Probing the protein orientation on charged self-assembled monolayers on gold nanohole arrays by SERS

Cation Chain Length of Nonhalogenated Ionic Liquids Matters in Enhancing SERS of Cytochrome c on Zr-Al-Co-O Nanotube Arrays

Surface-enhanced Raman scattering (SERS) is a remarkably powerful analytical technique enabling trace-level detection of biological molecules. The interaction of a probe molecule with the SERS substrate shows important distinctions in the SERS spectra, providing inherent fingerprint information on the probe molecule. Herein, nonhalogenated phosphonium-based ionic liquids (ILs) containing cations with varying chain lengths were used as trace additives to amplify the interaction between the cytochrome c (Cyt c) and Zr-Al-Co-O (ZACO) nanotube arrays, strengthening the SERS signals. An increased enhancement factor (EF) by 2.5-41.2 times compared with the system without ILs was achieved. The improvement of the SERS sensitivity with the introduction of these ILs is strongly dependent on the cation chain length, in which the increasing magnitude of EF is more pronounced in the system with a longer alkyl chain length on the cation. Comparing the interaction forces measured by Cyt c-grafted atomic force microscopy (AFM) probes on ZACO substrates with those predicted by the extended Derjaguin-Landau-Verwey-Overbeek (XDLVO) theory, the van der Waals forces became increasingly dominant as the chain length of the cations increased, associated with stronger Cyt c-ZACO XDLVO interaction forces. The major contributing component, van der Waals force, stems from the longer cation chains of the IL, which act as a bridge to connect Cyt c and the ZACO substrate, promoting the anchoring of the Cyt c molecules onto the substrate, thereby benefiting SERS enhancement.

Deciphering the Roles of Interfacial Amino Acids in Inter-Protein Charge Transport

Elucidating charge transport (CT) through proteins is critical for gaining insights into ubiquitous CT chain reactions in biological systems and developing high-performance bioelectronic devices. While intra-protein CT has been extensively studied, crucial knowledge about inter-protein CT via interfacial amino acids is still absent due to the structural complexity. Herein, by loading cytochrome c (Cyt c) on well-defined peptide self-assembled monolayers to mimic the protein-protein interface, we provide a precisely controlled platform for identifying the roles of interfacial amino acids in solid-state CT via peptide-Cyt c junctions. The terminal amino acid of peptides serves as a fine-tuning factor for both the interfacial interaction between peptides and Cyt c and the immobilized Cyt c orientation, resulting in a nearly 10-fold difference in current through peptide-Cyt c junctions with varied asymmetry. This work provides a valuable platform for studying CT across proteins and contributes to the understanding of fundamental principles governing inter-protein CT.

Raman spectroscopy and its plasmon-enhanced counterparts: A toolbox to probe protein dynamics and aggregation

Protein unfolding and aggregation are often correlated with numerous diseases such as Alzheimer's, Parkinson's, Huntington's, and other debilitating neurological disorders. Such adverse events consist of a plethora of competing mechanisms, particularly interactions that control the stability and cooperativity of the process. However, it remains challenging to probe the molecular mechanism of protein dynamics such as aggregation, and monitor them in real-time under physiological conditions. Recently, Raman spectroscopy and its plasmon-enhanced counterparts, such as surface-enhanced Raman spectroscopy (SERS) and tip-enhanced Raman spectroscopy (TERS), have emerged as sensitive analytical tools that have the potential to perform molecular studies of functional groups and are showing significant promise in probing events related to protein aggregation. We summarize the fundamental working principles of Raman, SERS, and TERS as nondestructive, easy-to-perform, and fast tools for probing protein dynamics and aggregation. Finally, we highlight the utility of these techniques for the analysis of vibrational spectra of aggregation of proteins from various sources such as tissues, pathogens, food, biopharmaceuticals, and lastly, biological fouling to retrieve precise chemical information, which can be potentially translated to practical applications and point-of-care (PoC) devices. This article is categorized under: Therapeutic Approaches and Drug Discovery > Emerging Technologies Diagnostic Tools > Diagnostic Nanodevices Nanotechnology Approaches to Biology > Nanoscale Systems in Biology.

Chemical conjugation to differentiate monosaccharides by Raman and surface enhanced Raman spectroscopy

Sugars play important roles in numerous biological processes, from providing energy to modifying proteins to alter their function. Glycosylation, the attachment of a sugar residue to a protein, is the most common post translational modification. Identifying the glycans on a protein is a useful tool both for pharmaceutical development as well as probing the proteome and glycome further. Sugars, however, are difficult analytes to probe due to their isomeric nature. In this work, Raman spectroscopy and surface enhanced Raman spectroscopy (SERS) are used to identify different monosaccharide species based on the vibrational modes of these isomeric analytes. The weak scattering of the sugars was overcome through conjugation with phenylboronic acid to provide a larger Raman scattering cross section and induce slight changes in the observed spectra associated with the structure of the monosaccharides. Spontaneous Raman, SERS in flow, and static SERS detection were performed in order to discriminate between arabinose, fructose, galactose, glucose, mannose, and ribose, as well as provide a method for identification and quantification for these sugar conjugates.

