Evaluation of enzymatic activity on nanoscale polystyrene-block-polymethylmethacrylate diblock copolymer domains

Understanding structural and functional changes of polymeric surface-bound proteins is extremely important as polymers play an increasingly significant role as arrays and substrates in proteomics applications. We carried out, for the first time, quantitative activity measurements of horseradish peroxidase (HRP) enzymes immobilized selectively on the polystyrene domains of microphase-separated polystyrene-block-polymethylmethacrylate ultrathin films. The specific enzymatic activity of HRP adsorbed on the diblock copolymer surface was evaluated and compared to that of HRP in free solution. We demonstrate that the polymeric surface-bound HRP molecules maintain approximately 85% of their activity in free solution. The unique advantages of diblock copolymer templates, involving nanoscale self-assembly and largely retained protein functionality, make the spontaneously constructed enzyme nanoarrays highly suitable as proteomics substrates. Our novel assembly method of providing functional enzymes on diblock copolymer thin films can be greatly beneficial for high-throughput and high-density protein assays.     

Measurement of cell migration on surface-bound fibronectin gradients

A novel technique for the quantitative observation of cell migration along linear gradient substrates functionalized with adhesive proteins is presented. Gradients of the cell adhesion molecule fibronectin are generated by the cross diffusion of functionalizable alkanethiols on gold and characterized by X-ray photoelectron spectroscopy and surface plasmon resonance. Two distinct migration assays are described that characterize the movement of either sparsely populated noncontacting cells or a confluent monolayer of cells into free space. The drift speed of bovine aortic endothelial cells is measured and shown to increase along a fibronectin gradient when compared to a uniform control substrate using both assays. The results of these experiments establish reproducible conditions for studies of cell migration on gradients of surface-bound ligands.     

Direct Comparison of Lysine versus Site-Specific Protein Surface Immobilization in Single-Molecule Mechanical Assays**

Single-molecule force spectroscopy (SMFS) is powerful for studying folding states and mechanical properties of proteins, however, it requires protein immobilization onto force-transducing probes such as cantilevers or microbeads. A common immobilization method relies on coupling lysine residues to carboxylated surfaces using 1-ethyl-3-(3-dimethyl-aminopropyl) carbodiimide and N-hydroxysuccinimide (EDC/NHS). Because proteins typically contain many lysine groups, this strategy results in a heterogeneous distribution of tether positions. Genetically encoded peptide tags (e.g., ybbR) provide alternative chemistries for achieving site-specific immobilization, but thus far a direct comparison of site-specific vs. lysine-based immobilization strategies to assess effects on the observed mechanical properties was lacking. Here, we compared lysine- vs. ybbR-based protein immobilization in SMFS assays using several model polyprotein systems. Our results show that lysine-based immobilization results in significant signal deterioration for monomeric streptavidin-biotin interactions, and loss of the ability to correctly classify unfolding pathways in a multipathway Cohesin-Dockerin system. We developed a mixed immobilization approach where a site-specifically tethered ligand was used to probe surface-bound proteins immobilized through lysine groups, and found partial recovery of specific signals. The mixed immobilization approach represents a viable alternative for mechanical assays on in vivo-derived samples or other proteins of interest where genetically encoded tags are not feasible.     

Activity study of self-assembled proteins on nanoscale diblock copolymer templates

Novel methods for affixing functional proteins on surfaces with high areal density have the potential to promote basic biological research as well as various bioarray applications. The use of polymeric templates under carefully balanced thermodynamic conditions enables spontaneous, self-assembled protein immobilization on surfaces with spatial control on the nanometer scale. To assess the full potential of such nanometer-scale protein platforms in biosensing applications, we report for the first time the biological activity of proteins on diblock copolymer platforms. We utilized horseradish peroxidase, mushroom tyrosinase, enhanced green fluorescent protein, bovine immunoglobulin G, fluorescein isothiocyanate conjugated anti-bovine IgG, and protein G as model systems in our protein activity studies. When specific catalytic functions of HRP and MT, immobilized on selective domains of microphase-separated PS-b-PMMA, are evaluated over a long period of time, these enzymes retain their catalytic activity and stability for well over 3 months. By performing confocal fluorescence measurements of self-fluorescing proteins and interacting protein/protein systems, we have also demonstrated that the binding behavior of these proteins is unaffected by surface immobilization onto PS-b-PMMA diblock copolymer microdomains. Our polymer platforms provide highly periodic, high-density, functional, stable surface-bound proteins with spatial control on the nanometer scale. Therefore, our diblock copolymer-guided protein assembly method can be extremely beneficial for high-throughput proteomic applications.     

