Instrumental biosensors: new perspectives for the analysis of biomolecular interactions

Nonspecific Binding-Fundamental Concepts and Consequences for Biosensing Applications

Nature achieves differentiation of specific and nonspecific binding in molecular interactions through precise control of biomolecules in space and time. Artificial systems such as biosensors that rely on distinguishing specific molecular binding events in a sea of nonspecific interactions have struggled to overcome this issue. Despite the numerous technological advancements in biosensor technologies, nonspecific binding has remained a critical bottleneck due to the lack of a fundamental understanding of the phenomenon. To date, the identity, cause, and influence of nonspecific binding remain topics of debate within the scientific community. In this review, we discuss the evolution of the concept of nonspecific binding over the past five decades based upon the thermodynamic, intermolecular, and structural perspectives to provide classification frameworks for biomolecular interactions. Further, we introduce various theoretical models that predict the expected behavior of biosensors in physiologically relevant environments to calculate the theoretical detection limit and to optimize sensor performance. We conclude by discussing existing practical approaches to tackle the nonspecific binding challenge in vitro for biosensing platforms and how we can both address and harness nonspecific interactions for in vivo systems.

A microwell array structured surface plasmon resonance imaging gold chip for high-performance label-free immunoassay

Surface plasmon resonance imaging (SPRi) offers a compelling method for high-throughput, real-time, and label-free biomolecular interaction studies and immunoassays, but its performance suffers from limited intrinsic sensitivity and low-contrast SPRi images. Herein we report a high-performance SPRi chip featuring patterned microwell array constructed by photolithography of adhesive polydopamine (PDA) thin film on conventional gold chip. The chip allows for the facile construction of region-defined sensing array on its surface with improved intrinsic SPRi sensitivity due to the intensified surface plasmon wave (SPW) in the microwells. The immunoassay performance of the as-designed SPRi chip is evaluated by using anti-ochratoxin A (anti-OTA) monoclonal antibody as a model target. The results show that this microwell array structured gold chip exhibits ca. 18%-32% higher signal intensity than the conventional gold chip when detecting anti-OTA at different concentrations, and the noise remains at the same level, showing enhanced intrinsic sensitivity. Meanwhile, this microwell-structured chip affords clear and high-contrast SPRi images with well-defined sensing areas, which greatly facilitates the extraction and quantitative analysis of detection signals while efficiently suppressing the disturbance from background areas.

Simultaneously performing optical and electrical responses from a plasmonic sensor based on gold/silicon Schottky junction

Making the chemical or biological sensors simpler and more compatible with other measurements is a key enabling technology for commercial application. In this work, we propose a plasmonic refractive-index sensor only based on gold/silicon Schottky junction to simultaneously perform optical and electrical read-out responses. Via exciting surface plasmon resonance (SPR), the designed device shows a few characteristic reflection valleys and greatly enhances the narrowband light absorption. Calculated results indicate that the SPR resonance wavelength can be tuned in the wavelength range of 1100-2000 nm by manipulating the period, width of the Si nanochannel and the incident angle of light. When the analyte is changed, the SPR resonance wavelength generated at the bottom surface of the Au layer barely shifts, while the one at the top surface shows a significant linear shift. The optimally designed system shows an optical response with a refractive index sensitivity of over 1000 nm per refractive index unit (nm/RIU). Moreover, the electrodynamic calculation of the hot electrons predicts the electrical response can be up to 14.5 mA/(W·RIU) for an example of detecting trichloromethane, where the employed light can be a monochromatic light and the sensing operation can be much simpler relative to the conventional spectral work mode.

A group II intron-encoded protein interacts with the cellular replicative machinery through the β-sliding clamp

Group II introns are self-splicing mobile genetic retroelements. The spliced intron RNA and the intron-encoded protein (IEP) form ribonucleoprotein particles (RNPs) that recognize and invade specific DNA target sites. The IEP is a reverse transcriptase/maturase that may bear a C-terminal endonuclease domain enabling the RNP to cleave the target DNA strand to prime reverse transcription. However, some mobile introns, such as RmInt1, lack the En domain but nevertheless retrohome efficiently to transient single-stranded DNA target sites at a DNA replication fork. Their mobility is associated with host DNA replication, and they use the nascent lagging strand as a primer for reverse transcription. We searched for proteins that interact with RmInt1 RNPs and direct these RNPs to the DNA replication fork. Co-immunoprecipitation assays suggested that DnaN (the β-sliding clamp), a component of DNA polymerase III, interacts with the protein component of the RmInt1 RNP. Pulldown assays, far-western blots and biolayer interferometry supported this interaction. Peptide binding assays also identified a putative DnaN-interacting motif in the RmInt1 IEP structurally conserved in group II intron IEPs. Our results suggest that intron RNP interacts with the β-sliding clamp of the DNA replication machinery, favouring reverse splicing into the transient ssDNA at DNA replication forks.