On the Sensitivity and Affinity of Gold, Silver, and Platinum Surfaces against the SARS-CoV-2 Virus: A Comparative Computational Study

The novel coronavirus disease and its complications have motivated the design of new sensors with the highest sensitivity, and affinity for the detection of the SARS-CoV-2 virus is considered in many research studies. In this research article, we employ full atomistic molecular dynamics (MD) models to study the interactions between the receptor binding domain (RBD) and spike protein of the coronavirus and different metals such as gold (Au), platinum (Pt), and silver (Ag) to analyze their sensitivity against this virus. The comparison between the RBD interactions with ACE2 (angiotensin-converting enzyme 2) and different metals indicates that metals have remarkable effects on the structural features and dynamical properties of the RBD. The binding site of the RBD has more affinity to the surfaces of gold, platinum, and silver than to the other parts of the protein. Moreover, the initial configuration of the RBD relative to the metal surface plays an important role in the stability of metal complexes with the RBD. The binding face of the protein to the metal surface has been changed in the presence of different metals. In other words, the residues of the RBD that participate in RBD interactions with the metals are different irrespective of the initial configurations in which the [Asn, Thr, Tyr], [Ser, Thr, Tyr], and [Asn, Asp, Tyr] residues of the protein have a greater affinity to Ag, Au, and Pt, respectively. The corresponding metals have a considerable affinity to the RBD, which due to strong interactions with the protein can change the secondary structure and structural features. Based on the obtained results during the complexation process between the protein and metals, the helical structure of the protein changes to the bend and antiparallel β-sheets. The calculated binding energies for the RBD complexes with silver, gold, and platinum are -95.03, -138.03, and -133.96 kcal·mol-1, respectively. The adsorption process of the spike protein on the surfaces of different metals represents similar results and indicates that the entire spike protein of the coronavirus forms a more stable complex with the gold surface compared with other metals. Moreover, the RBD of the spike protein has more interactions with the surfaces than with the other parts of the protein. Therefore, it is possible to predict the properties of the coronavirus on the metal surface based on the dynamical behavior of the RBD. Overall, our computational results confirm that the gold surface can be considered as an outstanding substrate for developing new sensors with the highest sensitivity against SARS-CoV-2.

Molecularly imprinted electrochemical sensor for the ultrasensitive detection of cytochrome c

Cytochrome c (Cyt c) is an important biomarker for the early stage of apoptosis that plays a role in the diagnosis and therapy of several diseases including cancer. Here, an electrochemical sensor based on molecularly imprinted polymer (MIP) for the ultrasensitive detection of Cyt c is studied. It is prepared by electropolymerization of o-phenylenediamine in the presence of Cyt c as template, followed by solvent extraction, resulting in the formation of Cyt c recognition sites. The MIP is characterised by cyclic voltammetry and differential pulse voltammetry, using ferrocenecarboxylic acid as redox probe. Voltammetric data indicates that the MIP-sensor behaves as an electrode with partially blocked surface. The partition isotherm obtained fits the Langmuir model, indicating a high affinity for Cyt c, with an association constant K_a = 5 × 10 ¹¹ M^-1. DPV measurements allow to achieve extremely high analytical sensitivity and low detection limit, in the femtomolar range, with negligible unspecific adsorption. Satisfactory analytical recovery tests performed in the presence of possible interfering proteins and in diluted human serum confirmed the selectivity of the MIP-sensor as well as its potential applicability for real samples analysis.

Phosphonium-Based Ionic Liquid Significantly Enhances SERS of Cytochrome c on TiO2 Nanotube Arrays

Surface-enhanced Raman scattering (SERS) is an attractive technique for studying trace detection. It is of utmost importance to further improve the performance and understand the underlying mechanisms. An ionic liquid (IL), the anion of which is derived from biomass, [P6,6,6,14][FuA] was synthesized and used as a trace additive to improve the SERS performance of cytochrome c (Cyt c) on TiO2 nanotube arrays (TNAs). An increased and better enhancement factor (EF) by four to five times as compared to the system without an IL was obtained, which is better than that from using the choline-based amino acid IL previously reported by us. Dissociation of the ILs improved the ionic conductivity of the system, and the long hydrophobic tails of the [P6,6,6,14]+ cation contributed to a strong electrostatic interaction between Cyt c and the TNA surface, thereby enhancing the SERS performance. Atomic force microscopy did verify strong electrostatic interactions between the Cyt c molecules and TNAs after the addition of the IL. This work demonstrates the importance of introducing the phosphonium-based IL to enhance the SERS performance, which will stimulate further development of more effective ILs on SERS detection and other relevant applications in biology.

