Non-invasive analysis of stored red blood cells using diffuse resonance Raman spectroscopy

A method to acquire the Raman spectra of sub-surface components using diffusely focused radiation in a microscope sampling configuration is described. This procedure generates Raman scattering at various sample depths by producing a converging beam at the back aperture of the objective lens. This method requires illumination of the sample with a defocused laser, while simultaneously increasing the number of CCD pixels that are binned along the spatial axis of the detector. We applied this diffuse sampling method to the analysis of stored red blood cells (RBCs). During storage, biochemical changes to RBCs occur (the "storage lesion"). However, there are no existing non-invasive methods to assess this. We evaluated the instrumental parameters needed to maximize the diffusely scattered signal, including pixel binning, slit width, and bandwidth. We demonstrated the effectiveness of this diffuse resonance Raman spectroscopy (DRRS) method by detecting RBCs through a blood bag segment (1 mm wall thickness). We directly compared the DRRS method to the more common stand-off Raman spectroscopy (SORS) method using both 633 nm and 785 nm excitation. Time-dependent DRRS spectra were used in a multivariate model for classification of RBCs in polymer segments by storage age. Young (6-8 day) RBCs were differentiated from old (35-40) RBCs with 100% sensitivity and 98.5% selectivity. These data indicated that DRRS is a promising, non-invasive technique for acquiring the spectra of sub-surface components, and is particularly applicable when the underlying sample can be resonantly enhanced.

Characterization of Storage-Induced Red Blood Cell Hemolysis Using Raman Spectroscopy

BACKGROUND

The therapeutic efficacy and safety of stored red blood cells (RBCs) relies on minimal in-bag hemolysis. The accuracy of current methods of measuring hemolysis can suffer as a result of specimen collection and processing artefacts.

OBJECTIVE

To test whether Raman spectroscopy could be used to assess hemolysis.

METHODS

RBCs were stored for as long as 42 days. Raman spectra of RBCs were measured before and after washing, and hemolysis was measured in supernatant by visible spectroscopy.

RESULTS

Raman spectra indicated increased concentrations of oxyhemoglobin (oxyHb) and methemoglobin (metHb), and decreased membrane fluidity with storage age. Changes in oxyHb and metHb were associated with the intraerythrocytic and extracellular fractions, respectively. Hemolysis increased in a storage age-dependent manner. Changes in Raman bands reflective of oxyHb, metHb, and RBC membranes correlated with hemolysis; the most statistically significant change was an increased intensity of metHb and decreased membrane fluidity.

CONCLUSIONS

These data suggest that Raman spectroscopy may offer a new label-free modality to assess RBC hemolysis during cold storage.

A rapid and simple chemical method for the preparation of Ag colloids for surface-enhanced Raman spectroscopy using the Ag mirror reaction

Colloidal silver (Ag) nanoparticles (AgNP) have been widely used for surface-enhanced Raman spectroscopy (SERS) applications. We report a simple, rapid and effective method to prepare AgNP colloids for SERS using the classic organic chemistry Ag mirror reaction with Tollens' reagent. The AgNP colloid prepared with this process was characterized using SEM, and the reaction conditions further optimized using SERS measurements. It was found that Ag mirror reaction conditions that included 20 mM AgNO3, 5 min reaction time, and 0.5 M glucose produced AgNP colloids with an average size of 319.1 nm (s.d ±128.1). These AgNP colloids exhibited a significant SERS response when adenine was used as the reporter molecule. The usefulness of these new AgNP colloids was demonstrated by detecting the nucleotides adenosine 5'-monophosphate (AMP), guanosine 5'-monophosphate (GMP), cytidine 5'-monophosphate (CMP), and uridine 5'-monophosphate (UMP). A detection limit of 500 nM for AMP was achieved with the as-prepared AgNP colloid. The bacterium Mycoplasma pneumoniae was also easily detected in laboratory culture with these SERS substrates. These findings attest to the applicability of this AgNP colloid for the sensitive and specific detection of both small biomolecules and microorganisms.

Label-Free Detection of Glycan-Protein Interactions for Array Development by Surface-Enhanced Raman Spectroscopy (SERS)

A glyco-array platform has been developed, in which glycans are attached to plasmonic nanoparticles through strain-promoted azide-alkyne cycloaddition. Glycan-protein binding events can then be detected in a label-free manner employing surface-enhanced Raman spectroscopy (SERS). As proof of concept, we have analyzed the binding of Gal1, Gal3, and influenza hemagglutinins (HAs) to various glycans and demonstrated that binding partners can be identified with high confidence. The attraction of SERS for optical sensing is that it can provide unique spectral signatures for glycan-protein complexes, confirm identity through statistical validation, and minimizes false positive results common to indirect methods. Furthermore, SERS is very sensitive and has multiplexing capabilities thereby allowing the simultaneous detection of multiple analytes.

Detection of neuraminidase stalk motifs associated with enhanced N1 subtype influenza A virulence via Raman spectroscopy

Oligonucleotides corresponding to neuraminidase (NA) stalk motifs that have been associated with enhanced influenza virulence have been identified using surface-enhanced Raman spectroscopy (SERS). 5'-Thiolated ssDNA oligonucleotides were immobilized onto a hexadecyltrimethylammonium bromide (CTAB) coated Au nanoparticles (AuNP). Three synthetic RNA sequences corresponding to specific amino acid deletions in the influenza NA stalk region were attached to the CTAB-modified AuNPs. Two of these sequences were specific to sequences with amino acid deletions associated with increased virulence, and one was a low virulence sequence with no amino acid deletions. Hybridization of synthetic matched and mismatched DNA-RNA complexes were detected based on the intrinsic SERS spectra. In addition, this platform was used to analyze RNA sequences isolated from laboratory grown influenza viruses having the NA stalk motif associated with enhanced virulence, including A/WSN/33/H1N1, A/Anhui/1/2005/H5N, and A/Vietnam/1203/2004/H5N1 strains. Multivariate feature selection methods were employed to determine the specific wavenumbers in the Raman spectra that contributed the most information for class discrimination. A one-way analysis of variance (ANOVA) test identified 884 and 1196 wavenumbers as being highly significant in the high and low virulence spectra, respectively (p < 0.01). A post-hoc Tukey Honestly Significance Difference (HSD) test identified the wavenumbers that played a major role in differentiating the DNA-RNA hybrid classes. An estimate of the spectral variability, based on the Wilcoxon rank sum test, found the major source of variation to be predominately between the different classes, and not within the classes, thus confirming that the spectra reflected real class differences and not sampling artifacts. The multivariate classification methods partial least squares discriminant analysis (PLS-DA) and support vector machine discriminant analysis (SVM-DA) were able to distinguish between different NA stalk-motifs linked to NA-enhanced influenza virus virulence (NA-EIV) with >95% sensitivity and specificity in both synthetic RNA sequences as well as the isolated viral RNA. This study demonstrates the feasibility of SERS for direct identification of influenza NA stalk mutations associated with virulence without sample amplification or labeling.

