A Sensitive SERS Quantitative Analysis Method for Amino Acids Using Ruhemann’s Purple as Molecular Probe in Triangle Nanosilver Sol Substrate

The stable silver nanotriangle (AgNT) sol was prepared by reduction of silver ions with sodium borohydride in the presence of H₂O₂ and sodium citrate. Under the action of NaCl, AgNTs were aggregated to a highly surface-enhanced Raman scattering (SERS) active substrate. In pH 6.0 Na₂HPO₄-NaH₂PO₄ buffer solution (PBS) at 80 °C water bath, ninhydrin reacted with amino acids to form blue-violet complex Ruhemann’s purple (RP), and the RP molecules adsorbed on the aggregated AgNT surfaces that exhibited a strong SERS peak at 657 cm^?1. The peak was linear to amino acid concentration in the range of 0.7–99.8 μmol/L, with a detection limit (DL) of 0.5 μmol/L. This SERS method was applied to detect amino acid in samples, with satisfactory results. In addition, the analytical system was also investigated by resonance Rayleigh scattering (RRS), absorption, and electron microscope techniques.     

Formation of Liquid-Crystalline Dispersions of Double-Stranded DNA–Chitosan Complexes

Right-handed helical double-stranded DNA molecules were shown to interact with chitosans to form under certain conditions (chitosan molecular weight, content of amino groups, distance between amino groups, ionic strength and pH of solution) cholesteric liquid-crystalline dispersions characterized by abnormal positive band in CD spectrum in the absorption region of DNA nitrogen bases. Conditions were found for the appearance of intense negative band in CD spectrum upon dispersion formation. In some cases, no intense band appeared in CD spectrum in spite of dispersion formation. These results indicate not only the multiple forms of liquid-crystalline dispersions of DNA–chitosan complexes but also a possibility to control the spatial properties of these complexes. The multiplicity of liquid-crystalline forms of DNA–chitosan complexes was attempted to explain by the effect of character of dipoles distribution over the surface of DNA molecules on the sense of spatial twist of cholesteric liquid crystals resulting from molecules of the complexes.     

Investigation of molecular structure of bombesin and its modified analogues nonadsorbed and adsorbed on electrochemically roughened silver surface

This work describes the molecular structure of bombesin (BN) and its analogs on the basis of the absorption infrared and Raman results described below. In these analogues is replaced one ([D-Phe12]BN, [Tyr4]BN, and [Lys3]BN) or two ([Tyr4,D-Phe12]BN, [D-Phe12,Leu14]BN, and [Leu13-(R)-Leu14]BN) amino acid residues within the peptide chain with a synthetic amino acid, creating antagonists to bombesin, which are useful in the treatment of cancer. It is also used surface enhanced Raman scattering (SERS) to study the differences and changes in the vibrational spectra of BN and its analogs, which were attached to an electrochemically roughened silver surface as these peptides interacted with target proteins. This work explores the use of SERS for molecules anchored to a macroscopic silver surface to interrogate the interaction of these peptides with protein receptors. The results presented here show that all peptides coordinate to the macroscopic silver surface through an indole ring and the methylene group of Trp8, the C==O fragment, and an amide bond; however, the orientation of these fragments on the electrochemically roughened silver surface and the strength of the interactions with this surface is slightly different for each peptide. For example, the interaction of --CH2-- of [D-Phe12]BN, [Tyr4,D-Phe12]BN, [D-Phe12,Leu14]BN, [Leu13-(R)-Leu14]BN, and [Lys3]BN with the silver surface perturbed the vertical orientation of the Trp8 indole ring on this surface. Hence, the indole ring adopted a close to perpendicular orientation on the silver surface for BN and [Tyr4]BN, only.     

Theoretical and pH dependent surface enhanced Raman spectroscopy study on caffeine

The surface enhanced Raman spectroscopy (SERS) spectrum of caffeine is recorded on a silver colloid at different pH values. It is discussed on the basis of the SERS "surface selection rules" in order to characterize its vibrational behavior on such a biological artificial model. To improve the previous assignments in the Raman spectrum and for a reliable, detailed analysis of SERS spectra, density functional theory calculations (structural parameters, harmonic vibrational wavenumbers, total electron density, and natural population analysis of the molecule) are performed for the anhydrous form of caffeine and the results are discussed. The predicted geometry and vibrational Raman spectra are in good agreement with the experimental data. The flat orientation of the mainly chemisorbed caffeine attached through the pi electrons and the lone pair of nonmethylated N atoms of the imidazole ring are proposed to occur at neutral and basic pH values. At acid pH values caffeine is probably adsorbed on the Ag surface through one or both oxygen atoms, more probably through the O atom of the conjugated carbonyl group with an end-on orientation. However, the changes in the overall SERS spectral pattern seem to indicate the electromagnetic mechanism as being the dominant one.     