Complementary Powerful Techniques for Investigating the Interactions of Proteins with Porous TiO2 and Its Hybrid Materials: A Tutorial Review

Understanding the adsorption and interaction between porous materials and protein is of great importance in biomedical and interface sciences. Among the studied porous materials, TiO₂ and its hybrid materials, featuring distinct, well-defined pore sizes, structural stability and excellent biocompatibility, are widely used. In this review, the use of four powerful, synergetic and complementary techniques to study protein-TiO_2-based porous materials interactions at different scales is summarized, including high-performance liquid chromatography (HPLC), atomic force microscopy (AFM), surface-enhanced Raman scattering (SERS), and Molecular Dynamics (MD) simulations. We expect that this review could be helpful in optimizing the commonly used techniques to characterize the interfacial behavior of protein on porous TiO₂ materials in different applications.

Selective Separation of Highly Similar Proteins on Ionic Liquid-Loaded Mesoporous TiO2

Separating proteins from their mixtures is an important process in a great variety of applications, but it faces difficult challenges as soon as the proteins are simultaneously of similar sizes and carry comparable net charges. To develop both efficient and sustainable strategies for the selective separation of similar proteins and to understand the underlying molecular mechanisms to enable the separation are crucial. In this work, we propose a novel strategy where the cholinium-based amino acid [Cho][Pro] ionic liquid (IL) is used as the trace additive and loaded physically on a mesoporous TiO₂ surface for separating two similar proteins (lysozyme and cytochrome c). The observed selective adsorption behavior is explained by the hydration properties of the [Cho][Pro] loaded on the TiO₂ surface and their partially dissociated ions under different pH conditions. As the pH is increased from 5.0 to 9.8, the degree of hydration of IL ions also increases, gradually weakening the interaction strength of the proteins with the substrates, more for lysozymes, leading to their effective separation. These findings were further used to guide the detection of the retention behavior of a binary mixture of proteins in high-performance liquid chromatography, where the introduction of ILs did effectively separate the two similar proteins. Our results should further stimulate the use of ILs in the separation of proteins with a high degree of mutual similarity.

Molecular Mechanistic Insights into the Ionic-Strength-Controlled Interfacial Behavior of Proteins on a TiO2 Surface

By adjusting the ionic strengths through changing the concentration of the buffer ions, the molecular force and the interfacial behavior of cytochrome c (Cyt c) and TiO₂ are systematically studied. The molecular forces determined by combining the adhesion force and adsorption capacity are found to first increase and then decrease with the increasing ionic strength, with a peak obtained at an ionic strength between 0.8 and 1.0 M. The mechanism is explained based on the dissociation and hydration of ions at the interfaces, where the buffer ions could be completely dissociated at ionic strengths of <0.8 M but were partially associated when the ionic strength increased to a high value (>1.2 M), and the strongest hydration was observed around 1.0 M. The hydrodynamic size and the zeta potential value representing the effective contact area and protein stability of the Cyt c molecule, respectively, are also affected by the hydration and are proportional to the molecular forces. The interfacial behavior of Cyt c molecules on the TiO₂ surface, determined through surface-enhanced Raman scattering (SERS), is extremely affected by the ionic strength of the solution as the ion dissociation and hydration also increase the electron transfer ability, where the best SERS enhancement is observed at the ionic strength of around 1.0 M, corresponding to the largest molecular force. Our results provide a detailed understanding at the nanoscale on controlling the protein interfacial behavior with solid surfaces, adjusted by the buffer ions.

SARS-CoV-2 Receptor Binding Domain as a Stable-Potential Target for SARS-CoV-2 Detection by Surface-Enhanced Raman Spectroscopy

In this work, we report a new approach for detecting SARS-CoV-2 RBD protein (RBD) using the surface-enhanced Raman spectroscopy (SERS) technique. The optical enhancement was obtained thanks to the preparation of nanostructured Ag/Au substrates. Fabricated Au/Ag nanostructures were used in the SERS experiment for RBD protein detection. SERS substrates show higher capabilities and sensitivity to detect RBD protein in a short time (3 s) and with very low power. We were able to push the detection limit of proteins to a single protein detection level of 1 pM. The latter is equivalent to 1 fM as a detection limit of viruses. Additionally, we have shown that the SERS technique was useful to figure out the presence of RBD protein on antibody functionalized substrates. In this case, the SERS detection was based on protein-antibody recognition, which led to shifts in the Raman peaks and allowed signal discrimination between RBD and other targets such as Bovine serum albumin (BSA) protein. A perfect agreement between a 3D simulated model based on finite element method and experiment was reported confirming the SERS frequency shift potential for trace proteins detection. Our results could open the way to develop a new prototype based on SERS sensitivity and selectivity for rapid detection at a very low concentration of virus and even at a single protein level.