Multiband and Ultrahigh Figure-of-Merit Nanoplasmonic Sensing with Direct Electrical Readout in Au-Si Nanojunctions

Nanoplasmonic sensors are heralding exciting advances as clinical diagnostics as they facilitate label-free, real-time, and ultrasensitive monitoring in a small footprint. But in essence, almost all of them still largely rely on expensive and bulky spectroscopy/imaging instrumentation and methodology, which has become the major impediment for point-of-care (POC) testing implantation. In this context, an ultracompact optical sensor is achieved with direct electrical read-out capacity by combining plasmonic sensing resonance and optical-signal-transducing into a unity integrated device. Benefiting from the convergence of high figure-of-merit (∼190) resonance and hot electron enhanced photoelectric conversions on the near-flat Au-Si nanotrench framework, the device is demonstrated to yield a detection limit on the order of 10^-6 RIU in a broadband operating wavelength window (700-1700 nm). Such a compact, silicon process compatible, and ultrasensitive optoelectronic sensing platform holds great potentials for future clinical POC detection and on-chip microspectrometer applications.

Passivated aluminum nanohole arrays for label-free biosensing applications

We report the fabrication and performance of a surface plasmon resonance aluminum nanohole array refractometric biosensor. An aluminum surface passivation treatment based on oxygen plasma is developed in order to circumvent the undesired effects of oxidation and corrosion usually found in aluminum-based biosensors. Immersion tests in deionized water and device simulations are used to evaluate the effectiveness of the passivation process. A label-free bioassay based on biotin analysis through biotin-functionalized dextran-lipase conjugates immobilized on the biosensor-passivated surface in aqueous media is performed as a proof of concept to demonstrate the suitability of these nanostructured aluminum films for biosensing.

Activation of Src family tyrosine kinases by ferric ions

The Src-family tyrosine kinases (SFKs) are oncogenic enzymes that contribute to the initiation and progression of many types of cancer. In normal cells, SFKs are kept in an inactive state mainly by phosphorylation of a consensus regulatory tyrosine near the C-terminus (Tyr(530) in the SFK c-Src). As recent data indicate that tyrosine modification enhances binding of metal ions, the hypothesis that SFKs might be regulated by metal ions was investigated. The c-Src C-terminal peptide bound two Fe(3+) ions with affinities at pH4.0 of 33 and 252μM, and phosphorylation increased the affinities at least 10-fold to 1.4 and 23μM, as measured by absorbance spectroscopy. The corresponding phosphorylated peptide from the SFK Lyn bound two Fe(3+) ions with much higher affinities (1.2pM and 160nM) than the Src C-terminal peptide. Furthermore, when Lyn or Hck kinases, which had been stabilised in the inactive state by phosphorylation of the C-terminal regulatory tyrosine, were incubated with Fe(3+) ions, a significant enhancement of kinase activity was observed. In contrast Lyn or Hck kinases in the unphosphorylated active state were significantly inhibited by Fe(3+) ions. These results suggest that Fe(3+) ions can regulate SFK activity by binding to the phosphorylated C-terminal regulatory tyrosine.

Chain-specific antibodies for laminin-511

Mouse monoclonal antibodies (mAbs) that bind to specific chains of laminin-511 (LM-511) have been developed. Antibody 2F12 binds to the LMα5 chain, 3G10 binds to the LMβ1 chain and 3C12 binds to the LMγ1 chain. These antibodies can be used to purify LM-511, to detect LM-511 in cell extracts or to detect the location of LM-511 in tissue by immunohistochemistry. In combination, the antibodies recognize all three chains of LM-511 and combinations of the antibodies can be used to quantitate levels of LM-511 in physiological fluids. One of the antibodies (3G10) is a potent inhibitor of the activity of LM-511 in cell adhesion, spreading and proliferation assays.

Real-time label-free surface plasmon resonance biosensing with gold nanohole arrays fabricated by nanoimprint lithography

In this work we present a surface plasmon resonance sensor based on enhanced optical transmission through sub-wavelength nanohole arrays. This technique is extremely sensitive to changes in the refractive index of the surrounding medium which result in a modulation of the transmitted light. The periodic gold nanohole array sensors were fabricated by high-throughput thermal nanoimprint lithography. Square periodic arrays with sub-wavelength hole diameters were obtained and characterized. Using solutions with known refractive index, the array sensitivities were obtained. Finally, protein absorption was monitored in real-time demonstrating the label-free biosensing capabilities of the fabricated devices.