Aptamer‐Based SERS Assay of ATP and Lysozyme by Using Primer Self‐Generation

A simple bifunctional surface‐enhanced Raman scattering (SERS) assay based on primer self‐generation strand‐displacement polymerization (PS‐SDP) is developed to detect small molecules or proteins in parallel. Triphosphate (ATP) and lysozyme are used as the models of small molecules and proteins. Compared to traditional bifunctional methods, the method possesses some remarkable features as follows: 1) by virtue of the simple PS‐SDP reaction, a bifunctional aptamer assembly binding of trigger 1 and trigger 2 was used as a functional structure for the simultaneous sensing of ATP or lysozyme. 2) The concept of isothermal amplification bifunctional detection has been first introduced into SERS biosensing applications as a signal‐amplification tool. 3) The problem of high background induced by excess bio‐barcodes is circumvented by using magnetic beads (MBs) as the carrier of signal‐output products and massive of hairpin DNA binding with SERS active bio‐barcodes relied on Au nanoparticles (Au NPs), SERS signal is significantly enhanced. Overall, with multiple amplification steps and one magnetic‐separation procedure, this flexible biosensing system exhibited not only high sensitivity and specificity, with the detection limits of ATP and lysozyme of 0.05 nM and 10 fM , respectively.     

基于分子印迹与表面增强拉曼散射的蛋白质疾病标志物检测研究进展

异常的蛋白质表达与疾病的发生与发展密切相关,因此蛋白质已作为疾病标志物广泛应用于疾病的早期诊断、治疗监测和预后评估.然而,临床样本中的蛋白质疾病标志物通常含量极低,并存在高丰度的基质干扰,对检测方法的特异性和灵敏度提出挑战.目前,蛋白质疾病标志物的检测方法主要是免疫分析.但是,免疫分析主要依赖抗体进行特异性识别,而抗体...     

Influence of antibody immobilization strategy on molecular recognition force microscopy measurements

A systematic evaluation of the effects of antibody immobilization strategy on the binding efficiency and selectivity (e.g., ability to distinguish between specific and nonspecific interactions) of immunosurfaces prepared with F(ab') antibody fragments of rabbit Immunoglobulin G (IgG) is described. F(ab') was attached to gold surfaces either (1) directly via the formation of a gold-thiolate bond or (2) indirectly through a series of a bifunctional linkers containing an alkane chain or ethylene glycol spacer. Immobilization of F(ab') via the sulfhydryl reactive group located opposite the antigen binding site ensured optimum orientation of the antigen binding site. X-ray photoelectron spectroscopy (XPS) and surface plasmon resonance (SPR) were used to confirm surface modification with the bifunctional linkers and antibody immobilization, respectively. Binding efficiency assays performed with SPR indicated that increasing the length of the linker increased the antigen binding efficiency. Atomic force microscopy (AFM) adhesion force measurements indicated that AFM probes functionalized with directly immobilized F(ab') more effectively discriminated between specific and nonspecific surface-bound proteins than probes modified indirectly via linker-immobilized F(ab'). In addition, a greater number of antibody-antigen binding events were observed with directly immobilized F(ab')-functionalized probes.     

Inhibition assay of yeast cell walls by plasmon resonance Rayleigh scattering and surface-enhanced Raman scattering imaging

We report on plasmon resonance Rayleigh scattering (PRRS) and surface enhanced Raman scattering (SERS) imaging for inhibition assay of yeast cell walls. This assay reveals that the proteins having alkali sensitive linkage bound to β1,3 glucan frameworks in cell walls are involved in SERS activity. The result is further confirmed by comparison of genetically modified cells and wild type cells. Finally, we find that PRRS and SERS spots do not appear on cell walls when daughter cells are enough smaller than parent ones, but appear when size of daughter cells are comparable to parent cells. This finding indicates the relationship between expression of the proteins that generate SERS spots and cell division. These results demonstrate that PRRS and SERS imaging can be a convenient and sensitive method for analysis of cell walls.     