Thermochemical studies on the interaction between sodium n-dodecyl sulphate and catalases

The enthalpies of interaction between bovine catalase and sodium n-dodecyl sulphate (SDS) in aqueous solutions of pH 3.2,6.4 and 10.0 have been measured over a range of SDS concentrations by microcalorimetry at 25°C. The enthalpies increase with decreasing pH and with increasing SDS concentration and largely arise from the interations between the anionic head group of SDS and the cactionic amino acid residues on the protein. Chemically modified catalase in which a proportion of carboxylic acid groups have been coupled with either glycine methyl ester or ethylenediamine have been prepared and characterized in terms of their enzymic activities, spectral properties and sedimentation behaviour. The enthalpies of interaction of these catalases with SDS have been studied at pH 6.4. The results of the experiments suggest that the enthalpies of interaction with SDS can be correlated with the ratio of cationic to anionic amino acid residues on the surface of the catalase molecules and hence the nominal net surface charge. The variation in the enthalpy of interaction of catalases with surface charge, as a consequence of variation in pH, differs from the variation with charge at constant pH possibly due to the thermal effect of proton binding to the catalase—complexes.     

Adsorption of polyethyleneimine on silver nanoparticles and its interaction with a plasmid DNA: a surface-enhanced Raman scattering study

Raman spectroscopy is applied in this work to study the adsorption of poly(ethyleneimine) (PEI) on Ag nanoparticles obtained by reduction with citrate, as well as to the study of the interaction between PEI and a plasmid. The surface-enhanced Raman spectroscopy (SERS) affords important information about the interaction and orientation of the polymer on the particles. In particular we have found that this polymer interacts with the surface through their amino groups in an interaction which also involves a change in the protonation state of amino groups as well as an increase of the chain order. This interaction implies a charge-transfer effect as deduced from the strong resonant effect in Raman spectra obtained at different excitation wavelengths. The complex formed by PEI and a plasmid, obtained by encoding the HBV (hepatitis B virus) genome inside the EcoRI restriction site of pGEM vector, was also studied by SERS. The interaction between both polymers leads to a conformational change affecting both macromolecules that can be detected by Raman at different excitation wavelengths. PEI undergoes a change to a more disordered structure as well as an increase of the number of protonated amino groups. The plasmid undergoes a structural change from A-DNA structure to B-DNA, along with a change in the superhelicity resulting in a more lineal structure when the plasmid interacts with PEI.     

A sensitive surface‐enhanced Raman scattering method for chondroitin sulfate with Victoria blue 4R molecular probes in nanogold sol substrate

Using silver nanoparticles (AgNPs) as the nanocatalyst, l ‐cysteine rapidly reduced HAuCl₄ to make a stable gold nanoparticle sol (Ag/AuNP) that had a high surface‐enhanced Raman scattering (SERS) activity in the presence of Victoria blue 4R (VB4r) molecular probes. Under the selected conditions, chondroitin sulfate (Chs) reacted with the VB4r probes to form associated complexes that caused the SERS effect to decrease to 1618 cm^?1. The decreased SERS intensity was linear to the Chs concentration in the range 3.1–500 ng/ml, with a detection limit of 1.0 ng/ml Chs. Accordingly, we established a simple and sensitive SERS quantitative analysis method to determine Chs in real samples, with a relative standard deviation of 1.47–3.16% and a recovery rate of 97.6–104.2%.     

Variability in ionization state,stoichiometry and aggregation in histidine complexes with formic acid

The crystal structures of the complexes of L and DL histidine with formic acid have been determined as part of an effort to define biologically and evolutionarily important interactions and aggregation patterns. In terms of ionization state and stoichiometry they may be described as L-histidine formate formic acid and DL-histidine formate monohydrate respectively. In the L-histidine complex, amino acid molecules arranged in head-to-tail sequences centred around 2₁ screw axes are interconnected by formic acid molecules and formate ions. Histidine-formate interactions in the structure gives rise to a characteristic interaction pattern involving a linear array of alternating imidazole groups and formate ions. In DL-histidine formale monohydrate, head-to-tail sequences involving glide related molecules are interconnected through main chain-side chain interactions leading to amino acid layers. The layers are held together by formate ions and water molecules arranged in strings along which the ion and the molecule alternate. The patterns of amino acid aggregation in histidine complexes exhibit considerably higher variability than those in complexes involving arginine and lysine do. X-ray studies on crystalline complexes involving amino and peptides Part XXIX.     

