Investigation of the interaction of DNA and neutral red by fluorescence spectroscopic analysis

The binding characteristics of neutral red (NR) with DNA were investigated by fluorescence spectrometry. Chemometrics approach as singular value decomposition (SVD) was used to evaluate the number of spectral species in the drug-DNA binding process, and then the intrinsic binding constant of 1.6 × 104 in base pairs and the binding site number of 0.97 were obtained from the Scatchard plot.     

Investigation of the interaction of carbofuran and DNA by voltammetry and fluorescence with the aid of chemometrics

<正>The interactions of carbofuran and DNA were studied using voltammetry and fluorescence spectroscopy.The formation of carbofuran-DNA makes the current peak of DNA decreased by voltammetry method.The binding number(n) and constant(K_a) for complex carbofuran-DNA were calculated to be 1.06±0.04 and 0.11±0.03mol~(-1) L,respectively by fluorescence measurement.Chemometrics approach,such as singular value decomposition(SVD) was used to evaluate the number of spectral species in the drug-DNA binding process.And the pure spectra and concentration profiles in the kinetic system were clearly deduced by multivariate curve resolution alternating least squares(MCR-ALS) with the initial estimates by evolving factor analysis(EFA).     

MICELLIZATION STUDIES OF DODECYL BENZENESULFONIC ACID AND ITS INTERACTION WITH POLYVINYLPYRROLIDONE

Dodecyl benzenesulfonic acid (DBSA) surfactant was used in the present study to find the effect of concentration on its electrical conductance in solution from 293-323K above and below the critical micelle concentration (CMC). The micellization parameters i.e. degree of counter ion binding (β), aggregation number (n) and number of counter ion micelle(m) were measured. The interaction of DBSA with polyvinylpyrrolidone (PVP) was also studied at 293K throughconductance and surface tension measure ments. A number of important parameters i.e. critical aggregation concentration (CAC), Gibb‘s free energy (△G) and binding ratio (R) were determined and the effect of NaCl on the CAC and polymer saturation point (PSP) was also investigated.     

Studies on the binding of vinpocetine to human serum albumin by molecular spectroscopy and modeling

The interaction between vinpocetine(VPC) and human serum albumin(HSA) in physiological buffer(pH 7.40) was investigated by fluorescence,FT-IR,UV-vis absorption and molecular modeling.VPC effectively quenched the intrinsic fluorescence of HSA via static quenching.The binding site number n and apparent binding constant K_a,corresponding thermodynamic parametersΔG,ΔH andΔS at different temperatures were calculated.The synchronous fluorescence and FT-IR spectra were used to investigate the structural change of HSA molecules with addition of VPC.Molecular modeling indicated that VPC could bind to the site I of HSA and hydrophobic interaction was the major acting force,which was in agreement with the binding mode study.     

Selective binding of bile salts by β-cyclodextrin derivatives with appended quinolyl arms

Two β-cyclodextrin derivatives bearing appended quinolyl and isoquinolyl arms,i.e.mono-(6-quinolyl- 6-deoxy)-β-cyclodextrin(1) and mono-(6-isoquinolyl-6-deoxy)-β-cyclodextrin(2) were synthesized in satisfactory yields and fully characterized.Their original conformations and binding behaviors toward four bile salt guests,that is,sodium cholate(CA),sodium deoxycholate(DCA),sodium glycocholate (GCA),and sodium taurocholate(TCA),were investigated by means of fluorescence,circular dichroism and 2D NMR spectroscopy.The study of solution structures revealed that both quinolyl and isoquinolyl arms were located outside the cyclodextrin cavity.The results obtained from the fluorescence titrations showed that the binding abilities of hosts 1 and 2 with selected bile salts varied in an order of DCA > CA > GCA.The selective binding of hosts toward bile salt guests was discussed from the viewpoints of induced-fit and multiple binding.     

Characterization of the Interaction between Bovine Serum Albumin and Lomefloxacin by Capillary Zone Electrophoresis

Three capillary zone electrophoresis (CZE) methods of the frontal analysis (FA), vacancypeak (VP) and simplified Hummel-Dreyer (SHD) were applied to investigate interaction betweenbovine serum albumin (BSA) and lomefloxacin, the experimental condition was established after alarge number of tests. Based on the site-binding model, the binding parameters were measuredaccording to the site model by Scatchard.     