Detection of proteins on silica-silver core-shell substrates by surface-enhanced Raman spectroscopy

We have employed the proposed Silica-Silver Core-Shell (SSCS) SERS-active substrates to detect four model proteins: lysozyme (a protein without chromophore), cytochrome c (a protein with chromophore of heme), fluorescein isothiocyanate (FITC)-anti human IgG (labeled with FITC) and atto610-biotin/avidin (recognition with labeled small molecules). SERS spectra of these proteins and Raman labels on the SSCS substrates show both high sensitivity and reproducibility, which are due to electromagnetic SERS enhancement with additional localization field within closely packed Ag nanoparticles decorated on the SiO(2) nanoparticles and the aggregation of SiO(2)@Ag particles. We have found that the SERS intensities of atto610-biotin/avidin adsorbed on the SSCS substrates are about 20 times stronger than those from Ag plating on Au-decorated substrate. Moreover, the broad surface plasmon resonance (SPR) of the proposed substrates will extend SERS applications to more biological molecules with different laser excitations.     

Differential SERS activity of gold and silver nanostructures enabled by adsorbed poly(vinylpyrrolidone)

We report that poly(vinylpyrrolidone) (PVP), a common stabilizer of colloidal dispersions of noble metal nanostructures, has a dramatic effect on their surface-enhanced Raman scattering (SERS) activity and enables highly selective SERS detection of analytes of various type and charge. Nanostructures studied include PVP-stabilized Au-Ag nanoshells synthesized by galvanic exchange reaction of citrate-reduced Ag nanoparticles (NPs), as well as solid citrate-reduced Ag and Au NPs, both before and after stabilization with PVP. All nanostructures were characterized in terms of their size, surface plasmon resonance wavelength, surface charge, and chemical composition. While the SERS activities of the parent citrate-reduced Ag and Au NPs are similar for rhodamine 6G (R6G) and 1,2-bis(4-pyridyl)ethylene (BPE) at various pH values, PVP-stabilized nanostructures demonstrate large differences in SERS enhancement factors (EFs) between these analytes depending on their chemical nature and protonation state. At pH values higher than BPE's pK(a2) of 5.65, where the analyte is largely unprotonated, the PVP-coated Au-Ag nanoshells showed a high SERS EF of >10(8). In contrast, SERS EFs were 10(3)- to 10(5)-fold lower for the protonated form of BPE at lower pH values, or for the usually highly SERS-active cationic R6G. The differential SERS activity of PVP-stabilized nanostructures is a result of discriminatory binding of analytes within-adsorbed PVP monolayer and a subsequent increase of analyte concentration at the nanostructure surface. Our experimental and theoretical quantum chemical calculations show that BPE binding with PVP-stabilized Au-Ag nanoshells is stronger when the analyte is in its unprotonated form as compared to its cationic, protonated form at a lower pH.     

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.     

Distance-Dependent Metal-Enhanced Intrinsic Fluorescence of Proteins Using Polyelectrolyte Layer-by-Layer Assembly and Aluminum Nanoparticles

Previously reported studies indicate that aluminum nanostructured substrates can potentially find widespread use in metal-enhanced fluorescence (MEF) applications particularly in the UV or near-UV spectral region toward label-free detection of biomolecules. MEF largely depends on several factors, such as chemical nature, size, shape of the nanostructure and its distance from the fluorophore. A detailed understanding of the MEF and its distance-dependence are important for its potential application in biomedical sensing. Our goal is to utilize intrinsic protein fluorescence for label-free binding assays. This is made possible by the use of metallic nanostructures which provide localized excitation and enhanced fluorescence of UV fluorophores and will also provide a way to separate the surface-bound proteins from the bulk samples. We evaluated varied probe distances from plasmonic nanostructures by the well-established layer-by-layer (LbL) technique. The investigated proteins were adsorbed on different numbers of alternate layers of poly(styrene sulfonate) (PSS) and poly(allylamine hydrochloride) (PAH). Bovine serum albumin (BSA) was electrostatically attached to the positively charged PAH layer, and goat and rabbit IgG were attached to negatively charged PSS layer. We obtained a maximum of a ~ 9 fold increase in fluorescence intensity from BSA at a distance of ~9 nm from the Al nanostructured surface. Approximately 6- and 7- fold increases were observed from goat and rabbit IgG at a distance of ~8 nm, respectively. The minimum lifetimes were about 3-fold shorter than those on bare control quartz slides for all three proteins. The time-resolved intensity decays were analyzed with a lifetime distribution model to understand the distance effect on the metal-fluorophore interaction in detail. The present study indicates the distance dependence nature of metal-enhanced intrinsic fluorescence of proteins and potential of LbL assembly to control the metal-to-fluorophore distance in the UV wavelength region.     