Self-Organized Ag Nanorings Antenna Substrates for Surface-Enhanced Raman Spectroscopy

We investigate the surface-enhanced Raman spectroscopy of Ag nanorings antenna in both experiment and simulation. Self-organized Ag nanorings antenna were formed on quartz glass wafers by a simple chemistry reaction without any template. The three-dimensional finite-difference time-domain simulation calculations indicate that the electric field enhancement of Ag nanoring antenna is strongly dependent on the gap distance. A very strong surface plasmon coupling in the gap region of Ag nanoring antenna is observed, whose field intensity is enhanced four times compared to that for Ag nanodomes antenna with the same gap distance. Surface-enhanced Raman scattering (SERS) measurements have shown that the SERS intensity acquired from the Ag nanoring antenna is about 16 times stronger than that obtained from Ag nanodomes antenna. These results pave the way to design plasmonic nanostructures for practical applications that require coupled metallic nanoparticles with enhanced electric fields.     

Rich spectroscopic and molecular dynamic studies on the interaction of cytotoxic Pt(II) and Pd(II) complexes of glycine derivatives with calf thymus DNA

Some amino acid derivatives, such as R-glycine, have been synthesized together with their full spectroscopic characterization. The sodium salts of these bidentate amino acid ligands have been interacted with [M(bpy)(H₂O)₂](NO₃)₂ giving the corresponding some new complexes with formula [M(bpy)(R-gly)]NO₃ (where M is Pt(II) or Pd(II), bpy is 2,2′-bipyridine and R-gly is butyl-, hexyl- and octyl-glycine). Due to less solubility of octyl derivatives, the biological activities of butyl and hexyl derivatives have been tested against chronic myelogenous leukemia cell line, K562. The interaction of these complexes with highly polymerized calf thymus DNA has been extensively studied by means of electronic absorption, fluorescence and other measurements. The experimental results suggest that these complexes positive cooperatively bind to DNA presumably via groove binding. Molecular dynamic results show that the DNA structure is largely maintained its native structure in hexylglycine derivative–water mixtures and at lower temperatures. The simulation data indicates that the more destabilizing effect of butylglycine is induced by preferential accumulation of these molecules around the DNA and due to their more negative free energy of binding via groove binding.     

Interface-Induced Ag Monolayer Film for Surface-Enhanced Raman Scattering Detection of Water-Insoluble Enrofloxacin

Water-insoluble molecules usually show poor surface-enhanced Raman scattering (SERS) signals, because they are hardly adsorbed on the surface of most commonly used SERS substrates, such as aqueous Ag or Au colloids. In this work, a highly sensitive and reproducible Ag monolayer film (Ag MLF) SERS substrate prepared by self-assembly of Ag nanoparticles (Ag NPs) on water/oil interface can realize the trace SERS detection of water-insoluble enrofloxacin. The positively charged phase transfer catalyst can transfer the negatively charged Ag nanoparticles in aqueous solution to the water/oil interface. At the same time, the water-insoluble enrofloxacin can also be attracted to the interface because of its lipophilic group. The type/volume of the oil phase and phase transfer catalyst and the vortex mixing time were all optimized to maximize the SERS effect of Ag MLF. Results showed that trace water-insoluble enrofloxacin can be identified by Ag MLF and its detection sensitivity was significantly improved. The proposed novel Ag MLF can be further applied to detect other water-insoluble molecules in SERS.

     

Role of transition metal ferrocyanides (II) in chemical evolution

Due to ease of formation of cyanide under prebiotic conditions, cyanide ion might have formed stable complexes with transition metal ions on the primitive earth. In the course of chemical evolution insoluble metal cyano complexes, which settled at the bottom of primeval sea could have formed peptide and metal amino acid complexes through adsorption processes of amino acids onto these metal cyano complexes.Adsorption of amino acids such as glycine, aspartic acid, and histidine on copper ferrocyanide and zinc ferrocyanide have been studied over a wide pH range of 3.6 – 8.5. Amino acids were adsorbed on the metal ferrocyanide complexes for different time periods. The progress of the adsorption was followed spectro-photometrically using ninhydrin reagent. Histidine was found to show maximum adsorption on both the adsorbents at neutral pH. Zinc ferrocyanide exhibits good sorption behaviour for all the three amino acids used in these investigations.     

