A streptavidin surface on planar glass substrates for the detection of biomolecular interaction

Nanoplasmonic probes of RNA folding and assembly during pre-mRNA splicing

RNA splicing plays important roles in transcriptome and proteome diversity. Herein, we describe the use of a nanoplasmonic system that unveils RNA folding and assembly during pre-mRNA splicing wherein the quantification of mRNA splice variants is not taken into account. With a couple of SERS-probes and plasmonic probes binding at the boundary sites of exon-2/intron-2 and intron-2/exon-3 of the pre-mature RNA of the β-globin gene, the splicing process brings the probes into the plasmonic bands. For plasmonic probes, a plasmon shift increase of ∼29 nm, corresponding to intron removal and exon-2 and exon-3 connection to form the mRNA molecule, is measured by plasmonic coupling. The increased scattering intensity and surface-enhanced Raman scattering (SERS) fingerprinting reveal the clear dynamics of pre-mRNA splicing. Moreover, a time-resolved experiment of individual RNA molecules exhibited a successful splicing and an inhibited splicing event by 33 μM biflavonoid isoginkgetin, a general inhibitor of RNA splicing. The results suggest that the RNA splicing is successfully monitored with the nanoplasmonic system. Thus, this platform can be useful for studying RNA nanotechnology, biomolecular folding, alternative splicing, and maturation of microRNA.

Detection of Bacillus thuringiensis Cry1Ab protein based on surface plasmon resonance immunosensor

Two novel surface plasmon resonance immunosensors were fabricated for detection of the Bacillus thuringiensis Cry1Ab protein and to demonstrate their performance in analyzing Cry1Ab protein in crop samples. Sensor 2 was modified by 1,6-hexanedithiol, Au/Ag alloy nanoparticles, 3-mercaptopropionic acid, and protein A (or not [sensor 1]), with Cry1Ab monoclonal antibody. As a result, both of the immunosensors exhibited satisfactory linear responses in the Cry1Ab protein concentration ranges of 10 to 500ngml(-1) and 8 to 1000ngml(-1), and the detection limits were 5.0 and 4.8ngml(-1), respectively. The immunosensors possessed good specificity and acceptable reproducibility. In addition, crop samples could be analyzed after a simple treatment. The transgenic crops could be easily identified from the conventional ones by the two immunosensors.

Multiplex approaches in protein microarray technology

The success of genome sequencing projects has provided the basis for systematic analysis of protein function and has led to a shift from the description of single molecules to the characterization of complex samples. Such a task would not be possible without the provision of appropriate high-throughput technologies, such as protein microarray technology. In addition, the increasing number of samples necessitates the adaptation of such technologies to a multiplex format. This review will discuss protein microarray technology in the context of multiplex analysis and highlight its current prospects and limitations.

Unique diagnostic and therapeutic roles of porphyrins and phthalocyanines in photodynamic therapy, imaging and theranostics

Porphyrinic molecules have a unique theranostic role in disease therapy; they have been used to image, detect and treat different forms of diseased tissue including age-related macular degeneration and a number of different cancer types. Current focus is on the clinical imaging of tumour tissue; targeted delivery of photosensitisers and the potential of photosensitisers in multimodal biomedical theranostic nanoplatforms. The roles of porphyrinic molecules in imaging and pdt, along with research into improving their selective uptake in diseased tissue and their utility in theranostic applications are highlighted in this Review.

Combined microslit electrokinetic measurements and reflectometric interference spectroscopy to study protein adsorption processes

Streaming potential/current measurements for the characterization of charge formation processes at solid/liquid interfaces were combined with reflectometric interference spectroscopy. The simultaneous determination of electrosurface characteristics and the optical thickness of interfacial layers provides information on structural variations of adsorbed or covalently bound polymers and on charge dependent adsorption and desorption phenomena at solid/liquid interfaces. To demonstrate the potentialities of this extended approach for biointerfacial studies the authors report a series of experiments on the adsorption of the plasma protein fibrinogen at poly(octadecene-alt-maleic acid) thin films.