The multivariate detection limit for Mycoplasma pneumoniae as determined by nanorod array-surface enhanced Raman spectroscopy and comparison with limit of detection by qPCR

Mycoplasma pneumoniae is a cell wall-less bacterial pathogen of the human respiratory tract that accounts for up to 20% of community-acquired pneumonia. At present, the standard for detection and genotyping is quantitative polymerase chain reaction (qPCR), which can exhibit excellent sensitivity but lacks standardization and has limited practicality for widespread, point-of-care use. We previously described a Ag nanorod array-surface enhanced Raman spectroscopy (NA-SERS) biosensing platform capable of detecting M. pneumoniae in simulated and true clinical throat swab samples with statistically significant specificity and sensitivity. We report here that differences in sample preparation influence the integrity of mycoplasma cells for NA-SERS analysis, which in turn impacts the resulting spectra. We have established a multivariate detection limit (MDL) using NA-SERS for M. pneumoniae intact-cell sample preparations. Using an adaptation of International Union of Pure and Applied Chemistry (IUPAC)-recommended methods for analyzing multivariate data sets, we found that qPCR had roughly 10× better detection limits than NA-SERS when expressed in CFU ml(-1) and DNA concentration (fg). However, the NA-SERS MDL for intact M. pneumoniae was 5.3 ± 1.0 genome equivalents (cells per μl). By comparison, qPCR of a parallel set of samples yielded a limit of detection of 2.5 ± 0.25 cells per μl. Therefore, for certain standard metrics NA-SERS provides a multivariate detection limit for M. pneumoniae that is essentially identical to that determined via qPCR.

Identification of mycobacteria based on spectroscopic analyses of mycolic acid profiles

This report examines lipophilic extracts containing mycolic acids isolated from tuberculosis (MTB) and non-tuberculosis (NTM) mycobacterial strains using chromatography, mass spectrometry (MS), nuclear magnetic resonance (NMR), and Raman spectroscopy. Gas chromatography-MS was used to identify major fatty acid mycolate components, while proton NMR confirmed the presence of characteristic cis- and trans-cyclopropane rings within different mycolic acid sub-types. Surface-enhanced Raman (SERS) spectra were obtained from the mycolic acids extracted from the bacterial cell envelopes of the MTB or NTM mycobacterial species. The Raman spectral profiles were used to develop a classification method based on chemometrics for identification of the mycobacterial species. Multivariate statistical analysis methods, including principal component analysis (PCA), hierarchical cluster analysis (HCA), and partial least squares discriminant analysis (PLS-DA) of the SERS spectra enabled differentiation of NTM mycobacteria from one another with 100% accuracy. These methods are also sensitive enough to differentiate clinically-isolated MTB strains that differed only by the presence or absence of a single extracytoplasmic sigma factor with 83-100% sensitivity and 80-100% specificity. The current work is the first report on discrimination of mycobacteria strains based on the SERS spectra of the constituent mycolic acids in lipophilic extracts. These results suggest that SERS can be used as an accurate and sensitive method for species and strain discrimination in mycobacteria.

Identification of virulence determinants in influenza viruses

To date there is no rapid method to screen for highly pathogenic avian influenza strains that may be indicators of future pandemics. We report here the first development of an oligonucleotide-based spectroscopic assay to rapidly and sensitively detect a N66S mutation in the gene coding for the PB1-F2 protein associated with increased virulence in highly pathogenic pandemic influenza viruses. 5'-Thiolated ssDNA oligonucleotides were employed as probes to capture RNA isolated from six influenza viruses, three having N66S mutations, two without the N66S mutation, and one deletion mutant not encoding the PB1-F2 protein. Hybridization was detected without amplification or labeling using the intrinsic surfaced-enhanced Raman spectrum of the DNA-RNA complex. Multivariate analysis identified target RNA binding from noncomplementary sequences with 100% sensitivity, 100% selectivity, and 100% correct classification in the test data set. These results establish that optical-based diagnostic methods are able to directly identify diagnostic indicators of virulence linked to highly pathogenic pandemic influenza viruses without amplification or labeling.

Layer-by-layer polyelectrolyte encapsulation of Mycoplasma pneumoniae for enhanced Raman detection

Mycoplasma pneumoniae is a major cause of respiratory disease in humans and accounts for as much as 20% of all community-acquired pneumonia. Existing mycoplasma diagnosis is primarily limited by the poor success rate at culturing the bacteria from clinical samples. There is a critical need to develop a new platform for mycoplasma detection that has high sensitivity, specificity, and expediency. Here we report the layer-by-layer (LBL) encapsulation of M. pneumoniae cells with Ag nanoparticles in a matrix of the polyelectrolytes poly(allylamine hydrochloride) (PAH) and poly(styrene sulfonate) (PSS). We evaluated nanoparticle encapsulated mycoplasma cells as a platform for the differentiation of M. pneumoniae strains using surface enhanced Raman scattering (SERS) combined with multivariate statistical analysis. Three separate M. pneumoniae strains (M129, FH and II-3) were studied. Scanning electron microscopy and fluorescence imaging showed that the Ag nanoparticles were incorporated between the oppositely charged polyelectrolyte layers. SERS spectra showed that LBL encapsulation provides excellent spectral reproducibility. Multivariate statistical analysis of the Raman spectra differentiated the three M. pneumoniae strains with 97-100% specificity and sensitivity, and low (0.1-0.4) root mean square error. These results indicated that nanoparticle and polyelectrolyte encapsulation of M. pneumoniae is a potentially powerful platform for rapid and sensitive SERS-based bacterial identification.