Hydrated Ionic Liquids Boost the Trace Detection Capacity of Proteins on TiO2 Support

Trace detection based on surface-enhanced Raman scattering (SERS) has attracted considerable attention, and exploiting efficient strategies to stretch the limit of detection and understanding the mechanisms on molecular level are of utmost importance. In this work, we use ionic liquids (ILs) as trace additives in a protein-TiO2 system, allowing us to obtain an exceptionally low limit of detection down to 10-9 M. The enhancement factors (EFs) were determined to 2.30 × 104, 6.17 × 104, and 1.19 × 105, for the three systems: one without ILs, one with ILs in solutions, and one with ILs immobilized on the TiO2 substrate, respectively, corresponding to the molecular forces of 1.65, 1.32, and 1.16 nN quantified by the atomic force microscopy. The dissociation and following hydration of ILs, occurring in the SERS system, weakened the molecular forces but instead improved the electron transfer ability of ILs, which is the major contribution for the observed excellent detection. The weaker diffusion of the hydrated IL ions immobilized on the TiO2 substrate did provide a considerably greater EF value, compared to the ILs in the solution. This work clearly demonstrates the importance of the hydration of ions, causing an improved electron transfer ability of ILs and leading to an exceptional SERS performance in the field of trace detection. Our results should stimulate further development to use ILs in SERS and related applications in bioanalysis, medical diagnosis, and environmental science.

Recent Advances in the Fabrication and Functionalization of Flexible Optical Biosensors: Toward Smart Life-Sciences Applications

Over the last 30 years, optical biosensors based on nanostructured materials have obtained increasing interest since they allow the screening of a wide variety of biomolecules with high specificity, low limits of detection, and great sensitivity. Among them, flexible optical platforms have the advantage of adapting to non-planar surfaces, suitable for in vivo and real-time monitoring of diseases and assessment of food safety. In this review, we summarize the newest and most advanced platforms coupling optically active materials (noble metal nanoparticles) and flexible substrates giving rise to hybrid nanomaterials and/or nanocomposites, whose performances are comparable to the ones obtained with hard substrates (e.g., glass and semiconductors). We focus on localized surface plasmon resonance (LSPR)-based and surface-enhanced Raman spectroscopy (SERS)-based biosensors. We show that large-scale, cost-effective plasmonic platforms can be realized with the currently available techniques and we emphasize the open issues associated with this topic.

A ten-minute, single step, label-free, sample-to-answer assay for qualitative detection of cytokines in serum at femtomolar levels

Label-free electronic affinity based immuno-sensing is an attractive candidate as a platform technology for analyzing biomarkers due to the ease of miniaturization and minimal use of reagents. Electronic based sensing approaches, however, have lagged behind their optical counterparts in terms of detection limit, selectivity, and reliability. Also, the matrix dependent nature of electronic sensing modalities makes difficult the analysis of biomarkers in high salt concentration samples such as serum due to charge screening. We present a novel sensing platform, the micro-well sensor, that works by functionalizing nanoscale volume wells with antibodies and monitoring the impedance change inside the wells due binding of target protein. This detection modality is advantageous to many label-free electronic sensors in that signal power scales with increase in salt concentration, thus improving the sensitivity of the platform. We demonstrate rapid label-free qualitative detection of cytokines within ten minutes at femtoMolar concentrations and a dynamic range of 3 orders of magnitude in serum samples. We describe the design, fabrication, and characterization of the micro-well sensor in serum samples using inflammatory protein biomarkers.

Surface-enhanced resonance Raman spectroscopy of heme proteins on a gold grid electrode

The combination of surface-enhanced resonance Raman spectroscopy (SERRS) and electrochemistry is an ideal tool to study the redox process of the heme proteins and is often performed on silver electrodes. In this manuscript, we present an approach using a microstructured gold surface that serves as the electrochemical working electrode, and at the same time, acts as SERS active substrate. The cell requires a micromolar concentration of sample at the electrode surface. Even if the performance of the gold grid as SERS substrate exhibited a smaller enhancement factor than expected for silver, oxidized and reduced spectra of proteins (Сyt c, Hb and Mb) monolayers could be obtained and the characteristic redox dependent shifts of the marker bands ν₁₉, ν₄ and ν₁₀ were seen. The easy modification protocol and the higher stability of the gold electrode towards oxidative currents are the advantages of the present spectroeletrochemical cell. Finally, FDTD simulations confirm that the roughness of the gold grid has an effect on the Raman enhancement of the adsorbed proteins.