Control of specific attachment of proteins by adsorption of polymer layers

This study concerns the design of protein-resistant polymer adsorbed layers for the control of surface binding of biospecific recognition entities. Polymer surface layers were prepared using the adsorption of poly(allylamine hydrochloride) (PAH), poly(l-lysine) (PL), and branched and linear polyethyleneimine (PEI) and further modified by the covalent attachment of biotin for specific avidin attachment. The adsorption of PAH, PL, and PEI on silicon substrates was studied as a function of pH and ionic strength using ellipsometry. Average dry layer thicknesses of approximately 10, approximately 5, approximately 9, and approximately 3 A (+/-1 A) were obtained when polymer adsorption occurred from solutions at pH 9.5 that contained 0.5 M NaCl for PAH, PL, branched PEI, and linear PEI, respectively. These polymers showed significant differences in their efficiency to suppress nonspecific avidin adsorption. At low ionic strength, avidin adsorption occurred on all polymer-coated surfaces at basic pH values, despite the same positive electrostatic charge for protein globules and the surface. Though the net electrostatic repulsion between avidin molecules and branched PEI was efficiently screened in a protein solution of pH 7 and 0.15 M NaCl, branched-PEI coatings of high molecular weight were unique in their ability to provide avidin-resistant surfaces as a result of steric hindrance from the branched architecture of adsorbed polymer chains. All polymers studied were effective in suppressing avidin adsorption at pH 3 as a result of protonation of the avidin surface functional groups at this pH. Branched-PEI-coated surfaces were also effective for the suppression of smaller positively charged proteins such as lysozyme and ribonuclease A at pH 7 and 0.15 M NaCl. They were also resistant to the adsorption of negatively charged proteins such as BSA and fibrinogen at pH 7 and 0.75 M NaCl. Furthermore, by using PEI-modified protein-repellent surfaces, selective binding of avidin was achieved to surface-bound silver nanoparticles, which should provide a promising application for the label-free detection of biological species using surface-enhanced Raman scattering (SERS).     

Label-free and direct protein detection on 3D plasmonic nanovoid structures using surface-enhanced Raman scattering

In this paper we use surface-enhanced Raman spectroscopy (SERS) on 3D metallic structures for label-free detection and characterization of proteins of interest at low concentrations. The substrates are prepared via nanopatterning with latex nano/microparticles and Cr and Ag sputtering, yielding stable, tunable, and mechanically flexible plasmonic structures. The nanovoids generate a SERS signal of the proteins of interest that is background free and independent of the protein charge. Concentrations as low as 0.05 μg mL⁻¹ could be detected for 4 different proteins. The proteins also exhibit significantly different SERS spectra on these substrates, which is an important feature for future label-free direct detection schemes.     

Surface tailoring for controlled protein adsorption: effect of topography at the nanometer scale and chemistry

Protein adsorption behavior is at the heart of many of today's research fields including biotechnology and materials science. With understanding of protein-surface interactions, control over the conformation and orientation of immobilized species may ultimately allow tailor-made surfaces to be generated. In this contribution protein-surface interactions have been examined with particular focus on surface curvature with and without surface chemistry effects. Silica spheres with diameters in the range 15-165 nm with both hydrophilic and hydrophobic surface chemistries have been used as model substrates. Two proteins differing in size and shape, bovine serum albumin (BSA) and bovine fibrinogen (Fg), have been used in model studies of protein binding with detailed secondary structure analysis being performed using infrared spectroscopy (IR) on surface-bound proteins. Although trends in binding affinity and saturation values were similar for both proteins, albumin is increasingly less ordered on larger substrates, while fibrinogen, in contrast, loses secondary structure to a greater extent when adsorbing onto particles with high surface curvature. These effects are compounded by surface chemistry, with both proteins becoming more denatured on hydrophobic surfaces. Both surface chemistry and topography play key roles in determining the structure of the bound proteins. A model of the binding characteristics of these two proteins onto surfaces having differing curvature and chemistry is presented. We propose that properties of an adsorbed protein layer may be guided through careful consideration of surface structure, allowing the fabrication of materials/surface coatings with tailored bioactivity.     