Detection of genetic markers related to high pathogenicity in influenza by SERS

We have developed a method for the detection of genetic markers associated with high pathogenicity in influenza. The assay consists of an array of 5'-thiolated ssDNA oligonucleotides immobilized on the surface of a Ag nanorod substrate that serve as capture probes for the detection of synthetic RNA sequences coding for a genetic mutation in the influenza PB1-F2 protein. Hybridization of the DNA probes to their complementary RNA sequences was detected using surface-enhanced Raman spectroscopy (SERS). Multivariate statistical analysis was used to differentiate the spectra of the complementary DNA probe-RNA target hybrids from those of the non-complementary DNA probes containing a single base pair polymorphism. Hierarchical cluster analysis (HCA) was able to distinguish with 100% accuracy the spectra of the complementary DNA probe-RNA target from the spectra of the immobilized DNA probes alone, or the DNA probes incubated with non-complementary RNA sequences. Linearity of response and limits of sensitivity of the SERS-based assays were determined using a partial least squares (PLS) regression model; detection limits computed by PLS was determined to be ~10 nM. The binding affinity of the DNA probes to their complementary RNA sequences was confirmed using enzyme-linked immunosorbent assay (ELISA); however, the detection limits observed using ELISA were approximately 10× higher (~100 nM) than those determined by PLS analysis of the SERS spectra.

Ag nanorod based surface-enhanced Raman spectroscopy applied to bioanalytical sensing

Recent progress in substrate nanofabrication has led to the development of Ag nanorod arrays as uniform, reproducible, large area SERS-active substrates with high signal enhancement. These novel nanostructures fabricated by oblique angle vapor deposition (OAD) offer a robust platform for the rapid detection of biological agents and open new perspectives for the development and integration of biomedical diagnostic for clinical and therapeutic applications. Ag nanorod arrays have been investigated as SERS-active substrates for the detection and identification of pathogens, including bacteria and viruses, as well as to evaluate the potential of this biosensing platform for bio-recognition of high affinity events using oligonucleotide-modified substrates. This review summarizes the various nanostructured substrates designed for SERS-based applications, highlights the nanofabrication methodology used to produce Ag nanorod arrays, outlines their morphological and physical properties, and provides a summary of the most recent uses of these substrates for clinical diagnostic and biomedical applications.

Direct optical detection of viral nucleoprotein binding to an anti-influenza aptamer

We have demonstrated label-free optical detection of viral nucleoprotein binding to a polyvalent anti-influenza aptamer by monitoring the surface-enhanced Raman (SERS) spectra of the aptamer-nucleoprotein complex. The SERS spectra demonstrated that selective binding of the aptamer-nucleoprotein complex could be differentiated from that of the aptamer alone based solely on the direct spectral signature for the aptamer-nucleoprotein complex. Multivariate statistical methods, including principal components analysis, hierarchical clustering, and partial least squares, were used to confirm statistically significant differences between the spectra of the aptamer-nucleoprotein complex and the spectra of the unbound aptamer. Two separate negative controls were used to evaluate the specificity of binding of the viral nucleoproteins to this aptamer. In both cases, no spectral changes were observed that showed protein binding to the control surfaces, indicating a high degree of specificity for the binding of influenza viral nucleoproteins only to the influenza-specific aptamer. Statistical analysis of the spectra supports this interpretation. AFM images demonstrate morphological changes consistent with formation of the influenza aptamer-nucleoprotein complex. These results provide the first evidence for the use of aptamer-modified SERS substrates as diagnostic tools for influenza virus detection in a complex biological matrix.

Detection of viral nucleoprotein binding to anti-influenza aptamers via SERS

A highly sensitive surface-enhanced Raman (SERS)-based method for detection of influenza viral nucleoproteins is described. The intrinsic SERS spectrum of the aptamer-nucleoprotein complex provides direct evidence of binding between a polyvalent anti-influenza aptamer and the nucleoproteins of three influenza strains.

Removal of surface contamination and self-assembled monolayers (SAMs) from silver (Ag) nanorod substrates by plasma cleaning with argon

Surface contamination of surface-enhanced Raman (SERS)-active metallic substrates has been a limitation to the utility of SERS as an analytical technique, potentially affecting surface coverage, spectral reproducibility, and analytical limits of detection. We have developed a simple and versatile cleaning method for SERS-active Ag nanorod arrays that consists of a short (4 min) exposure of the substrate to an Ar(+) plasma in a low-pressure environment. The findings presented here demonstrate that this cleaning procedure essentially eliminates organic background contamination. This procedure works equally well for self-assembled monolayers of thiolates that strongly adsorb onto Au and Ag surfaces. For SERS-active surfaces composed of arrays of Ag nanorods prepared by oblique-angle vapor deposition, we investigated the (1) Raman band intensities, (2) nanorod morphology via scanning electron microscopy, and (3) surface hydrophobicity via static contact angle measurements, as a function of exposure time of the Ag nanorods to the Ar(+) plasma. Short (4 min) exposure to Ar(+) plasma eliminated background contamination but decreased the observed SERS intensity for re-adsorbed analytes by approximately a factor of 2 while leaving the nanorod morphology essentially unchanged. Prolonged exposure to Ar(+) plasma (>10 min) resulted in substantial morphological changes of the Ag nanorod lattice and led to a decrease in the observed SERS intensities by a factor of 10. The results presented here suggest that Ar(+) plasma cleaning is an efficient process for removing carbonaceous and organic contamination as well as thiolate monolayers from SERS-active Ag surfaces, as long as the plasma conditions and exposure times are carefully monitored.