2-萘-(OCH2CH2)n-金刚胺与6-单取代环糊精衍生物的光诱导电子转移反应

A number of naphthalene donor compounds that possess an adamantanamine binding moiety and an (OCH2CH2)n (nn1, 2, 3, 4, 6, 8) spacer were synthesized. The fluorescence quenching between these donor substrates and mono-6-O-p-nitrobenzoyl-β-cyclodextrin (pNBCD) and mono-6-O-m-nitrobenzoyl-β-cyclodextrin(mNBCD) was studied in detail. It was found that very efficient fluorescence quenching could occur in these supramolecular systems. This quenching was attributed to the photoinduced electron transfer inside the supramolecular assembly between the naphthalene donors and cyclodextrin acceptors. Detailed Stern-Volmer constants were measured and they were partitioned into dynamic Stern-Volmer quenching constants and static binding constants. It was demonstrated that the binding constants between all the naphthalene compounds and cyclodextrins are the same as they possess the same binding site, i.e., adamantanamine.     

Synthesis and Crystal Structure of CoCl（ieaa）（C10H7—ieai）（C10H7NH2）

1 INTRODUCTION A number of isonitroso-b-diketones and isonitroso-b-ketoesters such as isonitrosoacetyl- acetone(Hiaa), isonitrosobenzoylacetone(Hiba) and isonitrosoethylacetoacetate (Hieaa) have been employed as reagents in spectrophotometric determination of iron, palladium and ruthenium[1]. Transition metal complexes of such ligands[2] are potential models for metal binding sites in ferroverdin[3]. They were found as dyes and light-absorbing agents for the acceleration of the sol…     

Interactions of ginsenosides with DNA duplexes： A study by electrospray ionization mass spectrometry and UV absorption spectroscopy

The non-covalent complexes of duplexes DNA and 9 ginsenosides（1 aglycone and 8 glycosides） were investigated using electrospray ionization mass spectrometry（ESI-MS） in the gas phase. The results of relative binding affinities in negative ion mode revealed that several factors impact on the duplexbinding properties of ginsenosides. Glycosylations of 20（S）-protopanaxadiol ginsenosides at the position C-20 and 20（S）-protopanaxatriol classification at the position C-6 enhanced the fraction of bound DNA sharply. A rhamnose moiety shows little lower binding intensities than glucose at the same position.Ginsenosides of 20（S）-protopanaxatriol result in subtle higher binding affinities toward the duplex DNA than 20（S）-protopanaxadiol family. However, glycosylation with two sugar moieties does not show a higher binding affinity than with only one moiety. The collision-induced dissociation experimental data demonstrate the gas-phase stability and fragmentation patterns of the ginsenoside/DNA complexes are related to the glycoside number. Positive ion ESI mass spectra of the complexes were also recorded. The result of ESI-MS suggests that hydrogen bonds are the dominate interaction between ginsenosides and DNA. Similar results were obtained in solution-phase by UV spectroscopy, which exhibit a hyperchromism and blue-shift effect when DNA solution was titrated by individual ginsenoside.     

Interaction of Surface-active Fluorescence Probes with Bovine Serum Albumin

The binding between three surface-active substituted 3H-indole fluorescence probes and bovine serum albumin (BSA) in aqueous solution was studied using fluorescence quenching. The binding constants of 3H-indole molecules with BSA were obtained. According to the Foerster resonance energy transfer theory, the distances between 3H-indole molecules and tryptophan of BSA were calculated. The results show that the oligoethyloxyethylene chain of 3H-indole molecules is longer, the binding between them is stronger, the energy transfer efficiency is higher, and the distance between tryptophan and 3H-indole is nearer.     

4-(4-羟基丁基－2－炔氧基)－3-（苯磺酰基）－1，2，5－噁二唑－2－氧化物与牛血清白蛋白结合作用的光谱法研究

The interaction between 4-(4-hydroxybut-2-ynyloxy)-3-(phenylsulfonyl)-1,2,5-oxadiazole-2-oxide(FB)andbovine serum albumin(BSA)was studied by spectroscopic methods including fluorescence and UV-Vis absorptionspectroscopy.The quenching mechanism of fluorescence of BSA by FB was considered to be a dynamic quenchingprocedure.The number of binding sites n and apparent binding constant K were measured by fluorescence quench-ing method.The results indicate that there is FB molecular binding with BSA,and forming 1∶1 complex.Thethermodynamic parameters such as ΔH,ΔG and ΔS,etc.,were calculated.The results indicate that the binding reac-tion is mainly entropy-driven and hydrophobic forces play major role in the binding reaction.The distance r be-tween donor(BSA)and acceptor(FB)was obtained according to Frster theory of non-radioactive energy transfer.     