A spectroscopic study of the interaction of the VO2+ cation with the two components of chondroitin sulfate

The interaction of the vanadyl (IV) cation with N-acetyl-D-galactosamine, D-galactosamine, and D-glucuronic acid has been investigated by electron absorption spectroscopy at different mental to ligand ratios and pH values. In the case of D-glucuronic acid, a more detailed study was undertaken, using differential IR spectroscopy in solution. The results show that the cation interacts with the two nitrogenated molecules only at higher pH values, generating 2∶1 lig-and to metal complexes in which coordination occurs through two pairs of deprotonated OH groups of the rings. In the case of D-glucuronic acid, the IR-measurements allowed a wider insight into the structural characteristics of the complexes generated in acidic media. The involvement of the glycosidic oxygen atom in coordination, is suggested at pH=3.     

Functional CD2 mutants unable to bind to, or be stimulated by, LFA-3.

To define epitopes on the CD2 (T11, the T cell erythrocyte receptor) molecule that are necessary for interaction with lymphocyte function-associated Ag-3 (LFA-3), we have expressed the human wild-type CD2 cDNA and mutant CD2 cDNA in a murine Ag-specific T cell hybridoma that responds to human HLA-DR Ag. Here we have expressed mutations at amino acid 91 and 92 of CD2 in the T cell hybridoma. The mutated CD2 molecules were functional in that pairs of anti-CD2 mAb that continued to bind were able to stimulate IL-2 production by the hybridomas. However, CD2 mutants with either the 91 or 92 amino acid substitution had lost the ability to bind to or be activated by either SRBC, which bear an LFA-3 homologue, or by murine L cells expressing human LFA-3. Unlike hybridomas expressing the wild-type CD2 molecule, there was no enhanced response to Ag stimulation. Taken together, these data suggest that the mutated CD2 molecules were no longer able to bind to, or to utilize, LFA-3 for activation. We have previously demonstrated that a mutation at amino acid 51 of CD2 results in loss of binding to LFA-3. Whether these two regions of CD2, discrete and separable by amino acid sequence, form one or more binding sites for LFA-3 remains to be determined.     

SERS quantitative detection of trace human chorionic gonadotropin using a label‐free Victoria blue B as probe in the aggregated immunonanogold sol substrate

Nanogold particles (NG) were modified by anti‐rabbit antibody (RAb) against human chorionic gonadotropin to obtain an immunonanogold probe (ING). In pH 7.0 Na₂HPO₄‐citrate buffer solution containing KCl, ING probes formed large aggregates in which Victoria blue B (VBB) molecules were adsorbed on the surface and which exhibited strong surface‐enhanced Raman scattering (SERS) at a peak of 1612 cm^–1. After addition of human chorionic gonadotropin (hCG) an immune reaction with the ING probe occurred to form dispersive ING–hCG complexes with non‐SERS activity that led to a decreased SERS peak at 1612 cm^–1. The decreased SERS intensity was linear to the concentration of hCG over 2.4–73.2 ng/mL. The ING reaction was studied in detail by SERS, scanning electron microscope (SEM), resonance Rayleigh scattering (RRS), surface plasmon resonance (SPR) absorption and laser scattering techniques. SERS quenching was observed and discussed. Copyright © 2014 John Wiley & Sons, Ltd.     

Interaction of Antimalarial Drug Quinacrine with Nucleic Acids of Variable Sequence Studied by Spectroscopic Methods

Abstract

The interaction of antimalarial drug quinacrine (QA) with polynucleotides is studied by UV- visible absorption, fluorescence and surface-enhanced Raman spectroscopy(SERS). The polynucleotides employed for such a study were calf thymus DNA, poly(A).poly(T), poly(A).poly(U), poly(C).poly(G) and poly(dG-dC).poly(dG-dC). Absorption and fluorescence spectra of QA complexes indicate that an interaction with the biomolecule is taking place, although different interaction mechanisms are probable depending on the sequence. The SERS spectra also reflect spectral changes which depend on the polymer sequence and that can be correlated to those observed by fluorescence, with the advantage of the detailed structural information provided by this vibrational technique. QA interacts with polynucleotides through its diprotonated form and by ring stacking. The strength of such interaction is extremely sequence dependent, thus suggesting different interaction mechanisms in each case. The SERS technique allows the simultaneous study of those polynucleotide moieties that are directly involved in the interaction thanks to the short-range character of the SERS spectroscopy. The interaction of QA with the above nucleic acids lead to a different change in the chain stability and flexibility which is further related to the different denaturation tendency of the polymer in the presence of the metal surface.     