Detection of Mycoplasma pneumoniae in simulated and true clinical throat swab specimens by nanorod array-surface-enhanced Raman spectroscopy

The prokaryote Mycoplasma pneumoniae is a major cause of respiratory disease in humans, accounting for 20% of all community-acquired pneumonia and the leading cause of pneumonia in older children and young adults. The limitations of existing options for mycoplasma diagnosis highlight a critical need for a new detection platform with high sensitivity, specificity, and expediency. Here we evaluated silver nanorod arrays (NA) as a biosensing platform for detection and differentiation of M. pneumoniae in culture and in spiked and true clinical throat swab samples by surface-enhanced Raman spectroscopy (SERS). Three M. pneumoniae strains were reproducibly differentiated by NA-SERS with 95%-100% specificity and 94-100% sensitivity, and with a lower detection limit exceeding standard PCR. Analysis of throat swab samples spiked with M. pneumoniae yielded detection in a complex, clinically relevant background with >90% accuracy and high sensitivity. In addition, NA-SERS correctly classified with >97% accuracy, ten true clinical throat swab samples previously established by real-time PCR and culture to be positive or negative for M. pneumoniae. Our findings suggest that the unique biochemical specificity of Raman spectroscopy, combined with reproducible spectral enhancement by silver NA, holds great promise as a superior platform for rapid and sensitive detection and identification of M. pneumoniae, with potential for point-of-care application.

Identification of individual genotypes of measles virus using surface enhanced Raman spectroscopy

A spectroscopic assay based on surface-enhanced Raman spectroscopy (SERS) has been developed for rapid genotyping of the measles virus (MeV). Silver nanorods fabricated using an oblique angle vapor deposition method acted as the SERS-active substrate. The SERS spectra of four separate MeV genotypes, i.e. A, H1, D4 and D9, and two separate negative media control samples were analyzed using multivariate statistical methods. Principal components analysis (PCA) and hierarchical cluster analysis (HCA) successfully separated three of the four MeV genotypes studied. The MeV genotypes used in this study had >96% sequence similarity as monitored using the MeV hemagglutinin (H) gene, and the clustering seen in PCA and HCA mirrored this sequence diversity. For example, the MeV genotypes with the highest sequence diversity (~3%, A and H1) were the most widely separated in the PCA scores plot and HCA dendogram. Conversely, the MeV genotypes with the lowest sequence diversity (~0.5%, D4 and D9) could not be statistically differentiated. However, a supervised chemometric method, partial least squares-discriminant analysis (PLS-DA) was able to separate each of the four MeV strains, the two negative controls, and the background, with >90% sensitivity and >96% selectivity based solely on their inherent SERS spectra. These results demonstrate that SERS, in combination with multivariate statistical methods, is a highly sensitive and rapid viral identification and classification method that can be applied to MeV genotyping.

Rapid and sensitive detection of rotavirus molecular signatures using surface enhanced Raman spectroscopy

Human enteric virus infections range from gastroenteritis to life threatening diseases such as myocarditis and aseptic meningitis. Rotavirus is one of the most common enteric agents and mortality associated with infection can be very significant in developing countries. Most enteric viruses produce diseases that are not distinct from other pathogens, and current diagnostics is limited in breadth and sensitivity required to advance virus detection schemes for disease intervention strategies. A spectroscopic assay based on surface enhanced Raman scattering (SERS) has been developed for rapid and sensitive detection of rotavirus. The SERS method relies on the fabrication of silver nanorod array substrates that are extremely SERS-active allowing for direct structural characterization of viruses. SERS spectra for eight rotavirus strains were analyzed to qualitatively identify rotaviruses and to classify each according to G and P genotype and strain with >96% accuracy, and a quantitative model based on partial least squares regression analysis was evaluated. This novel SERS-based virus detection method shows that SERS can be used to identify spectral fingerprints of human rotaviruses, and suggests that this detection method can be used for pathogen detection central to human health care.

Quantitative surface-enhanced Raman spectroscopy based analysis of microRNA mixtures

We have developed a rapid, sensitive, and quantitative method for identification of microRNA (miRNA) sequences in multicomponent mixtures using surface-enhanced Raman spectroscopy (SERS). The method uses Ag nanorod array substrates prepared by oblique angle vapor deposition as the SERS platform. We show that Ag nanorod-based SERS spectra are uniquely characteristic for each miRNA sequence studied, and that the spectral reproducibility is sufficient for quantitative analysis of miRNA profiles in multicomponent mixtures using partial least squares (PLS) regression analysis. This method was applied to individual sample mixtures consisting of two, three, and five miRNAs. Separate PLS models were generated for the two-, three-, and five-component mixtures from >150 calibration spectra covering a concentration range of 6 to 150 microM for each miRNA. The PLS models were externally validated with independent test samples resulting in root mean square errors of prediction (RMSEP) of 7.4, <7.4, and <10 microM for the two-, three-, and five-component models, respectively. These results demonstrate the applicability of SERS for quantitative detection and profiling of miRNAs and suggest that SERS may prove to be a novel, label-free method for identification of disease biomarkers.

Structure and conformation of the disulfide bond in dimeric lung surfactant peptides SP-B1–25 and SP-B8–25

Raman spectroscopy was used to determine the conformation of the disulfide linkage between cysteine residues in the homodimeric construct of the N-terminal alpha helical domain of surfactant protein B (dSP-B(1-25)). The conformation of the disulfide bond between cysteine residues in position 8 of the homodimer of dSP-B(1-25) was compared with that of a truncated homodimer (dSP-B(8-25)) of the peptide having a disulfide linkage at the same position in the alpha helix. Temperature-dependent Raman spectra of the S-S stretching region centered at approximately 500 cm(-1) indicated a stable, although highly strained disulfide conformation with a chi(CS-SC) dihedral angle of +/-10 degrees for the dSP-B(1-25) dimer. In contrast, the truncated dimer dSP-B(8-25) exhibited a series of disulfide conformations with the chi(CS-SC) dihedral angle taking on values of either +/-30 degrees or 85+/-20 degrees . For conformations with chi(CS-SC) close to the +/-90 degrees value, the Raman spectra of the 8-25 truncated dimers exhibited chi(SS-CC) dihedral angles of 90/180 degrees and 20-30 degrees . In the presence of a lipid mixture, both constructs showed a nu(S-S) band at approximately 488 cm(-1), corresponding to a chi(CS-SC) dihedral angle of +/-10 degrees . Polarized infrared spectroscopy was also used to determine the orientation of the helix and beta-sheet portion of both synthetic peptides. These calculations indicated that the helix was oriented primarily in the plane of the surface, at an angle of approximately 60-70 degrees to the surface normal, while the beta structure had approximately 40 degrees tilt. This orientation direction did not change in the presence of a lipid mixture or with temperature. These observations suggest that: (i) the conformational flexibility of the disulfide linkage is dependent on the amino acid residues that flank the cysteine disulfide bond, and (ii) in both constructs, the presence of a lipid matrix locks the disulfide bond into a preferred conformation.

