Surface-enhanced Raman spectroscopic studies of coactivator-associated arginine methyltransferase 1

We report, for the first time, the surface-enhanced Raman spectra of an important enzyme, coactivator-associated arginine methyltransferase 1 (CARM1), involved in various biological activities such as tumor suppressor function and stem cell differentiation. We have employed surface-enhanced Raman scattering (SERS) to obtain insight into the structural details of CARM1 by adsorbing it to silver (Ag) nanoparticles. The enzyme retains its activity even after its adsorption onto Ag nanoparticles. We observe strong SERS modes arising from amide vibrations and aromatic ring amino acids. The SERS spectra revealed amide I bands at 1637 cm(-1) and 1666 cm(-1), which arise as a result of the alpha helix of the protein and the polypeptide backbone vibration of a random coil, respectively. In order to confirm the amide vibrations, we have performed SERS on deuterated CARM1, which exhibits a clear red shift in amide band positions. The SERS spectra may provide useful information, which could be harnessed to study the functional interactions of CARM1 with small molecule modulators.     

UV polymerization of self-assembled monolayers of a novel diacetylene on silver: a spectroscopic analysis by surface plasmon resonance and surface enhanced Raman scattering

UV polymerization of self-assembled monolayers of a novel carbazolyl-diacetylene (CDS9) chemisorbed on silver films was demonstrated by surface plasmon resonance (SPR) and surface enhanced Raman scattering (SERS) experiments. SPR tests performed during UV exposure permitted one to observe the growth of the absorption coefficient, associated with the formation of the polymeric backbone. The Raman spectra of polymerized monolayers exhibited the bands associated with the C=C stretching modes of the conjugated backbone, typical of the blue and red polymeric phases usually present in polydiacetylenes, with a clear predominance of the red form. Moreover, the strong surface enhancement of the Raman band corresponding to the aromatic C=C stretching modes suggested that carbazolyl groups arrange nearly perpendicularly to the metal surface. In contrast, the absence of a SERS signal in the region of conjugated C[triple bond]C bond stretchings confirmed a polymerization scheme with conjugated triple bonds nearly parallel to the plane of the metal.     

Surface-enhanced Raman scattering and the adsorption behavior of (RS)-phenylsuccinic acid

The surface geometry of (RS)-phenylsuccinic acid molecule was studied by analysis of the SERS spectra of aromatic dicarboxylic acid adsorbed on silver colloid surfaces. For a reliable analysis of the SERS spectrum, we also performed density functional theoretical calculations. The SERS spectral features indicated that the RSPSA molecules should bound to the silver as dicarboxylate, with a strongly tilted orientation with respect to the normal to the surface. Such a tilted orientation was presumed to occur by the simultaneous sigma and pi-type coordination of carboxylate groups to silver surface caused by the steric hindrance and electrostatic repulsion between the two carboxylate groups, and thereby RSPSA on silver was easily displaced with aromatic carboxylic acids. A sigma-type coordination therefore seemed to be more important than a pi-type coordination for aromatic carboxylic acid derivatives to assemble on a silver surface. The large enhancement of in-plane bending, out of plane bending and ring breathing modes in the surface-enhanced Raman scattering spectrum indicates that the molecule is adsorbed on the silver surface in a 'at least vertical' configuration, with the ring perpendicular to the silver surface.     

Structures and bonding on a colloidal silver surface of the various length carboxyl terminal fragments of bombesin