On the adsorption behavior of biotin-binding proteins on gold and silica

Streptavidin (SAv), avidin (Av), and neutravidin (NAv) have become widely used molecular tools in biotechnology thanks to their remarkable affinity for biotin. Their tetravalency renders these molecules particularly interesting for the functionalization of solid-liquid interfaces. Using the quartz crystal microbalance with dissipation monitoring, we systematically investigate the deposition of biotin-binding proteins to two surfaces that are popular in biotechnology: gold and silica. We find that simple physisorption of biotin-binding proteins is a viable method to confer biotin-binding functionality to gold surfaces. Both SAv and Av form dense, stable protein monolayers that retain biotin-binding activity and are largely inert to the unspecific binding of bovine serum albumin. Furthermore, we report that SAv resists adsorption to silica over a wide range of pH and ionic strength. The contrast in the binding behavior of SAv on silica and on gold suggests a simple strategy for the selective biofunctionalization of nano- or microstructured surfaces.

Efficient biosensor interfaces based on space-controlled self-assembled monolayers

In this paper we demonstrate control over the spacing of surface-modifying probe molecules through the use of labile dendron spacers. During this process, anchor molecules are first adsorbed to a surface, with dendron modifiers attached. Steric interactions of the bulky dendrons control the density of anchor molecules bound to the surface. The dendron branches are subsequently detached from the anchor molecules, and the anchors are chemically modified with probe molecules, resulting in a surface with controlled spacing between probe molecules. Control over this spacing is important when the probe size is small in comparison with the target molecule. This importance is demonstrated for the binding of protein (streptavidin) targets to the probe (biotin) surface. The effect of probe space control on the efficiency of target capture is evaluated by examining the binding of streptavidin to thiolated biotin for a series of mixed monolayers. Surface modification is monitored by Fourier transform infrared reflection absorption spectroscopy (FTIR-RAS). The relative concentration of probe molecules at the surface is measured using X-ray photoelectron spectroscopy (XPS) measurements. Thiolated-biotin surfaces with optimized spacing show an increased capture efficiency for streptavidin relative to surfaces with nonoptimal or no control over probe spacing, as measured by surface plasmon resonance (SPR) spectroscopy. These results are of potential significance for the optimization and fabrication of micro- and nanoarrays used in chemical and biochemical measurements.

An advanced biosensor for the prediction of estrogenic effects of endocrine-disrupting chemicals on the estrogen receptor alpha

A label-free and time-resolved biosensor based on reflectometric interference spectroscopy (RIfS) has been developed to evaluate the agonistic or antagonistic effects of potential ligands with unknown behavior. The biosensor utilizes the specific interaction between the estrogen receptor alpha (ER alpha) and short specific peptides. The unique feature of these peptides allows the investigation of the behavior of ligands and the discrimination between the agonistic and antagonistic effects caused by conformational changes of the receptor. Thus, this developed biosensor allows not only the differentiation between ligands and nonligands of a receptor, but also the potential of these ligands to influence conformational changes in the receptor, leading to activation or inhibition of the receptor-dependent pathways. Owing to the robustness of the direct optical detection principle used, the biosensor is applicable to complex biological matrices, even crude cell extracts. Moreover, the reliability of the biosensor, including regeneration steps when performing subsequent measurements, has been verified.

Characterisation of morphology of self-assembled PEG monolayers: a comparison of mixed and pure coatings optimised for biosensor applications

For detection of low concentrations of analytes in complex biological matrices using optical biosensors, a high surface loading with capture molecules and a low nonspecific binding of nonrelevant matrix molecules are essential. To tailor biosensor surfaces in such a manner, poly(ethylene glycols) (PEG) in varying lengths were immobilised covalently onto glass-type surfaces in different mixing ratios and concentrations, and were subsequently modified with three different kinds of receptors. The nonspecific binding of a model protein (ovalbumin, OVA) and the maximum loading of the respective analytes to these prepared surfaces were monitored using label-free and time-resolved reflectometric interference spectroscopy (RIfS). The three different analytes used varied in size: 150 kDa for the anti-atrazine antibody, 60 kDa for streptavidin and 5 kDa for the 15-bp oligonucleotide. We investigated if the mixing of PEG in different lengths could increase the surface loadings of analyte mimicking a three-dimensional matrix as was found using dextrans as sensor coatings. In addition, the effect on the surface loading was investigated with regard to the size of the analyte molecule using such mixed PEGs on the sensor surface. For further characterisation of the surface coatings, polarisation modulation infrared reflection absorption spectroscopy, atomic force microscopy, and ellipsometry were applied.