A general model-based approach to two-dimensional infrared correlation spectroscopy incorporating the global phase angle

We describe a theoretical framework for a model-based approach to two-dimensional correlation spectroscopy that is generally applicable to any arbitrary model function. The method is based on the correlation between spectral data and a set of model waveforms with a varying correlation index, the global phase angle Theta. When experimental spectral intensity variations are expressed as sinusoidal, exponential, Lorentzian, or quadratic functions, the proposed approach allows us to estimate the quantitative values of the target parameters in those expressions. In addition, this method enables us to assess the sequential order in a series of bands undergoing non-identical intensity changes in a dynamic data set. We present both simulated and experimentally obtained data that illustrate that the deviations from linearity of the absorption band intensity waveforms are clearly detected and can be quantitatively estimated using quadratic functions.

Micelle Density Regulated by a Reversible Switch of Protein Secondary Structure

Protein secondary structures may exhibit reversible transitions that occur in an abrupt and controllable manner. In this report, we demonstrate that such transitions may be utilized in the design of a "smart" protein micellar system, in which a stimulus-induced change in protein structure triggers a rapid change in micelle compacticity and size. Specifically, recombinant DNA methods were used to prepare a protein triblock copolymer containing a central hydrophilic block and two hydrophobic end blocks derived from elastin-mimetic peptide sequences. Below the copolymer inverse transition temperature (T(t)), dilute solutions of this amphiphilic protein formed monodispersed micelles in a narrow range of R(H) of approximately 100 nm. When the the temperature was raised above T(t), an abrupt increase in micelle internal density was observed with a concomitant reduction in micelle size. This reversible change in micelle compacticity was triggered by helix-to-sheet protein folding transition. Significantly, these protein polymer-based micelles, which are rapidly responsive to environmental stimuli, establish a new mechanism for the design of controlled drug delivery vehicles.

Aligned silver nanorod arrays as substrates for surface-enhanced infrared absorption spectroscopy

Preferentially aligned silver nanorod arrays prepared by oblique angle vapor deposition were evaluated as substrates for surface-enhanced infrared absorption (SEIRA) spectroscopy. These nanorod arrays have an irregular surface lattice and are composed of tilted, cylindrically shaped nanorods that have an average length of 868 nm +/- 95 nm and an average diameter of 99 nm +/- 29 nm. The overall enhancement factor for chemisorbed organic films of para-nitrobenzoic acid (PNBA) deposited onto the Ag nanorod arrays analyzed by external reflection SEIRA was calculated to be 31 +/- 9 compared to infrared reflection-absorption spectroscopy (IRRAS) obtained from a 500 nm Ag film substrate. This enhancement is attributed to the unique optical properties of the nanorod arrays as well as the increased surface area provided by the nanorod substrate. SEIRA reflection-absorbance intensity was observed with both p- and s-polarized incident radiation with angles of incidence ranging from 25 degrees to 80 degrees . The largest intensity was achieved with p-polarization and incident angles larger than 75 degrees . Polarization-dependent ultraviolet/visible/near-infrared (UV/Vis/NIR) spectra of the nanorod arrays demonstrate that the red-shifted surface plasmon peaks of the elongated nanorods may be partially responsible for the observed SEIRA response. The SEIRA detection limit for the Ag nanorod arrays was estimated to be 0.08 ng/cm(2). Surface-enhanced Raman scattering (SERS) and SEIRA analysis of chemisorbed PNBA utilizing the same nanorod substrate is demonstrated.

Membrane-mimetic films of asymmetric phosphatidylcholine lipid bolaamphiphiles

Membrane-spanning phospholipid bolaamphiphiles either alone or as a constituent of a multicomponent lipid membrane may prove to be facile building blocks for generating robust bioactive membrane-mimetic assemblies. We have previously reported the synthesis of asymmetric dialkyl phospholipid bolaamphiphiles that contain ester linked phosphatidylcholine and amine functionalities at opposite chain ends. In this report, we describe the synthesis of phospholipid bolaamphiphiles that are conjugated to biotin via the terminal amine with or without a poly(ethylene oxide) spacer arm of varying chain length. The behavior of biotinylated bolaamphiphiles as a self-assembled monolayer at an air-water interface was characterized by epi-fluorescence microscopy and revealed that domain structure and pi-A isotherms were substantially influenced by linker type and size. Substrate bound assemblies were produced by Langmuir-Blodgett deposition onto planar substrates coated with an avidin derivatized polyelectrolyte multilayer. Significantly, external reflectance infrared spectroscopy confirmed the fabrication of bolaamphiphile thin films that display extended stability in vitro.

Polarized Surface Enhanced Raman and Absorbance Spectra of Aligned Silver Nanorod Arrays

Polarized surface-enhanced Raman scattering (SERS) and UV-vis absorbance spectra were measured for a nonplanar Ag nanorod array substrate prepared by oblique angle vapor deposition. The anisotropy of the SERS polarization was shown to differ from that of the polarized UV-vis absorbance. The maximum SERS intensity was observed in the polarization direction perpendicular to the long axis of the Ag nanorods, while the UV-vis absorbance was strongly polarized along the direction of the long axis of the nanorod array. Analysis of the polarization data showed that molecular orientation was not the cause of the anisotropic SERS scattering. Rather, the SERS anisotropy was primarily attributed to the lateral arrangement of the three-dimensional tilted nanorod lattice in which highly localized plasmon modes are created by strong electromagnetic coupling between adjacent metallic nanorods.