Raman (RS) and surface-enhanced Raman scattering spectra (SERS) were measured for various length carboxyl terminal fragments (X-14 of amino acid sequence) of bombesin ( BN): BN13-14, BN12-14, BN11-14, BN10-14, BN9-14, and BN8-14 in silver colloidal solutions. Density functional theory (DFT) calculations of Raman wavenumbers and intensities with extended basis sets (B3LYP/6-31++G**) were performed with the aim of providing the definitive band allocations to the normal coordinates. The proposed band assignment is consistent with the assignment for similar compounds reported in the literature. The nonadsorbed and adsorbed molecular structures were deducted by detailed spectral analysis of the RS and SERS spectra, respectively. This analysis also allowed us to propose the particular surface geometry and orientation of these peptides on silver surface, and their specific interaction with the surface. For example, a SERS spectrum of BN8-14 indicates that the interaction of a thioether atom and Trp8 with the silver surface is favorable and may dictate the orientation and conformation of adsorbed peptide. One of the most prominent and common features in all of the fragments' SERS spectra is a approximately 692 cm (-1) band due to nu(C-S) accompanied by two or three bands of different C-S conformers for all, except BN8-14, which suggests that all of the above-mentioned compounds adsorb on the silver surface through the thioether atom and that the attachment of Trp8 produces limitation in a number of possible C-S conformers adopted on this surface. Our results also show clearly that His12 and CO do not interact with the colloid surface, which supports our earlier results.     

Surface-enhanced Raman study of the interactions between tripodal cationic polyamines and polynucleotides

Raman and surface-enhanced Raman spectra of new DNA/RNA-binding compounds consisting of three imidazole (Im) and three pyridine (Py) rings connected by tripodal polyaminomethylene linkages were obtained by the near-infrared excitation at 1064 nm. Study of interactions of Im and Py polyamines with single-stranded RNA polynucleotides (poly?A, poly?G, poly?C, poly?U), double-stranded DNA polynucleotides (poly?dAdT-poly?dAdT, poly?dGdC-poly?dGdC) and calf thymus DNA (ct-DNA) by surface-enhanced Raman spectroscopy (SERS) reveals unambiguous enhancement of the Raman scattering from the small molecules as well as appearance of new bands in spectra associated mainly with nucleobases. The SERS experiments point toward comparable interactions of Im and Py polyamines with single-stranded purine and pyrimidine polynucleotides. Furthermore, SERS experiments with double stranded polynucleotides reveal the base-pair dependent selectivity of Im and Py, whereby interactions within both, major and minor groove are indicated for poly?dAdT-poly?dAdT, at variance to preferred binding of Im and Py to only major groove of poly?dGdC-poly?dGdC. SERS spectra of Im and Py with ct-DNA imply that protonated amino groups of these compounds preferentially interact with N7 atoms (adenine, guanine) while nitrogen in aromatic rings of polyamines might be attracted to C6-NH(2) (adenine), all sites being located at the major groove of the DNA helix. Wavenumber downshift of the imidazole (Im) and pyridine (Py) ring vibrations supports aromatic stacking interactions of imidazole and pyridine aromatic moieties with DNA base-pairs.     

Monosodium glutamate in its anhydrous and monohydrate form: differentiation by Raman spectroscopies and density functional calculations

Monosodium glutamate (MSG), a common flavor enhancer, is detected in aqueous solutions by Raman and surface-enhanced Raman (SERS) spectroscopies at the micromolar level. The presence of different species, such as protonated and unprotonated MSG, is demonstrated by concentration and pH dependent Raman and SERS experiments. In particular, the symmetric bending modes of the amino group and the stretching modes of the carboxy moiety are employed as marker bands. The protonation of the NH(2) group at acidic pH values, for example, is detected in the Raman spectra. From the measured SERS spectra, a strong chemical interaction of MSG with the colloidal particles is deduced and a geometry of MSG adsorbed on the silver surface is proposed. In order to assign the observed Raman bands, calculations employing density functional theory (DFT) were performed. The calculated geometries, harmonic vibrational wavenumbers and Raman scattering activities for both MSG forms are in good agreement with experimental data. The set of theoretical data enables a complete vibrational assignment of the experimentally detected Raman spectra and the differentiation between the anhydrous and monohydrate forms of MSG.     

Surface- and resonance-enhanced micro-Raman spectroscopy of xanthene dyes: from the ensemble to single molecules.