Influence of Structured Water Layers on Protein Adsorption Process: A Case Study of Cytochrome c and Carbon Nanotube Interactions and Its Implications

Cytochrome c, an essential protein of the electron transport chain, is known to be capable of amplifying the toxicity of carbon nanomaterials via free-radical generation. To understand their interaction, as well as the more general protein-nanoparticle interaction at molecular levels, we investigate the adsorptions between cytochrome c and carbon nanotubes (CNTs) in dynamic and thermodynamic ways using molecular dynamics simulations. The results reveal a well-defined three-phase process separated by two transition points: the diffusion phase where the protein diffuses in the water box, the lockdown phase I where the protein inserts into the surface-bound water layers and rearranges its conformation to fit to the surface of the CNT, and the lockdown phase II where cytochrome c repels the water molecules standing in its way to the surface of CNT and reaches stable adsorption states. The structured water layers affect the movement of atoms by electrostatic forces. In lockdown phase I, the conformation adjustment of the protein dominates the adsorption process. The most thermally favorable adsorption conformation is determined. It shows that except for the deformation of short β sheets and some portions of α helixes, most of the secondary structures of cytochrome c remain unchanged, implying that most of the functions of cytochrome c are preserved. During these processes, the energy contributions of the hydrophilic residues of cytochrome c are much larger than those of hydrophobic residues. Interestingly, the structured water layers at the CNT surface allow more hydrophilic residues such as Lys to get into close contact with the CNT, which plays a significant role during the anchoring process of adsorption. Our results demonstrate that the heme group is in close contact with the CNT in some of the adsorbed states, which hence provides a way for electron transfer from cytochrome c to the CNT surface.

Single molecule protein patterning using hole mask colloidal lithography

The ability to manipulate single protein molecules on a surface is useful for interfacing biology with many types of devices in optics, catalysis, bioengineering, and biosensing. Control of distance, orientation, and activity at the single molecule level will allow for the production of on-chip devices with increased biological activity. Cost effective methodologies for single molecule protein patterning with tunable pattern density and scalable coverage area remain a challenge. Herein, Hole Mask Colloidal Lithography is presented as a bench-top colloidal lithography technique that enables a glass coverslip to be patterned with functional streptavidin protein onto patches from 15-200 nm in diameter with variable pitch. Atomic force microscopy (AFM) was used to characterize the size of the patterned features on the glass surface. Additionally, single-molecule fluorescence microscopy was used to demonstrate the tunable pattern density, measure binding controls, and confirm patterned single molecules of functional streptavidin.

Dynamic Liquid Surface Enhanced Raman Scattering Platform Based on Soft Tubular Microfluidics for Label-Free Cell Detection

Cell detection is of great significance for biomedical research. Surface enhanced Raman scattering (SERS) has been widely applied to the detection of cells. However, there is still a lack of a general, low-cost, rapid, and sensitive SERS method for cell detection. Herein, a dynamic liquid SERS platform, which combines label-free SERS technique with soft tubular microfluidics for cell detection, is proposed. Compared with common static solid and static liquid measurement, the dynamic liquid SERS platform can present dynamical mixing, precise control of the mixing time, and continuous spectra collection. By characterizing the model molecules, the proposed dynamic liquid SERS platform has successfully demonstrated good stability and repeatability with 1.90% and 4.98% relative standard deviation (RSD), respectively. Three cell lines including one normal breast cell line (MCF-10A) and two breast cancer cell lines (MCF-7 and MDA-MB-231) were investigated in this platform. 270 cell spectra were selected as the training set for the classification of the models based on the K-Nearest Neighbor (K-NN) algorithm. In three independent experiments, three types of cells were identified by a test set containing 180 cell spectra with sensitivities above 83.3% and specificities above 91.6%. The accuracy was 94.1 ± 1.14% among three independent cell identifications. The dynamic liquid SERS platform has shown higher signal intensity, better repeatability, less pretreatment, and obtainment of more spectra with less time consumption. It will be a powerful detection tool in the area of cell research, clinical diagnosis, and food safety.