Hemoglobin is expressed by alveolar epithelial cells

Hemoglobin gene expression in non-erythroid cells has been previously reported in activated macrophages from adult mice and lens cells, and recent studies indicate that alveolar epithelial cells can be derived from hematopoietic stem cells. Our laboratory has now produced strong evidence that hemoglobin is expressed by alveolar type II (ATII) cells and Clara cells, the primary producers of pulmonary surfactant. ATII cells are also closely involved in innate immunity within the lung and are stem cells that differentiate into alveolar type I cells. Reverse transcriptase-PCR was used to measure the expression of transcripts from the alpha- and beta-globin gene clusters in several human and rodent pulmonary epithelial cells. Surprisingly, the two major globin mRNAs characteristic of adult erythroid precursor cells were clearly expressed in human A549 and H441 cell lines, mouse MLE-15 cells, and primary ATII cells isolated from normal rat and mouse lungs. DNA sequencing verified that these PCR products were indeed the result of specific amplification of globin gene cDNAs. These alveolar epithelial cells also expressed the corresponding hemoglobin protein subunits as determined by Western blotting, and tandem mass spectrometry sequencing was used to verify the presence of both alpha- and beta-globin polypeptides in rat primary ATII cells. The function of hemoglobin expression by cells of the pulmonary epithelium will be determined by future studies, but this novel finding could potentially have important implications for the physiology and pathology of the lung.

Analysis of photoinitiated polymerization in a membrane mimetic film using infrared spectroscopy and near-IR Raman microscopy

A method has been developed to investigate the extent of polymer cross-linking that results following in situ photopolymerization of an acrylate-functionalized phospholipid assembly adsorbed onto a stabilized, membrane-mimetic film produced from a polyelectrolyte multilayer (PEM) on polytetrafluoroethylene (PTFE) grafts. The acrylate phospholipid monomer was synthesized, prepared as a unilamellar vesicle, and fused onto closed-packed acyl chains that make up the PEM membrane-mimetic barrier on the PTFE graft. Both broad band white light and 514.5 nm laser radiation were used as excitation sources for photoinitiation; eosin Y was used as the photoinitiator. The use of 514.5 nm excitation reduced the time for maximum polymerization of the acrylate lipid from 60 min to 240 s. Infrared spectroscopy was successfully used to analyze the extent of photopolymerization in simplified model acrylate lipid systems; however, this method could not be used to analyze acrylate polymerization in heterogeneous, multicomponent PEM membrane-mimetic barriers on PTFE grafts. A near-infrared Raman microscopy method based on the ratio of the integrated areas of the CC and CN vibrations was shown to provide equivalent information to the IR method for analysis of the extent of polymerization efficiency in acrylate lipids. In addition, it proved feasible to extend this near-IR Raman method to the in situ analysis of the extent of polymerization in a stabilized acrylate lipid membrane on a PEM film in a PTFE vascular graft. This work describes a new approach for generating and analyzing the robustness of a membrane-mimetic coating on biomaterial surfaces, and may improve our ability to predict the long-term stability of polymeric membrane-mimetic films on implantable medical devices.

Structure and properties of phospholipid-peptide monolayers containing monomeric SP-B(1-25) II. Peptide conformation by infrared spectroscopy

The conformation and orientation of synthetic monomeric human sequence SP-B(1-25) (mSP-B(1-25)) was studied in films with phospholipids at the air-water (A/W) interface by polarization modulation infrared reflectance absorption spectroscopy (PM-IRRAS). Modified two-dimensional infrared (2D IR) correlation analysis was applied to PM-IRRAS spectra to define changes in the secondary structure and rates of reorientation of mSP-B(1-25) in the monolayer during compression. PM-IRRAS spectra and 2D IR correlation analysis showed that, in pure films, mSP-B(1-25) had a major alpha-helical conformation plus regions of beta-sheet structure. These alpha-helical regions reoriented later during film compression than beta structural regions, and became oriented normal to the A/W interface as surface pressure increased. In mixed films with 4:1 mol:mol acyl chain perdeuterated 1,2-dipalmitoyl-sn-glycero-3-phosphocholine/1,2-dioleoyl-sn-glycero-3-[phospho-rac-(1-glycerol)] (sodium salt) (DPPC-d(62):DOPG), the IR spectra of mSP-B(1-25) showed that a significant, concentration-dependent conformational change occurred when mSP-B(1-25) was incorporated into a DPPC-d(62):DOPG monolayer. At an mSP-B(1-25) concentration of 10 wt.%, the peptide assumed a predominantly beta-sheet conformation with no contribution from alpha-helical structures. At lower, more physiological peptide concentrations, 2D IR correlation analysis showed that the propensity of mSP-B(1-25) to form alpha-helical structures was increased. In phospholipid films containing 5 wt.% mSP-B(1-25), a substantial alpha-helical peptide structural component was observed, but regions of alpha and beta structure reoriented together rather than independently during compression. In films containing 1 wt.% mSP-B(1-25), peptide conformation was predominantly alpha-helical and the helical regions reoriented later during compression than the remaining beta structural components. The increased alpha-helical structure of mSP-B(1-25) demonstrated here by PM-IRRAS and 2D IR correlation analysis in monolayers of 4:1 DPPC:DOPG containing 1 wt.% (and, to a lesser extent, 5 wt.%) peptide may be relevant for the formation of the intermediate order 'dendritic' surface phase observed in similar surface films by epi-fluorescence.

Characterization of the Low-Energy Electronic Excited States of Benzoyl-Substituted Ruthenocenes

Electronic absorption and resonance Raman spectral studies of benzoylruthenocene (BRc) and 1,1'-dibenzoylruthenocene (DRc) indicate that the low-energy electronic excited states of these 4d(6) metallocenes possess metal-to-ligand charge transfer (MLCT) character. While this MLCT contribution should weaken the metal-ring bonding in the excited state, neither compound is photosensitive in nonhalogenated solvents such as methanol, acetonitrile, and cyclohexane. In contrast, irradiating BRc and DRc in the good electron-accepting solvent, carbon tetrachloride, results in ring loss via a pathway that appears to originate from a charge-transfer-to-solvent excited state. Both metallocenes function as photoinitiators for the anionic polymerization of ethyl 2-cyanoacrylate, and the kinetics and mechanism of this process have been investigated. Comparing the present results on BRc and DRc with those reported earlier for the corresponding benzoyl-substituted ferrocene compounds reveals some interesting commonalities and differences between the excited-state properties of these 3d and 4d metallocenes.