Surface-enhanced resonance Raman scattering (SERRS) spectra of various rhodamine dyes, of pyronine G and thiopyronine adsorbed on isolated silver clusters were recorded at the ensemble level and at the single-molecule level with a high-resolution confocal laser microscope equipped with a spectrograph and a CCD-detector. Comparing single-molecule spectra with ensemble spectra, various inhomogeneous spectral features, such as line splitting, spectral wandering, spectral diffusion and abrupt spectral jumps between different metastable spectral states, are revealed positions and the relative intensities of the vibronic bands. Resonance enhancement is investigated with respect to single-molecule surface-enhanced Raman scattering (SERS) spectroscopy and is found to be responsible for approximately three orders of magnitude in sensitivity. A significant influence of the substituents on the single-molecule SERRS sensitivity is found, showing that various chemical effects are responsible for surface enhancement in addition to the electromagnetic enhancement effect.     

Glucose‐induced and fructose‐induced deboronation reaction of 4‐mercaptophenylboronic acid assembled on silver investigated by surface‐enhanced Raman scattering

We examined the deboronation reaction of 4‐mercaptophenylboronic acid (4MPBA) via fructose and glucose on silver surfaces by means of surface‐enhanced Raman scattering (SERS) at the excitation wavelengths of 488, 514, and 633 nm. The SERS spectra on silver nanoparticles clearly exhibited specific spectral signatures of thiophenol (TP) peaks, indicating a deboronation reaction of 4MPBA on the surfaces, whereas no strong TP peaks were observed on gold nanoparticles. The vibrational bands at 417, 999, 1021, and 1574 cm^?1 in the Ag SERS spectra could correspond to the in‐plane aromatic ring modes in TP. X‐ray photoelectron spectroscopy also supported the surface reaction on Ag by referring the B1s peaks at ~193 eV. The ratiometric Raman measurements of the band at 1574 cm^?1, with respect to that at 1587 cm^?1, revealed fructose and glucose quantification in the concentration range of 1–10 mm . We did not identify such changes for mannose, sucrose, and sialic acid. The SERS peaks of 4MPBA on roughened Ag plates also exhibited TP bands to show the time‐dependent spectral change. Our findings indicate that the deboronation of 4MPBA and conjugation with fructose and glucose may be facilitated efficiently on silver surfaces for their quantification. Copyright © 2016 John Wiley & Sons, Ltd.     

Oxadiazole‐2‐thiol Adsorption on Gold Nanorods: A Joint Theoretical and Experimental Study by Using SERS,XPS, and DFT

The chemisorption of 1,3,4‐oxadiazole‐2‐thiol (ODT) on gold nanorods has been investigated by using surface‐enhanced Raman spectroscopy (SERS) and density functional theory (DFT). Although most of the SERS spectra have remarkable similarity to the normal Raman spectra of the pure analyte, the adsorption of ODT on a gold surface leads to a drastic change in its Raman spectrum and distinct vibrational features are obtained with gold nanorods and spherical nanoparticles. Simulated Raman spectra for hybrid systems that consist of an oxadiazole moiety coordinated to a Au₂₀ gold cluster provided valuable information about the coordination mode and enabled us to assign vibration modes.     

Raman and SERS investigation of isolated sp carbon chains

Carbon chains with sp hybridization and a known distribution of lengths have been studied by Raman and Surface Enhanced Raman Scattering (SERS). With the support of density functional theory simulations the observed Raman features have been assigned to active modes of individual chains. SERS spectra show remarkable differences, attributed to the interaction between sp chains and Ag nanoparticles used as a SERS active medium. The results obtained for this model system permit in principle to explain a large number of Raman data from molecular and solid sp/sp² carbon systems.     