SERS Quantification and Characterization of Proteins and Other Biomolecules

Changes in protein expression levels and protein structure may indicate genomic mutations and may be related to some diseases. Therefore, the precise quantification and characterization of proteins can be used for disease diagnosis. Compared with several other alternative methods, surface-enhanced Raman scattering (SERS) spectroscopy is regarded as an excellent choice for the quantification and structural characterization of proteins. Herein, we review the main advance of using plasmonic nanostructures as SERS sensing platform for this purpose. Three design approaches, including direct SERS, indirect SERS, and SERS-encoded nanoparticles, are discussed in the direction of developing new precise approaches of quantification and characterization of proteins. While this Review is focused on proteins, in order to highlight concepts of SERS-based sensors also detection of other biomolecules will be discussed.

Site-Selective Surface-Enhanced Raman Detection of Proteins

Strategies for protein detection via surface-enhanced Raman spectroscopy (SERS) currently exploit the formation of randomly generated hot spots at the interfaces of metal colloidal nanoparticles, which are clustered together by intrusive chemical or physical processes in the presence of the target biomolecule. We propose a different approach based on selective and quantitative gathering of protein molecules at regular hot spots generated on the corners of individual silver nanocubes in aqueous medium at physiological pH. Here, the protein, while keeping its native configuration, experiences an intense local E-field, which boosts SERS efficiency and detection sensitivity. Uncontrolled signal fluctuations caused by variable molecular adsorption to different particle areas or inside clustered nanoparticles are circumvented. Advanced electron microscopy analyses and computational simulations outline a strategy relying on a site-selective mechanism with superior Raman signal enhancement, which offers the perspective of highly controlled and reproducible routine SERS detection of proteins.

Orientation-dependent nanostructure arrays based on anisotropic silicon wet-etching for repeatable surface-enhanced Raman scattering

Repeatable fabrication of sensitive plasmonic substrates through a simple procedure has become a major challenge for SERS-based sensing and imaging. Herein, a new class of high-performance SERS substrates, including pyramid, ridged-hexagon, and quasi-triangle nanostructures, is successfully fabricated based on the nanosphere lithography technique and anisotropic wet etching. Using the wafer-scale Cr-hole array as the etching mask, cavity-templates of various configurations are fabricated by the orientation-dependent wet etching technique, from where the nanostructure arrays are finally peeled-off. The anisotropic wet etching on (100), (110), and (111) silicon wafers has been systematically studied at the nanoscale revealing the formation mechanism of these cavity-templates. The peeled-off nanostructure arrays provide high-density tips and/or gaps (about 2.5 × 10(7) mm(-2)) and thus facilitate the generation of "hot spots". The distribution of the electromagnetic field is visualized by the finite difference time domain calculation. And the calculation results are validated by SERS characterization. The SERS enhancement factors of these substrates are in the order of 10(6)-10(7), with the maximum enhancement factor of 1.32 × 10(7) yielded by the ridged-hexagon arrays. The proposed nanostructure arrays present excellent homogeneity and reproducibility (with the largest relative standard deviation of 16.43%) for the reason that the SERS-active substrates are peeled-off from an identical template. The cost-effective fabrication, high sensitivity, good homogeneity and well-performed reproducibility demonstrate that these orientation-dependent NSs are good candidates for SERS-based in vitro and in situ detection and biosensing.

Research on the influence of alkyl ammonium bromides on the properties of Ag/AgBr/GO composites

The photocatalytic activities of as-synthesized Ag/AgBr/GO nanocomposites became weaker when alkyl chain became shorter, whereas an opposite change for their SERS enhancements.

Molecular simulations of cytochrome c adsorption on positively charged surfaces: the influence of anion type and concentration

The influence of anion type and concentration on the adsorption of cytochrome c onto the positively charged NH₂-SAM surface.

Surface-enhanced resonance Raman scattering of hemoproteins and those in complicated biological systems

The SERRS spectra of heme are influenced by structural changes, orientation, and selective adsorption on the Ag surface.

Controllable synthesis of graphene oxide–silver (gold) nanocomposites and their size-dependencies

The Raman scattering properties and catalytic activities of as-synthesized GO–metal composites were correlated with the size of metallic nanoparticles and exhibited size-dependent behavior.

Electrokinetic preconcentration of small molecules within volumetric electromagnetic hotspots in surface enhanced Raman scattering

The on-chip integration of a preconcentration chamber for ultrasensitive surface-enhanced Raman scattering (SERS) is shown. Small molecules are preconcentrated using 3D volumetric electromagnetic hotspots. The experimental results demonstrate an enhancement of the SERS signals of over two orders of magnitude, which allows the fingerprinting of neurotransmitter molecules at the nanomolar level and furthers the selective detection of oppositely charged molecules. This on-chip integration will provide new directions for ultrasensitive SERS applications.