Noncovalent interactions and coordination reactions in the systems consisting of copper(II) ions, aspartic acid and diamines

Interactions of aspartic acid between 1,3-diaminopropane (tn) and 1,4-diaminobutane (Put) in metal-free systems as well as in the systems including copper(II) ions were studied. The composition and overall stability constants of the complexes formed were determined by the potentiometric method. The interaction centres and coordination sites were identified by spectroscopic methods. Each of the ligands has both negative and positive interaction centres. In aspartic acid such centres are carboxyl groups and amine group, while in the polyamine molecules – protonated amine groups. The centres are also the potential sites of the coordination of metal ions. Analysis of the log K_e values of the adducts in the systems with polyamines has shown that the stability of the adducts in the metal-free systems depends on a significant degree on the steric factor that is the length of the polyamine. In some species the inversion effect, hitherto not reported in literature, was found. In the ternary systems including Cu(II) ions, only protonated species are formed, including molecular complexes with intermolecular interactions and metallation through the oxygen atoms of carboxyl groups and amine groups of the amino acid. In the adducts the protonated diamine is in the outer coordination sphere and is involved in noncovalent interactions with the anchoring CuH(Asp) or Cu(Asp) complexes.     

Molecular cloning of cDNA that encode MHC class I molecules from a New World primate (Saguinus oedipus). Natural selection acts at positions that may affect peptide presentation to T cells

To investigate the evolutionary pressures that drive the generation of polymorphism in primate MHC class I molecules, three cDNA that encode MHC class I alleles from a New World monkey, the cotton-top tamarin (Saguinus oedipus), were cloned and sequenced. These tamarin MHC class I alleles contained amino acid substitutions not found in any of the previously sequenced human MHC class I alleles. Moreover, the majority of these unique amino acid substitutions was located in the Ag recognition site at positions that have been shown to be critical in the presentation of viral peptides to T cells in mice and humans. These data suggest that selective pressures on MHC class I molecules preferentially act on the Ag recognition site and that the peptide binding or presenting functions of these molecules may drive the generation of MHC class I polymorphism. The novel Ag recognition sites of the tamarin MHC class I molecules, in addition to their restricted polymorphism, might account for the unusual susceptibility of the cotton-top tamarin to human pathogens.     

C-type lectin-like carbohydrate recognition of the hemolytic lectin CEL-III containing ricin-type -trefoil folds

CEL-III is a Ca(2+)-dependent hemolytic lectin, isolated from the marine invertebrate Cucumaria echinata. The three-dimensional structure of CEL-III/GalNAc and CEL-III/methyl alpha-galactoside complexes was solved by x-ray crystallographic analysis. In these complexes, five carbohydrate molecules were found to be bound to two carbohydrate-binding domains (domains 1 and 2) located in the N-terminal 2/3 portion of the polypeptide and that contained beta-trefoil folds similar to ricin B-chain. The 3-OH and 4-OH of bound carbohydrate molecules were coordinated with Ca(2+) located at the subdomains 1alpha, 1gamma, 2alpha, 2beta, and 2gamma, simultaneously forming hydrogen bond networks with nearby amino acid side chains, which is similar to carbohydrate binding in C-type lectins. The binding of carbohydrates was further stabilized by aromatic amino acid residues, such as tyrosine and tryptophan, through a stacking interaction with the hydrophobic face of carbohydrates. The importance of amino acid residues in the carbohydrate-binding sites was confirmed by the mutational analyses. The orientation of bound GalNAc and methyl alpha-galactoside was similar to the galactose moiety of lactose bound to the carbohydrate-binding site of the ricin B-chain, although the ricin B-chain does not require Ca(2+) ions for carbohydrate binding. The binding of the carbohydrates induced local structural changes in carbohydrate-binding sites in subdomains 2alpha and 2beta. Binding of GalNAc also induced a slight change in the main chain structure of domain 3, which could be related to the conformational change upon binding of specific carbohydrates to induce oligomerization of the protein.     

Synthesis of Peptide Mediated Au Core–Ag Shell Nanoparticles as Surface-Enhanced Raman Scattering Labels

As the fundamental understanding of metal–light interactions gains solid grounds, further research has been devoted to construct novel structures that take full advantage of such unique interactions, which is called plasmonics. In this report, the preparation of Au–Ag core–shell structures obtained by coating the Au surface with peptide and Raman reporter molecule and depositing an Ag layer on it is reported. The prepared Au–Ag NPs are tested for their surface-enhanced Raman scattering (SERS) performance. The negatively charged peptides with three different lengths, which are 3 (P1), 15 (P2), and 21 (P3) amino acid long, were chemically attached to 13 nm AuNPs along with Raman reporter molecule, carboxytetramethylrhodamine, and these modified AuNPs were coated with three different shell thickness of Ag metal. The prepared Au–Ag NPs were tested for their SERS performance and found that the Au–Ag NPs prepared with P2 and thickest shell performs best as SERS label.