“Parallel factor analysis of multi-excitation ultraviolet resonance Raman spectra for protein secondary structure determination”

Protein secondary structural analysis is important for understanding the relationship between protein structure and function, or more importantly how changes in structure relate to loss of function. The structurally sensitive protein vibrational modes (amide I, II, III and S) in deep-ultraviolet resonance Raman (DUVRR) spectra resulting from the backbone C–O and N–H vibrations make DUVRR a potentially powerful tool for studying secondary structure changes. Experimental studies reveal that the position and intensity of the four amide modes in DUVRR spectra of proteins are largely correlated with the varying fractions of α-helix, β-sheet and disordered structural content of proteins. Employing multivariate calibration methods and DUVRR spectra of globular proteins with varying structural compositions, the secondary structure of a protein with unknown structure can be predicted. A disadvantage of multivariate calibration methods is the requirement of known concentration or spectral profiles. Second-order curve resolution methods, such as parallel factor analysis (PARAFAC), do not have such a requirement due to the “second-order advantage.” An exceptional feature of DUVRR spectroscopy is that DUVRR spectra are linearly dependent on both excitation wavelength and secondary structure composition. Thus, higher order data can be created by combining protein DUVRR spectra of several proteins collected at multiple excitation wavelengths to give multi-excitation ultraviolet resonance Raman data (ME-UVRR). PARAFAC has been used to analyze ME-UVRR data of nine proteins to resolve the pure spectral, excitation and compositional profiles. A three factor model with non-negativity constraints produced three unique factors that were correlated with the relative abundance of helical, β-sheet and poly-proline II dihedral angles. This is the first empirical evidence that the typically resolved “disordered” spectrum represents the better defined poly-proline II type structure.     

Infrared and Raman spectra of N-acetyl-l-amino acid methylamides with aromatic side groups

Infrared and Raman spectra of N-acetyl-l-phenylalanine methylamide, N-acetyl-l-tyrosine methylamide and N-acetyl-l-tryptophan methylamide, as model compounds of aromatic amino acid residues in proteins, were measured in the solid state and in methanol solutions. Vibrational assignments of the spectra were made by utilizing the deuteration effect and by comparison with the spectra of related compounds which include toluene, p-cresol and 3-methylindole. The amide I, III and IV bands were strong in Raman scattering, but other characteristic amide bands were ill-defined. In the Raman spectra of methanol solutions, only the bands due to the aromatic side group vibrations were markedly observed, but those due to the peptide backbone vibrations were very weak, suggesting the coexistence of various molecular conformations in solution.     

Direct detection of DNA using 3D surface enhanced Raman scattering hotspot matrix

Silver nanoparticles (AgNPs) are evaporatively self‐assembled into the 3D surface enhanced Raman scattering (SERS) hotspot matrix with the assistant of glycerol to improve the spectral reproducibility in direct DNA detection. AgNPs and DNA in the glycerol‐stabilized 3D SERS hotspot matrix are found to form flexible sandwich structures through electrostatic interaction where neighboring AgNPs create uniform and homogeneous localized surface plasmon resonance coupling environments for central DNA. Nearly two orders of magnitude extra SERS enhancement, more stable peak frequency and narrower peak full width at half maximum can therefore be obtained in DNA SERS spectra, which ensures highly stable and reproducible SERS signals in direct detection of both single strand DNA and double strand DNA utilizing the 3D SERS hotspot matrix. By normalizing the SERS spectra using phosphate backbone as internal standard, identification of single base variation in oligonucleotides, determination of DNA hybridization events and recognition of chemical modification on bases (hexanethiol‐capped at 5’ end) have been demonstrated experimentally. This proposed 3D SERS hotspot matrix opens a novel perspective in manipulating plasmonic nanoparticles to construct SERS platforms and would make the surface enhanced Raman spectroscopy a more practical and reliable tool in direct DNA detection.     

Vibrational spectra of 1,2-diaminobenzene, 4,5-dimethyl-1,2-diaminobenzene and catechol and their SER spectra

The Raman and IR spectra of 1,2-diaminobenzene and 4,5-dimethyl-1,2-diaminobenzene are reported and assignments of fundamental modes proposed. The surface-enhanced Raman spectra (SERS) of catechol, 1,2-diaminobenzene and 4,5-dimethyl-1,2-diaminobenzene on gold and silver colloids were obtained. FT-SERS of the three molecules are also briefly reported.     