Orbital Interaction of Epoxidation on the Same Curvature Bonds of Single-walled Carbon Nanotubes

The epoxidation of different bonds with the same bond curvature in one nano-tube including armchair,zigzag and chiral tubes was studied. The calculated results showed that for the adducts with opened C–O–C configuration,the magnitude of the binding energies was related with their corresponding bonding characteristics in HOMO,and the larger binding energies were attributed to stronger orbital interaction between one O atom and the nanotube; whereas for the adducts with 3MR structures,the binding energies were related with the changes of C–C bond length and independent of the frontier orbital interaction before and after epoxidation.     

Studies on Reaction Mechanism Between Sparfloxacin and Bovine Serum Albumin

The binding of sparfloxacin and bovine serum albumin(BSA) in aqueous solution was studied by means of fluorescence and absorbance spectra, and the interactions influenced by Fe^3 and Cu^2 were explored. Based on the Scatchard‘s site binding model and fluorescence quenching, practical formulas for a small molecule ligand attaching to a bio-macromolecule are proposed. The binding parameters were measured according to the suggested models, and the binding distance, the transfer efficiency of energy between sparfloxacin and BSA were obtained in view of the F6rster theory of non-radiation energy transfer. The effect of sparfloxacin on the conformation of BSA was analyzed by means of synchronous fluorescence spectroscopy.     

Molecular Dynamics Simulation of the Binding Interaction between Hormone Glucagon Protein and Self-Assembled Monolayer Molecules

Restrained molecular dynamics simulations were performed to study the binding affinity of the peptide with alkanethiols of different tail-groups, S（CH2）7CH3, S（CH2）7OH and S（CH2）7COOH, which self-assembled on Au（111） surface in the presence of water molecules. The curves of binding affinity were calculated by fixing the center of mass of the peptide at various distances from the assembling surface. Simulation results show that the binding affin- ity is in the order as COOH-SAMs〉OH-SAMs〉CH3-SAMs, while 100% COOH-SAMs〉5% COOH-SAMS in concentration. The effects on binding affinity by different tail-groups were also studied. Results show that the binding affinity between COOH-SAMs and the peptide is bigger than those of the others and increasing the acidity of COOH-SAMs will result in stronger attractive power.     

Mechanisms of imidacloprid resistance in Nilaparvata lugens by molecular modeling

<正>Homology models of the ligand binding domain of the wild-type and Y151S mutant brown planthopper {Nilaparvata lugens)α1 and rat(Rattus norvegicus)β2 nicotinic acetylcholine receptor(nAChR) subunits were generated based on the crystal structure of acetylcholine binding protein of Lymnaea stagnalis.Neonicotinoid insecticide imidacloprid was docked into the putative binding site of wild-type and mutantα1β2 dimeric receptors by Surflex-docking,and the calculated docking energies were in agreement with experimental results.The resistance mechanisms and corresponding binding modes of imidacloprid on nAChRs containing the Y151S target-site mutation were discussed.     

Interaction specific binding hotspots in Endonuclease colicin-immunity protein complex from MD simulations

The binding of Endonuclease colicin 9 (E9) by Immunity protein 9 (Im9) was found to involve some hotspots from helix III of Im9 on protein-protein interface that contribute the dominant binding energy to the complex.In the current work,MD simulations of the WT and three hotspot mutants (D51A,Y54A and Y55A of Im9) of the E9-Im9 complexes were carried out to investigate specific interaction mechanisms of these three hotspot residues.The changes of binding energy between the WT and mutants of the complex were computed by the MM/PBSA method using a polarized force field and were in excellent agreement with experiment values,verifying that these three residues were indeed hotspots of the binding complex.Energy decomposition analysis revealed that binding by D51 to E9 was dominated by electrostatic interaction due to the presence of the carboxyl group of Asp51 which hydrogen bonds to K89.For binding by hotspots Y54 and Y55,van der Waals interaction from the aromatic side chain of tyrosine provided the dominant interaction.For comparison,calculation by using the standard (nonpolarizable) AMBER99SB force field produced binding energy changes from these mutations in opposite direction to the experimental observation.Dynamic hydrogen bond analysis showed that conformations sampled from MD simulation in the standard AMBER force field were distorted from the native state and they disrupted the inter-protein hydrogen bond network of the protein-protein complex.The current work further demonstrated that electrostatic polarization plays a critical role in modulating protein-protein binding.     