Structure and properties of phospholipid–peptide monolayers containing monomeric SP-B1–25

Epifluorescence microscopy was used to study the structure and phase behavior of phospholipid films containing a human-sequence monomeric SP-B(1-25) synthetic peptide (mSP-B(1-25)). Measurements were done directly at the air-water (A/W) interface on films in a Langmuir-Whilhelmy balance coupled to a fluorescence microscope and real-time detection system to yield an approximate optical resolution of 1 mum. Fluorescence was achieved by laser excitation of 2-(4,4-difluoro-5,7-dimethyl-4-bora-3a,4a-diaza-s-indacene-3-dodecanoyl)-1-hexadecanoyl-sn-glycero-3-PC (BODIPY-PC, concentration </=1 mol%). The presence of mSP-B(1-25) in films of 4:1 (mol/mol) 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC)/1,2-dioleoyl-sn-glycero-3-[phospho-rac-(1-glycerol)] (sodium salt) (DOPG) had a substantial effect on lipid morphology and phase behavior that depended on both surface pressure and peptide concentration (10, 5, and 1 wt.%). The mSP-B(1-25) peptide tended to fluidize phospholipid monolayers based on expanded molecular areas and reduced collapse pressures. In addition, epifluorescence measurements revealed the formation of solid-phase domains apparent as three-armed counterclockwise spirals separated from regions of fluid liquid-expanded phase domains in compressed phospholipid-peptide films. The appearance of these separated solid-phase domains resembled pure L-DPPC rather than the ensemble-type solid domains found in films of DPPC/DOPG alone and were most apparent when 10 wt.% mSP-B(1-25) was present. In contrast, films containing lower, more physiological mSP-B(1-25) contents of 5 and 1 wt.% exhibited a prominent intermediate 'dendritic' phase that increased in extent as surface pressure was raised. This phase was characterized by branching structures that formed a lattice-like mesh network with fluorescence intensities between a dye-depleted solid domain and a dye-enriched liquid phase. These results indicate that mSP-B(1-25) at near-physiological levels produces morphological changes in phospholipid monolayers analogous to those observed for native SP-B(1-79).

Deacylated pulmonary surfactant protein SP-C transforms from alpha-helical to amyloid fibril structure via a pH-dependent mechanism: an infrared structural investigation

Bovine pulmonary surfactant protein C (SP-C) is a hydrophobic, alpha-helical membrane-associated lipoprotein in which cysteines C4 and C5 are acylated with palmitoyl chains. Recently, it has been found that the alpha-helix form of SP-C is metastable, and under certain circumstances may transform from an alpha-helix to a beta-strand conformation that resembles amyloid fibrils. This transformation is accelerated when the protein is in its deacylated form (dSP-C). We have used infrared spectroscopy to study the structure of dSP-C in solution and at membrane interfaces. Our results show that dSP-C transforms from an alpha-helical to a beta-type amyloid fibril structure via a pH-dependent mechanism. In solution at low pH, dSP-C is alpha-helical in nature, but converts to an amyloid fibril structure composed of short beta-strands or beta-hairpins at neutral pH. The alpha-helix structure of dSP-C is fully recoverable from the amyloid beta-structure when the pH is once again lowered. Attenuated total reflectance infrared spectroscopy of lipid-protein monomolecular films showed that the fibril beta-form of dSP-C is not surface-associated at the air-water interface. In addition, the lipid-associated alpha-helix form of dSP-C is only retained at the surface at low surface pressures and dissociates from the membrane at higher surface pressures. In situ polarization modulation infrared spectroscopy of protein and lipid-protein monolayers at the air-water interface confirmed that the residual dSP-C helix conformation observed in the attenuated total reflectance infrared spectra of transferred films is randomly or isotropically oriented before exclusion from the membrane interface. This work identifies pH as one of the mechanistic causes of amyloid fibril formation for dSP-C, and a possible contributor to the pathogenesis of pulmonary alveolar proteinosis.

Effect of hydrophobic surfactant proteins SP-B and SP-C on binary phospholipid monolayers: II. Infrared external reflectance-absorption spectroscopy

In situ external reflection infrared spectroscopy at the air-water interface was used to study the influence on phospholipid structure of an endogenous mixture of the two hydrophobic surfactant proteins, SP-B and SP-C, which are thought to play pivotal roles in the adsorption and function of pulmonary surfactant. Mixtures studied were 1:1, 2:1, and 7:1 (mol:mol) DPPC-d(62):DPPG, and 7:1 DPPC-d(62):DOPG, alone and in the presence of 0.5-10 wt % mixed SP-B/C purified chromatographically from calf lung surfactant extract. Perdeuteration of DPPC produced a shift in vibrational frequencies so that it could be differentiated spectroscopically from the phosphoglycerol component in the surface monolayer. CH(2) antisymmetric and symmetric stretching bands ( approximately 2920 and 2852 cm(-1)) along with the analogous CD(2) stretching bands ( approximately 2194 and 2089 cm(-1)) were analyzed, and band heights and peak wavenumber positions were assessed as a function of monolayer surface pressure. Small, near-physiological contents of 1-2 wt % SP-B/C typically produced the maximum observed spectroscopic effects, which were abolished at high protein contents of 10 wt %. Analysis of CH(2) and CD(2) stretching bands and C-H/C-D band height ratios indicated that SP-B/C affected PC and PG lipids differently within the surface monolayer. SP-B/C had preferential interactions with DPPG in 1:1, 2:1, and 7:1 DPPC-d(62):DPPG films that increased its acyl chain order. SP-B/C also interacted specifically with DOPG in 7:1 DPPC-d(62):DOPG monolayers, but in this case an increase in CH(2) band heights and peak wavenumber positions indicated a further disordering of the already fluid DOPG acyl chains. CD(2) band height and peak wavenumber analysis indicated that SP-B/C had no significant effect on the structure of DPPC-d(62) chains in 7:1 films with DPPG or DOPG, and had only a slight tendency to increase the acyl chain order in 1:1 films of DPPC-d(62):DPPG. SP-B/C had no significant effect on DPPC-d(62) structure in films with DOPG. Infrared results also indicated that interactions involving SP-B/C and lipids led to exclusion of PC and PG lipids from the compressed interfacial monolayer, in agreement with our previous report on the phase morphology of lipid monolayers containing 1 wt % SP-B/C.