Multivariate evaluation of doxorubicin surface-enhanced Raman spectra

Multivariate evaluation of surface-enhanced Raman spectra of doxorubicin in plasma was performed. In a principal component analysis (PCA) all spectral features were modelled into three principal components. The major variation of the data was shown to be the variation of doxorubicin Raman signal together with the doxorubicin fluorescence, whereas the variation due to plasma was of minor importance. It was also shown that the surface-enhanced Raman scattering (SERS) measurements were independent on such factors as measurement occasion and silver colloids. The presented results show that with some improvements, quantification of doxorubicin directly in plasma could be possible.     

Vibrational study of the metal-adsorbate interaction of phenylacetic acid and alpha-phenylglycine on silver surfaces

Raman and SERS spectra of phenylacetic acid and alpha-phenylglycine on silver sols have been recorded at several concentrations and pH values. The alpha-phenylglycine has been also studied in D(2)O. The respective vibrational assignments have been proposed and the analysis of the SERS spectra has made it possible to conclude that phenylacetic acid links to the metal through its carboxylate group only, while alpha-phenylglycine links also through its amino group. In both cases the aromatic ring seems to be almost perpendicular to the metal surface. On the other hand, the contribution of the charge transfer (CT) mechanism to the enhancement of the SERS spectra has been calculated as well and it is found to be very important in both molecules. The band most enhanced by this mechanism is that of vibration 8a, mainly in alpha-phenylglycine.     

A DFT Investigation of Surface‐Enhanced Raman Scattering of Adenine and 2′‐Deoxyadenosine 5′‐Monophosphate on Ag20 Nanoclusters

We present a detailed analysis of the surface‐enhanced Raman scattering (SERS) of adenine and 2′‐deoxyadenosine 5′‐monophosphate (dAMP) adsorbed on an Ag₂₀ cluster by using density functional theory. Calculated Raman spectra show that spectral features of all complexes depend greatly on adsorption sites of adenine and dAMP. The complexes consisting of adenine adsorbed on the Ag₂₀ cluster through N3 reproduce the measured SERS spectra in silver colloids, and thus demonstrated that adenine interacts with the silver surface via N3. We also investigate the SERS spectrum of adenine at the junction between two Ag₂₀ clusters and demonstrate that adenine can bind to the clusters through N3 and the external amino group, while dAMP can be adsorbed on the cluster in an end‐on orientation with the ribose and phosphate groups near to or away from the silver cluster. In contrast to the adenine–Ag₂₀ complexes, the dAMP–Ag₂₀ complexes produce new and strong bands in the low‐ or high‐wavenumber region of the Raman spectra, due to vibrations of the ribose and phosphate groups. Furthermore, the spectrum of dAMP bound to the Ag₂₀ cluster via N7 approaches the experimental SERS spectra on silver colloids.     

Investigation of sport supplements quality by Raman spectroscopy and principal component analysis

In this work, sport supplements were investigated by Raman spectroscopy. Samples were obtained from health foods shops, gyms and sports centers covering a wide range of available supplement powders. A systematic comparison of Raman spectra of the analyzed supplements allowed identifying the supplement type through the characteristic vibrational modes of carbohydrates and proteins. The protein supplements were identified by Raman bands at 1650, 1250 and 1004 cm⁻¹, while the spectral range between 1200 and 800 cm⁻¹ was useful to identify the carbohydrate supplements. Due to the diversity in composition of sport supplements, a chemometric tool such as principal component analysis (PCA) was employed to assist in the interpretation of Raman spectra, allowing also the identification of compounds present in sport supplements. Especially, the Raman scattering of aromatic and aliphatic amino acids residues contributes to the existence of bands characteristic for the different types of proteins. This kind of information is very important for the quality control of these products, for detecting the presence of fraud or a sample composition in disagreement with the label, thus ensuring the provenance of the supplements.