Strategies for label-free optical detection

A large number of methods using direct detection with label-free systems are known. They compete with the well-introduced fluorescence-based methods. However, recent applications take advantage of label-free detection in protein-protein interactions, high-throughput screening, and high-content screening. These new applications require new strategies for biosensors. It becomes more and more obvious that neither the transduction principle nor the recognition elements for the biomolecular interaction process alone determine the quality of the biosensor. Accordingly, the biosensor system has to be considered as a whole. This chapter focuses on strategies to optimize the detection platform and the biomolecular recognition layer. It concentrates on direct detection methods, with special focus on optical transduction. Since even this restriction still leaves a large number of methods, only microrefractometric and microreflectometric methods using planar transducers have been selected for a detailed description and a listing of applications. However, since many review articles on the physical principles exist, the description is kept short. Other methods are just mentioned in brief and for comparison. The outlook and the applications demonstrate the future perspectives of direct optical detection in bioanalytics.

Diet-derived polyphenol metabolite enterolactone is a tissue-specific estrogen receptor activator

Numerous dietary compounds can modify gene expression by binding to the members of the nuclear receptor superfamily of transcription factors. For example, dietary polyphenols, such as soy isoflavones genistein and daidzein, modulate the activity of the estrogen receptors (ERs)-alpha and ERbeta. An additional class of dietary polyphenols that modulate cellular signaling pathways are lignans, compounds that are common constituents of Western diets. In this study, we show that a metabolite of dietary lignans, enterolactone, at physiological concentrations, activates ER-mediated transcription in vitro with preference for ERalpha. The effects of enterolactone are mediated by the ER ligand binding domain and are susceptible to antiestrogen treatment. Furthermore, the affinity of enterolactone toward ERalpha, measured by a novel ligand binding assay, is augmented in cell culture conditions. Moreover, our results demonstrate for the first time that enterolactone has estrogenic activity in vivo. In transgenic estrogen-sensitive reporter mice, enterolactone induces tissue-specific estrogen-responsive reporter gene expression as well as promotes uterine stromal edema and expression of estrogen-responsive endogenous genes (CyclinD1 and Ki67). Taken together, our data show that enterolactone is a selective ER agonist inducing ER-mediated transcription both in vitro in different cell lines and in vivo in the mouse uterus.

Direct force measurement of the stability of poly(ethylene glycol)-polyethylenimine graft films

The stability and passivity of poly(ethylene glycol)-polyethylenimine (PEG-PEI) graft films are important for their use as antifouling coatings in a variety of biotechnology applications. We have used AFM colloidal-probe force measurements combined with optical reflectometry to characterize the surface properties and stability of PEI and dense PEG-PEI graft films on silica. Initial contact between bare silica probes and PEI-modified surfaces yields force curves that exhibit a long-range electrostatic repulsion and short-range attraction between the surfaces, indicating spontaneous desorption of PEI in the aqueous medium. Further transfer of PEI molecules to the probe occurs with subsequent application of forces between FR = 300 and 500 microN/m. The presence of PEG reduces the adhesive properties of the PEI surface and prevents transfer of PEI molecules to the probe with continuous contact, though an initial desorption of PEI still occurs. Glutaraldehyde crosslinking of the graft films prevents both the initial desorption and subsequent transfer of the PEI, resulting in sustained attractive interaction forces of electrostatic origin between the negatively charged probe and the positively charged copolymer graft films.

Kinetic study of phosphorylation-dependent complex formation between the kinase-inducible domain (KID) of CREB and the KIX domain of CBP on a quartz crystal microbalance

We report quantitative analysis of peptide-peptide interactions on a 27 MHz quartz crystal microbalance (QCM) in aqueous solution. The KID (kinase-inducible domain) of transcription factor CREB (cyclic AMP response element binding protein) is known to interact with the KIX domain of coactivator CBP (CREB binding protein), facilitated by phosphorylation at Ser-133 of the KID. The KIX domain peptide (86 aa) was immobilized on the QCM gold electrode surface by means of a poly(ethylene glycol) spacer. Binding of the KID peptide (46 aa) to the KIX peptide was detected by frequency decreases (mass increases) of the QCM. Both maximum binding amount (Deltammax) and association constants (Ka) obtained from the QCM measurements increased as a result of phosphorylation of Ser-133 of the KID peptide. The Ka values for KIX peptide to the phosphorylated (pKID) and unphosphorylated KID peptides were (93+/-2) x 10(3) and (5+/-1) x 10(3) M(-1), respectively. This difference was explained by the dissociation rate constant (k(-1)) of the pKID being 20 times smaller than that of the KID, while association rate constants (k1) were independent of phosphorylation.

