using a Sodev O2D vibrating tube densimeter. The relative massic heat capacities of the aqueous systems were also determined, under the same temperature and pressure conditions, using a Picker Flow Microcalorimeter. All measurements were made on solutions containing rare earth salt in the concentration range 0.01 ⩽ m/(mol · kg⁻¹) ⩽ 0.2. Relative densities and relative massic heat capacities were used to calculate the apparent molar volumes and apparent molar heat capacities of the acidified salt solutions from which the apparent molar properties of the aqueous salt solutions were extracted by the application of Young's Rule. The concentration dependences of the isothermal apparent molar volumes and heat capacities of each aqueous salt solution were modelled using Pitzer ion-interaction equations. These models produced estimates of apparent molar volumes and apparent molar heat capacities at infinite dilution for each set of isothermal V_φ,2 and C_pφ,2 values. In addition, the temperature and concentration dependences of the apparent molar volumes and apparent molar heat capacities of the aqueous rare earth perchlorate salt solutions were modelled using modified Pitzer ion-interaction equations. The latter equations utilized the Helgeson, Kirkham, and Flowers equations of state to model the temperature dependences (at p=0.1 MPa) of apparent molar volumes and apparent molar heat capacities at infinite dilution. The results of the latter models were compared to those previously published in the literature.Apparent molar volumes and apparent heat capacities at infinite dilution for the trivalent metal cations Pr³⁺(aq), Gd³⁺(aq), Ho³⁺(aq), and Tm³⁺(aq) were calculated using the conventions V₂^∘(H⁺(aq)) ≡ 0 and C_p2^∘(H⁺(aq)) ≡ 0 and have been compared to other values reported in the literature.     

Measurements of excess molar enthalpy and excess molar heat capacity of (1-heptanol or 1-octanol)+(diethylamine or <Emphasis Type="Italic">s</Emphasis>-butylamine) mixtures at 298.15 K and 0.1 MPa

Experimental data of excess molar enthalpy (H _m^E) and excess molar heat capacity (C _pm^E) of binary mixtures containing (1-heptanol or 1-octanol)+(diethylamine or s-butylamine) have been determined as a function of composition at 298.15 K and at 0.1 MPa using a modified 1455 Parr solution calorimeter. The excess molar enthalpy data are negative and show parabolic format over the whole composition range; however, the excess molar heat capacity values, whose curves show a S-shape, are positive in the 0.0 to 0.7 molar fraction range and negative between the molar fraction values 0.7 to 1.0. The applicability of the ERAS-model to correlate the excess molar enthalpy data was tested. The calculated data values are in good agreement with the experimental ones. The experimental behavior of H _m^E is interpreted in terms of specific interactions between 1-alkanol and amine molecules.     

Temperature-dependent volumetric and viscometric properties of amino acids in aqueous solutions of an antibiotic drug

Volumetric and viscometric properties of glycine and methionine (amino acids) in a 0.2 vol. % amikacin sulphate (antibiotic drug) aqueous solution with the molality range of 0.025 mol kg^?1–0.25 mol kg^?1 were measured over the temperature range of 20°C–40°C at the interval of 5°C. Different parameters like apparent molar volume (? _V), apparent molar adiabatic compression (? _κ ), isentropic compression (κ _S) along with other acoustical parameters were calculated. Parameters like viscous relaxation time (τ), free volume (V _F), internal pressure (Π _I), and molar cohesive energy (MCE) were calculated from dynamic viscosity measurements. The ? _V values are positive in both cases, but with higher magnitude observed in methionine. These positive values of ? _V are indicative of strong solute-solvent interactions at all temperatures. In case of methionine there is a sharp initial increase in the ? _V values which become almost constant with further additions of the amino acid. Structural differences in the two amino acids studied are clearly reflected in the different nature of the plots of different parameters. In case of an amino acid-drug system, dynamic viscosity increase has been attributed to the increase in the hydrophilic-ionic and hydrophilic-hydrophilic interactions with the increase in the amino acid concentration which in turn may cause more frictional resistance to the flow of the solution. All other parameters are discussed in terms of solute-solvent and solvent-solvent interactions.     

Chromatographic Framework to Determine the Memantine Binding Mechanism on Human Serum Albumin Surface

In this work, the interaction of memantine with human serum albumin (HSA) immobilized on porous silica particles was studied using a biochromatographic approach. The determination of the enthalpy change at different pH values suggested that the protonated group in the memantine–HSA complex exhibits a heat protonation with a magnitude around 65 kJ mol^?1. This value agrees with the protonation of a guanidinium group, and confirmed that an arginine group may become protonated in the memantine–HSA complex formation. The thermodynamic data showed that memantine–HSA binding, for low temperature (<293 K), is dominated by a positive entropy change. This result suggests that dehydration at the binding interface and charge–charge interactions contribute to the memantine–HSA complex formation. Above 293 K, the thermodynamic data ΔH and ΔS became negative due to van der Waals interactions and hydrogen bonding which are engaged at the complex interface. The temperature dependence of the free energy of binding is weak because of the enthalpy–entropy compensation caused by a large heat capacity change, ΔC _p = ? 3.79 kJ mol^?1 K^?1 at pH = 7. These results were used to determine the potential binding site of this drug on HSA.     

Thermodynamic properties of resveratrol in dimethyl sulfoxide

In this article, the enthalpies of dissolution of resveratrol in dimethyl sulfoxide (DMSO) were measured using a RD496-2000 Calvet microcalorimeter at 298.15?K under atmospheric pressure. The differential enthalpy (??_dif H _m) and molar enthalpy (??_sol H _m) of dissolution of resveratrol in DMSO were determined, and the relationship between heat and the amount of solute was also established. Based on the thermodynamic and kinetic knowledge, the corresponding kinetic equation, half-life, ??_sol H _m, ??_sol S _m, ??_sol G _m, the relative partial molar enthalpy (??_sol H _m(partial)) and the relative apparent molar enthalpy (??_sol H _m(app)) of the dissolution process were obtained. The results showed that this study not only provided a simple method for the determination of the half-life for a drug, but also offered a theoretical reference for the clinical application of resveratrol.