Design of surface modifications for nanoscale sensor applications

Nanoscale biosensors provide the possibility to miniaturize optic, acoustic and electric sensors to the dimensions of biomolecules. This enables approaching single-molecule detection and new sensing modalities that probe molecular conformation. Nanoscale sensors are predominantly surface-based and label-free to exploit inherent advantages of physical phenomena allowing high sensitivity without distortive labeling. There are three main criteria to be optimized in the design of surface-based and label-free biosensors: (i) the biomolecules of interest must bind with high affinity and selectively to the sensitive area; (ii) the biomolecules must be efficiently transported from the bulk solution to the sensor; and (iii) the transducer concept must be sufficiently sensitive to detect low coverage of captured biomolecules within reasonable time scales. The majority of literature on nanoscale biosensors deals with the third criterion while implicitly assuming that solutions developed for macroscale biosensors to the first two, equally important, criteria are applicable also to nanoscale sensors. We focus on providing an introduction to and perspectives on the advanced concepts for surface functionalization of biosensors with nanosized sensor elements that have been developed over the past decades (criterion (iii)). We review in detail how patterning of molecular films designed to control interactions of biomolecules with nanoscale biosensor surfaces creates new possibilities as well as new challenges.

Allosteric transition induced by Mg²⁺ ion in a transactivator monitored by SERS

We demonstrate the utility of the surface-enhanced Raman spectroscopy (SERS) to monitor conformational transitions in protein upon ligand binding. The changes in protein's secondary and tertiary structures were monitored using amide and aliphatic/aromatic side chain vibrations. Changes in these bands are suggestive of the stabilization of the secondary and tertiary structure of transcription activator protein C in the presence of Mg(2+) ion, whereas the spectral fingerprint remained unaltered in the case of a mutant protein, defective in Mg(2+) binding. The importance of the acidic residues in Mg(2+) binding, which triggers an overall allosteric transition in the protein, is visualized in the molecular model. The present study thus opens up avenues toward the application of SERS as a potential tool for gaining structural insights into the changes occurring during conformational transitions in proteins.

Influence of protein size on surface-enhanced Raman scattering (SERS) spectra in binary protein mixtures

The size-dependent interactions of eight blood proteins with silver nanoparticles (AgNPs) in their binary mixtures were investigated using surface-enhanced Raman scattering (SERS). Principal component analysis (PCA) was performed on the SERS spectra of each binary mixture, and the differentiation ability of the mixtures was tested. It was found that the effect of relative concentration change on the SERS spectra of the binary mixtures of small proteins could be detected using PCA. However, this change was not observed with the binary mixtures of large proteins. This study demonstrated that the relative interactions of the smaller proteins with an average size of 50 nm AgNPs smaller than the large proteins could be monitored, and this information can be used for the detection of proteins in protein mixtures.

Convenient detection of the thiol functional group using H/D isotope sensitive Raman spectroscopy

Convenient detection of thiol groups using Raman spectroscopy.

Tuning the 3D plasmon field of nanohole arrays

Modern photonics is being revolutionized through the use of nanostructured plasmonic materials, which confine light to sub-diffraction limit resolution providing universal, sensitive, and simple transducers for molecular sensors. Understanding the mechanisms by which light interacts with plasmonic crystals is essential for developing application-focussed devices. The strong influence of grating coupling on electromagnetic field distribution, frequency and degeneracy of plasmon bands has now been characterized using hexagonal nanohole arrays. An equation for nanohole arrays was derived to demonstrate the strong influence of incidence and rotation angle on optical properties of 2D plasmonic crystals such as nanohole arrays. Consequently, we report experimental data that are in strong agreement with finite difference time-domain (FDTD) simulations that clearly demonstrate the influence of the grating coupling conditions on the optical properties (such as plasmon degeneracy and bandwidth), and on the distribution of the plasmon field around nanohole arrays (including tuneable penetration depths and highly localized fields). The tuneable 3D plasmon field allowed for controlled sensing properties and by increasing the angle of incidence to 30 degrees, the resonance wavelength was tuned from 1000 to 600 nm, and the sensitivity was enhanced by nearly 300% for a protein assay using surface plasmon resonance (SPR) and by 40% with surface-enhanced Raman scattering (SERS) sensors.

Phosphate mediated adsorption and electron transfer of cytochrome c. A time-resolved SERR spectroelectrochemical study

The study of proteins immobilized on biomimetic or biocompatible electrodes represents an active field of research as it pursues both fundamental and technological interests. In this context, adsorption and redox properties of cytochrome c (Cyt) on different electrode surfaces have been extensively reported, although in some cases with contradictory results. Here we report a SERR spectroelectrochemical study of the adsorption and electron transfer behaviour of the basic protein Cyt on electrodes coated with amino-terminated monolayers. The obtained results show that inorganic phosphate (Pi) and ATP anions are able to mediate high affinity binding of the protein with preservation of the native structure and rendering an average orientation that guarantees efficient pathways for direct electron transfer. These findings aid the design of Cyt-based bioelectronic devices and understanding the modulation by Pi and ATP of physiological functions of Cyt.