Effect of hydrophobic surfactant protein SP-C on binary phospholipid monolayers. Molecular machinery at the air/water interface

Fluorescent and modified dark-field microscopies were used to investigate the phase behavior of physiologically relevant lipid/protein monomolecular films containing surfactant protein C(SP-C). Synthetic human SP-C(1-34) was labeled at its N-terminus using the fluorescent probe 6-(((4(4,4-difluoro-5-(2-thienyl)-4-bora-3a,4a-diaza-s-indacene-3-yl)phenoxy)acetyl)amino)hexanoic acid (BODIPY/TR-X). Using dual fluorescent labeling (lipid and protein) in the monolayers, we have correlated (at physiologically small concentrations of the protein) the lipid phase separation and protein distribution in situ. A comparison of the lipid and protein dye fluorescent micrographs indicates that SP-C(1-34) is preferentially associated with the disordered lipid phase. Three concepts arise from our results. (1) The presence of SP-C alone does not result in the complete dissolution of condensed phase domains in a fashion that we have previously reported for the entire hydrophobic surfactant protein (SP-B/C) fraction (Biophys. J. 77 (1999) 903). Rather, the use of relatively high amounts ( approximately 10 wt.%) of the labeled SP-C protein is needed to reproduce the fluorescence monolayer morphology previously observed for small concentrations ( approximately 1 wt.%) of the natural SP-B/C mixture. (2) Scattered light, dark-field microscopy performed using grazing angle laser illumination reveals the presence of surface-associated, three-dimensional (3D) structures of micrometer-sized dimensions when the labeled BODIPY/TR-X:SP-C(1-34) protein is included in the monolayer, as previously observed with the naturally isolated SP-B/C mixture. The 3D structures are associated exclusively with the presence of the SP-C protein in disordered monolayer phases. (3) To explain these results, we have derived a molecular model accounting for the structure and physico-chemical properties of the SP-C protein in terms of its energetics. The molecular events involved in the SP-C-mediated production of the 3D surface particles are explained using the analogy of a simple molecular machine, namely a loaded spring. This interpretation is supported by an energetic analysis that suggests the major factor contributing to the formation of the 3D particles is the energy liberated by re-expansion of the surrounding phospholipid film into the area vacated by the SP-C protein as it re-orients away from the surface.

Effect of hydrophobic surfactant proteins SP-B and SP-C on phospholipid monolayers. Protein structure studied using 2D IR and beta correlation analysis

We have applied two-dimensional infrared (2D IR) and betanu correlation spectroscopy to in-situ IR spectroscopy of pulmonary surfactant proteins SP-B and SP-C in lipid-protein monolayers at the air-water interface. For both SP-B and SP-C, a statistical windowed autocorrelation method identified two separate surface pressure regions that contained maximum amide I intensity changes: 4-25 mN/m and 25-40 mN/m. For SP-C, 2D IR and betanu correlation analyses of these regions indicated that SP-C adopts a variety of secondary structure conformations, including alpha-helix, beta-sheet, and an intermolecular aggregation of extended beta-sheet structure. The main alpha-helix band split into two peaks at high surface pressures, indicative of two different helix conformations. At low surface pressures, all conformations of the SP-C molecule reacted identically to increasing surface pressure and reoriented in phase with each other. Above 25 mN/m, however, the increasing surface pressure selectively affected the coexisting protein conformations, leading to an independent reorientation of the protein conformations. The asynchronous 2D IR spectrum of SP-B showed the presence of two alpha-helix components, consistent with two separate populations of alpha-helix in SP-B-a hydrophobic fraction associated with the lipid chains and a hydrophilic fraction parallel to the membrane surface. The distribution of correlation intensity between the two alpha-helix cross peaks indicated that the more hydrophobic helix fraction predominates at low surface pressures whereas the more hydrophilic helix fraction predominates at high surface pressures. The different SP-B secondary structures reacted identically to increasing surface pressure, leading to a reorientation of all SP-B subunits in phase with one another.

Structures of yeast vesicle trafficking proteins

In protein transport between organelles, interactions of v- and t-SNARE proteins are required for fusion of protein-containing vesicles with appropriate target compartments. Mammalian SNARE proteins have been observed to interact with NSF and SNAP, and yeast SNAREs with yeast homologues of NSF and SNAP proteins. This observation led to the hypothesis that, despite low sequence homology, SNARE proteins are structurally similar among eukaryotes. SNARE proteins can be classified into two groups depending on whether they interact with SNARE binding partners via conserved glutamine (Q-SNAREs) or arginine (R-SNAREs). Much of the published structural data available is for SNAREs involved in exocytosis (either in yeast or synaptic vesicles). This paper describes circular dichroism, Fourier transform infrared spectroscopy, and dynamic light scattering data for a set of yeast v- and t-SNARE proteins, Vti1p and Pep12p, that are Q-SNAREs involved in intracellular trafficking. Our results suggest that the secondary structure of Vti1p is highly alpha-helical and that Vti1p forms multimers under a variety of solution conditions. In these respects, Vti1p appears to be distinct from R-SNARE proteins characterized previously. The alpha-helicity of Vti1p is similar to that of Q-SNARE proteins characterized previously. Pep12p, a Q-SNARE, is highly alpha-helical. It is distinct from other Q-SNAREs in that it forms dimers under many of the solution conditions tested in our experiments. The results presented in this paper are among the first to suggest heterogeneity in the functioning of SNARE complexes.