Investigation of initial pellicle formation on modified titanium dioxide (TiO2) surfaces by reflectometric interference spectroscopy (RIfS) in a model system

OBJECTIVES

Plaque accumulation, leading to inflammatory processes and bone loss, is one of the main reasons for failure of dental implants. Pellicle formation plays a key role in bacterial adhesion and plaque accumulation. The influence of experimental bioactive implant surface coatings on the initial process of pellicle formation was investigated in a model system.

METHODS

TiO2-films were modified by covalent binding of laminin and human epidermal growth factor (EGF) to promote adhesion of epithelial cells. Adsorption and dissociation behavior of bovine serum albumin (BSA) and salivary proteins on these surfaces were monitored by time-resolved reflectometric interference spectroscopy (RIfS).

RESULTS

The thickness of the irreversibly adsorbed salivary protein layer was reduced from 2.78 +/- 0.71 nm on unmodified TiO2 to 0.78 +/- 0.22 nm on laminin-coated surfaces and to 1.18 +/- 0.29 nm on EGF-coated surfaces. The percentage of initially adsorbed proteins remaining irreversibly bound was reduced from 51 +/- 8% on titanium to 23 +/- 5% by laminin coating and to 44 +/- 11% on EGF-coated surfaces. The highest reduction of protein adsorption (layer thickness lower than 0.05 nm) was achieved on DC-PEG-layers used as spacer for protein coupling.

SIGNIFICANCE

Laminin and EGF were shown to be promising candidates for use as biological coatings on the transmucosal part of titanium dental implants where the objective is to enhance epithelial adhesion and inhibit adsorption of salivary proteins and bacteria.

Direct optical sensors: principles and selected applications

In the field of bio and chemosensors a large number of detection principles has been published within the last decade. These detection principles are based either on the observation of fluorescence-labelled systems or on direct optical detection in the heterogeneous phase. Direct optical detection can be measured by remission (absorption of reflected radiation, opt(r)odes), by measuring micro-refractivity, or measuring interference. In the last case either Mach-Zehnder interferometers or measurement of changes in the physical thickness of the layer (measuring micro-reflectivity) caused, e.g., by swelling effects in polymers (due to interaction with analytes) or in bioassays (due to affinity reactions) also play an important role. Here, an overview of methods of microrefractometric and microreflectometric principles is given and benefits and drawbacks of the various approaches are demonstrated using samples from the chemo and biosensor field. The quality of sensors does not just depend on transduction principles but on the total sensor system defined by this transduction, the sensitive layer, data acquisition electronics, and evaluation software. The intention of this article is, therefore, to demonstrate the essentials of the interaction of these parts within the system, and the focus is on optical sensing using planar transducers, because fibre optical sensors have been reviewed in this journal only recently. Lack of selectivity of chemosensors can be compensated either by the use of sensor arrays or by evaluating time-resolved measurements of analyte/sensitive layer interaction. In both cases chemometrics enables the quantification of analyte mixtures. These data-processing methods have also been successfully applied to antibody/antigen interactions even using cross-reactive antibodies. Because miniaturisation and parallelisation are essential approaches in recent years, some aspects and current trends, especially for bio-applications, will be discussed. Miniaturisation is especially well covered in the literature.

Liposomes for microcompartmentation of enzymes and their influence on catalytic activity

Modular systems for protein coupling have been applied for anchoring enzyme molecules on liposome surfaces. Two cytoplasmic model enzymes, alpha-amylase from Escherichia coli (EC. 3.2.1.1) and guanylate kinase from Saccharomyces cerevisiae (EC. 2.7.4.8), were directly coupled by a histidine-tag or indirectly via strep-tag and streptavidin or streptactin linker to a liposome membrane. Though the catalytic properties of the enzymes are generally maintained, stability and specific activity of the enzymes are modified after coupling and are especially influenced by the lipid used for the liposome assembly.