A genetic approach for controlling the binding and orientation of proteins on nanoparticles

Although silver nanoparticles are excellent surface enhancers for Raman spectroscopy, their use to probe the conformation of large proteins at interfaces has been complicated by the fact that many polypeptides adsorb weakly or with a random orientation to colloidal silver. To address these limitations, we sought to increase binding affinity and control protein orientation by fusing a silver-binding dodecapeptide termed Ag4 to the C-terminus of maltose-binding protein (MBP), a well-characterized model protein with little intrinsic silver binding affinity. Quartz crystal microbalance measurements conducted with the MBP-Ag4 fusion protein revealed that its affinity for silver (Kd approximately 180 nM) was at least 1 order of magnitude higher than a control protein, MBP2, containing a non-silver-specific C-terminal extension. Under our experimental conditions, MBP-Ag4 SERS spectra exhibited 2-4 fold higher signal-to-background relative to MPB2 and contained a number of amino acid-assigned vibrational modes that were either weak or absent in control experiments performed with MBP2. Changes in amino acid-assigned peaks before and after MBP-Ag4 bound maltose were used to assess protein orientation on the surface of silver nanoparticles. The genetic route described here may prove useful to study the orientation of other proteins on a variety of SERS-active surfaces, to improve biosensors performance, and to control functional nanobiomaterials assembly.     

Chemical Strategies for Dendritic Magneto-plasmonic Nanostructures Applied to Surface-Enhanced Raman Spectroscopy

Chemical analyses in the field using surface-enhanced Raman scattering (SERS) protocols are expected to be part of several analytical procedures applied to water quality monitoring. To date, these endeavors have been supported by developments in SERS substrate nanofabrication, instrumentation portability, and the internet of things. Here, we report distinct chemical strategies for preparing magneto-plasmonic (Fe₃O₄ : Au) colloids, which are relevant in the context of trace-level detection of water contaminants due to their inherent multifunctionality. The main objective of this research is to investigate the role of poly(amidoamine) dendrimers (PAMAMs) in the preparation of SERS substrates integrating both functionalities into single nanostructures. Three chemical routes were investigated to design magneto-plasmonic nanostructures that translate into different ways for assessing SERS detection by using distinct interfaces. Hence, a series of magneto-plasmonic colloids have been characterized and then assessed for their SERS activity by using a model pesticide (thiram) dissolved in aqueous samples.     

Surface-enhanced Raman nanoparticle beacons based on bioconjugated gold nanocrystals and long range plasmonic coupling

We have developed a new class of surface-enhanced Raman scattering beacons (SERS beacons) that can be turned on and off by long-range plasmonic coupling, induced by biomolecular recognition and binding events. The beacons are based on colloidal gold nanocrystals in two sizes (40 and 60 nm) and are prepared by spectral encoding with a Raman reporter molecule, functionalized with thiolated DNA probes, and stabilized and protected by low molecular weight poly(ethylene glycol)s (PEGs). The results show the SERS signal intensities increase by 40-200-fold when the nanoparticle beacons are activated by plasmonic coupling, much higher than the bright-to-dark intensity ratios reported for traditional molecular beacons. Multivalent gold nanoparticles also have exquisite specificity and are able to recognize single-base mismatches or mutations. This class of SERS nanoparticle beacons has novel mechanisms for molecular detection and signal amplification, and its long-range coupling nature raises new opportunities in developing plasmonic probes to detect proteins, cells, and intact viruses.     

Aromatic amino acids providing characteristic motifs in the Raman and SERS spectroscopy of peptides

Raman and surface-enhanced Raman spectroscopies (SERS) are potentially important tools in the characterization of biomolecules such as proteins and DNA. In this work, SERS spectra of three cysteine-containing aromatic peptides: tryptophan-cysteine, tyrosine-cysteine, and phenylalanine-cysteine, bound to Au nanoshell substrates, were obtained, and compared to their respective normal Raman spectra. While the linewidths of the SERS peaks are significantly broadened (up to 70%), no significant spectral shifts (<6 cm (-1)) of the major Stokes modes were observed between the two modalities. We show that the Raman and SERS spectra of penetratin, a cell-penetrating peptide oligomer, can be comprised quite reliably from the spectra of its constituent aromatic amino acids except in the backbone regions where the spectral intensities are critically dependent on the length and conformations of the probed molecules. From this study we conclude that, together with protein backbone groups, aromatic amino acid residues provide the overwhelmingly dominant features in the Raman and SERS spectra of peptides and proteins when present. It follows that the Raman modes of these three small constructed peptides may likely apply to the assignment of Raman and SERS features in the spectra of other peptides and proteins.