Biosafety and bioapplication of nanomaterials by designing protein-nanoparticle interactions

The protein-nanoparticle (NP) interface is a current frontier of multiple disciplines, full of challenges and opportunities. The unique behaviors of nanomaterials (NMs) bring many exciting applications, and also raise safety concerns. Beyond bioapplications, various NMs could also enter human bodies from the environment. When entering human bodies, NPs interact with various biomolecules, especially proteins, forming a protein corona. This protein-NP complex is what the biosystems 'see' and 'respond to'. Therefore, understanding how NPs interact with proteins is crucial for both bioapplications and the biosafety of NMs. In this review, the current understanding of protein-NP interactions is summarized, including the theoretical background, experimental results, and computational progresses. Guidelines for improving bioapplication performance and reducing the potential biosafety hazard of NMs by designing the protein-NP interactions are discussed, along with future directions and challenges in this exciting field.

Self-assembled monolayers of NH2-terminated thiolates: order, pKa, and specific adsorption

Self-assembled monolayers (SAMs) of amino-terminated alkanethiols on Au were characterized by a combination of electrochemical (LSV, CV, and EIS) and spectroscopic (XPS and SER) techniques. Clear correlations were obtained between the apparent surface pKa values determined by impedimetric titrations and order parameters such as the content of trans conformers in the SAMs. These results contrast with previous studies that exhibit dispersions of up to 6 pH units in the reported pKa values. In addition, we determined that inorganic and organic phosphate species bind specifically to these SAMs mediating adsorption and heterogeneous electron transfer of positively charged macromolecules such as cytochrome c.

Position-specific chemical modification and quantitative proteomics disclose protein orientation adsorbed on silica nanoparticles

We describe a method for determining the orientation of cytochrome c, RNase A, and lysozyme on silica nanoparticles (SNPs) using chemical modification combined with proteolysis-mass spectrometry. The proteins interacted with SNPs through preferential adsorption sites, which are dependent on SNP diameter; 4 nm SNPs induce greater structural stabilization than 15 nm particles, presumably due to greater surface curvature of the former. These results suggest that nanoparticle size and protein structure influence protein orientation on SNPs.

Monitoring protein distributions based on patterns generated by protein adsorption behavior in a microfluidic channel

We report a unique monitoring technique of protein distributions based on distinctive patterns generated by protein adsorption behavior on a solid surface in a microfluidic channel. Bare gold and COOH-modified self-assembled monolayer (SAM) sensing surfaces were pre-adsorbed with one of four different proteins: lysozyme, albumin, transferrin, or IgG. Each surface provides a thermodynamically governed platform for immobilizing proteins and generates analyte-specific response patterns. Each surface has its own thermodynamic energy governing pre-adsorbed protein behaviors, so that sample proteins react with the pre-adsorbed ones to different extents depending on their sizes, isoelectric points (pI), and characteristics of the sensing surfaces. Modified surfaces were mounted and monitored in real time using surface plasmon resonance (SPR). Buffer-prepared sample matrices (α1-antitrypsin, haptoglobin, C-reactive protein (CRP), and IgM) characterized protein response patterns. Each surface generated distinctive patterns based on individual SPR angle shifts. We classified each sample with 95% accuracy using linear discriminant analysis (LDA). Our method also discriminated between different concentrations of CRP in the cocktail sample, detecting concentrations as low as 1 nM with 91.7% accuracy. This technique may be integrated with a microfluidic lab-on-a-chip system and monitor the distribution of a specific group of proteins in human serum.

Multiple aspects of the interaction of biomacromolecules with inorganic surfaces

The understanding of the mechanisms involved in the interaction of biological systems with inorganic materials is of interest in both fundamental and applied disciplines. The adsorption of proteins modulates the formation of biofilms onto surfaces, a process important in infections associated to medical implants, in dental caries, in environmental technologies. The interaction with biomacromolecules is crucial to determine the beneficial/adverse response of cells to foreign inorganic materials as implants, engineered or accidentally produced inorganic nanoparticles. A detailed knowledge of the surface/biological fluids interface processes is needed for the design of new biocompatible materials. Researchers involved in the different disciplines face up with similar difficulties in describing and predicting phenomena occurring at the interface between solid phases and biological fluids. This review represents an attempt to integrate the knowledge from different research areas by focussing on the search for determinants driving the interaction of inorganic surfaces with biological matter.