Application of atomic force microscopy and grating coupler for the characterization of biosensor surfaces

Atomic force microscopy (AFM) and an optical grating coupler system were used to improve the understanding of the biosensing layer on a Ta(2)O(5)-light-guiding surface. Exemplary, we investigated the immobilization of the protein avidin, the subsequent binding of biotinylated oligonucleotides and hybridization of a complementary 12-mer. The AFM measurements revealed the height of approximately 1.6 nm for a single avidin molecule, while the thickness of the avidin layer on the biosensor surface seemed to be 2.8-3.0 nm. This result lead to the conclusion that the protein was not forming a simple monolayer. However, the thickness of the avidin layer could not be determined directly, but only after shifting of protein by the tip of the AFM leading to grooves of 1 micro m(2) and approximately 3 nm depth. As the height of oxide particles forming the waveguide surface was also in the range of 1.5 nm, the depth of these grooves could also be a result of the deposition of proteins on top of the oxide particles. This was consistent with the increased roughness of the surface after protein binding. Thus, investigations with the grating coupler were used to determine quantitatively the amount of immobilized avidin. On a biotinylated surface the amount of immobilized avidin lead to the assumption of a complete monolayer, whereas simple adsorption proved to be less efficient. A binding ratio of 1:1.3 for avidin and a biotinylated oligonucleotide was achieved. Up to 83% of the bound single strand were accessible for a subsequent hybridization reaction with a 12-mer. These results supported the model of avidin being deposited mainly on top of the oxide particles leading to the picture of a 'rough' complete protein monolayer, which was postulated from the AFM investigations.

Label-free parallel screening of combinatorial triazine libraries using reflectometric interference spectroscopy

The parallel reflectometric interference spectroscopy is presented as a label-free optical detection method. A new setup was adapted to accommodate sample carriers in a 96-well microplate. It allows for the first time simultaneous plate imaging by a CCD camera for the parallel detection of specific biomolecular interaction in the microplate wells at heterogeneous phase using direct optical monitoring. The detection of binding events with time resolution enables a highly parallel functional biomolecular interaction analysis (BIA). The combination of this new screening setup with combinatorial solid-phase synthesis is performed in the wells of glass-bottom microplates to accomplish the synthesis and the screening platform within one device. As a model system for a solid-phase substance library, synthesis of a triazine library and the subsequent BIA with four different antibodies were carried out. The presented setup enables a time resolution of 18 s with a total screening time of less than 35 min including baseline adjustment, BIA, and regeneration of the screening device for 96 samples in parallel. The binding studies reveal a fast classification of the different monoclonal and polyclonal antibodies and enable the detection of triazines with high binding affinity. The presented prototype is the first parallelized optical label-free detection system for biomolecular interaction analysis that is suitable for a high-throughput screening based on the 96-well microplate format.

Online monitoring of solid-phase peptide syntheses on glass-type surfaces using white light interference

Label-free optical detection methods are of particular value for the investigation of biomolecular interactions. A label-free method based on reflectometric interference spectroscopy is described which enables both the on-line monitoring of solid phase peptide syntheses and subsequently the determination of antibody binding to these peptides without cleavage from the support. The method uses SiO(2) transducers that were modified with diaminopolyethylene glycol. The stepwise coupling of different amino acids to the transducer surface was investigated and the complete monitoring of the synthesis of a viral epitope was performed. The success of the synthesis was proven via binding of a specific monoclonal antibody to the transducer-bound product. In order to demonstrate specificity the binding was inhibited with the same peptide epitope added in solution. The approach is attractive especially in the field of high throughput screening since both the synthesis and the interaction with the biological receptor can be monitored using the same technique.

Single molecule research on surfaces: from analytics to construction and back

The study of single molecules opens a new dimension in understanding nature down to its finest ramifications. While much progress was achieved in the last decade concerning the detection techniques, suitable techniques for manipulating and handling the biomolecules still bear a challenge. Primarily, the task is keeping an individual, active molecule of a certain lifespan in the spot. Here, we will focus on techniques for the functional immobilization of (single) molecules on surfaces to enable their observation at one position over a time period. Presenting the main methods of reversible immobilization we will accentuate the chelator lipid concept as combining all features prerequisite for functional, reversible and well-defined immobilization. This will also show that single molecule research in principle is the synthesis of an insight into the function of nature and nano-biotechnology (manipulation): thus of analytics, construction, and back.