Adsorption Isotherms of Quercetin and Catechin Compounds on Quercetin-MIP

A molecular imprinted polymer(MIP)was prepared with quercetin as the template and methacrylic acid(MAA)as the functional monomer.Acetonitrile and methanol were used as the porogen with ethylene glycol dimethacrylate(EGDMA)as the crosslinker and 2,2'-azobis(isobutyronitrile)(AIBN)as the initiator.The experimental parameters of the equilibrium isotherms were estimated via linear and nonlinear regression analyses.The linear equation as the functions of the adsorption concentration of the single compound in its solution and the competitive adsorption of the single compound in its mixed compounds solution was then expressed,and the adsorption equilibrium data were correlated to Langmuir and Freundlich isotherm models.The mixture compounds show competitive adsorption on the specific binding sites of quercetin-MIP.Furthermore,the competitive Langmuir isotherms were applied to the mixture compounds.The adsorption concentrations of quercetin,( )catechin( C),and(-)epicatechin(EC)on the quercetin molecular imprinted polymer were compared.The quercetin-imprinted polymer shows extraordinarily higher adsorption ability for quercetin than for the two catechin compounds that were also assessed.     

Binding of nucleosides with the cytotoxic plant alkaloid sanguinarine: Spectroscopic and thermodynamic studies

In spite of a large number of studies of the interaction of the cytotoxic plant alkaloid sanguinarine(SAN) with nucleic acids,the anticancer mechanism of SAN is still not clear.In contrast to the large number of studies of the interaction mechanism of SAN with DNA,there have been relatively few studies of the interaction of SAN with nucleosides.In this work,the interaction of SAN with three nucleosides-thymidine(T),uridine(U),and adenosine(A)-was investigated using a combination of conventional fluorescence and UV-vis spectroscopic techniques;thermodynamic calculations were also carried out at physiological pH 7.2.The binding processes of SAN with the different nucleosides were characterized by hypochromic and bathochromic effects in the absorption spectra of SAN and by the quenching of the fluorescence intensity of SAN.The measurements of fluorescence lifetime,the variations of the absorption spectra of the fluorophore,and the dependence of the quenching on the temperature indicated that the fluorescence quenching is static.The Stern-Volmer plot is nonlinear and approximately quadratic showing that,in this process,one SAN molecule can bind with two nucleoside molecules.These studies,together with our earlier studies of the binding of SAN with cytidine(C) and guanosine(G),showed that the binding constants of SAN with the five nucleosides at T = 308.15,318.15,and 328.15 K decreased in the order C > G > T > U > A and at T = 298.15 K decreased in the order G > C > T > U > A,and that the binding of SAN with the various nucleosides is not only slightly exothermic but also entropy-driven.All these results together with fluorescence quenching experiments advance good evidence concerning the interaction of SAN with various nucleosides.Such studies of the interaction mechanism of alkaloids with DNA may promote the development of new drugs.     

Synthesis of a Pair of Derivatives of N-Methylpyrrole Polyamide

A pair of derivatives of tetrameric N-methylpyrrole polyamide were synthesized in order to develop a new method for the study of interaction of the polyamide derivatives with DNA. Indole acetic acid and nicotinic acid were introduced to the polyamide in the synthesized compound, which showed an expected red shift in the UV spectrum. These compounds may function as a potential tool in the detection of the polyamide binding to DNA.     

A High Performance Theory for Thermodynamic Study on the Binding of Human Serum Albumin with Erbium Chloride

A thermodynamic study of the interaction between erbium(III) chloride (Er3＋) and human serum albumin (HSA) was studied at pH＝7.0, 27 and 37 ℃ in phosphate buffer by isothermal titration calorimetry (ITC). The present study reports the thermodynamic parameters that govern HSA-Er3＋ interactions. The extended solvation theory was used to reproduce the enthalpies of HSA-Er3＋ interactions over the whole range of Er3＋ concentrations. The binding parameters recovered from the new model were attributed to the structural change of HSA and its biological activity. The results obtained indicate that there is a set of two identical binding sites for Er3＋ ions with negative cooperativity. The enhancement of complex formation by Er3＋ and concomitant increase in ∆S suggest that the metal ion plays a role in increasing the number of hydrophobic contacts. The binding parameters discovered from the extended solvation model indicate that the stability of HSA molecule is increased as a result of its interaction with Er3＋ ions.