The propeptides of VEGF-D determine heparin binding, receptor heterodimerization, and effects on tumor biology

VEGF-D is an angiogenic and lymphangiogenic glycoprotein that can be proteolytically processed generating various forms differing in subunit composition due to the presence or absence of N- and C-terminal propeptides. These propeptides flank the central VEGF homology domain, that contains the binding sites for VEGF receptors (VEGFRs), but their biological functions were unclear. Characterization of propeptide function will be important to clarify which forms of VEGF-D are biologically active and therefore clinically relevant. Here we use VEGF-D mutants deficient in either propeptide, and in the capacity to process the remaining propeptide, to monitor the functions of these domains. We report for the first time that VEGF-D binds heparin, and that the C-terminal propeptide significantly enhances this interaction (removal of this propeptide from full-length VEGF-D completely prevents heparin binding). We also show that removal of either the N- or C-terminal propeptide is required for VEGF-D to drive formation of VEGFR-2/VEGFR-3 heterodimers which have recently been shown to positively regulate angiogenic sprouting. The mature form of VEGF-D, lacking both propeptides, can also promote formation of these receptor heterodimers. In a mouse tumor model, removal of only the C-terminal propeptide from full-length VEGF-D was sufficient to enhance angiogenesis and tumor growth. In contrast, removal of both propeptides is required for high rates of lymph node metastasis. The findings reported here show that the propeptides profoundly influence molecular interactions of VEGF-D with VEGF receptors, co-receptors, and heparin, and its effects on tumor biology.

Identification of a Wnt-induced protein complex by affinity proteomics using an antibody that recognizes a sub-population of β-catenin

β-catenin is a signaling protein with diverse functions in cell adhesion and Wnt signaling. Although β-catenin has been shown to participate in many protein-protein interactions, it is not clear which combinations of β-catenin-interacting proteins form discrete complexes. We have generated a novel antibody, termed 4B3, which recognizes only a small subset of total cellular β-catenin. Affinity proteomics using 4B3, in combination with subcellular fractionation, has allowed us to define a discrete trimeric complex of β-catenin, α-catenin and the tumor suppressor APC, which forms in the cytoplasm in response to Wnt signaling. Depletion of the limiting component of this complex, APC, implicates the complex in mediating Wnt-induced changes in cell-cell adhesion. APC is also essential for N-terminal phosphorylation of β-catenin within this complex. Each component of β-catenin/APC/α-catenin complex co-exists in other protein complexes, thus use of a selective antibody for affinity proteomics has allowed us to go beyond the generation of a list of potential β-catenin-interacting proteins, and define when and where a specific complex forms.

Efficient immobilization and patterning of biomolecules on poly(ethylene terephthalate) films functionalized by ion irradiation for biosensor applications

The surface of a poly(ethylene terephthalate) (PET) film was selectively irradiated with proton beams at various fluences to generate carboxylic acid groups on the surface; the resulting functionalized PET surface was then characterized in terms of its wettability, chemical structure, and chemical composition. The results revealed that (i) carboxylic acid groups were successfully generated in the irradiated regions of the PET surface, and (ii) their relative amounts were dependent on the fluence. A capture biomolecule, anthrax toxin probe DNA, was selectively immobilized on the irradiated regions on the PET surface. Cy3-labeled DNA as a target biomolecule was then hybridized with the probe DNA immobilized on the PET surface. Liver-cancer-specific α-fetoprotein (AFP) antigen, as a target biomolecule, was also selectively immobilized on the irradiated regions on the PET surface. Texas Red-labeled secondary antibody was then reacted with an AFP-specific primary antibody prebound to the AFP antigen on the PET surface for the detection of the target antigen, using an indirect immunoassay method. The results revealed that (i) well-defined micropatterns of biomolecules were successfully formed on the functionalized PET surfaces and (ii) the fluorescence intensity of the micropatterns was dependent mainly on the concentrations of the target DNA hybridized to the probe DNA and the target AFP antigen immobilized on the PET films. The lowest detectable concentrations of the target DNA and target AFP antigen in this study were determined to be 4 and 16 ng/mL, respectively, with the PET film prepared at a fluence of 5 × 10(14) ions/cm(2).

A roadmap to generate renewable protein binders to the human proteome

Despite the wealth of commercially available antibodies to human proteins, research is often hindered by their inconsistent validation, their poor performance and the inadequate coverage of the proteome. These issues could be addressed by systematic, genome-wide efforts to generate and validate renewable protein binders. We report a multicenter study to assess the potential of hybridoma and phage-display technologies in a coordinated large-scale antibody generation and validation effort. We produced over 1,000 antibodies targeting 20 SH2 domain proteins and evaluated them for potency and specificity by enzyme-linked immunosorbent assay (ELISA), protein microarray and surface plasmon resonance (SPR). We also tested selected antibodies in immunoprecipitation, immunoblotting and immunofluorescence assays. Our results show that high-affinity, high-specificity renewable antibodies generated by different technologies can be produced quickly and efficiently. We believe that this work serves as a foundation and template for future larger-scale studies to create renewable protein binders.

Characterization of a novel JNK (c-Jun N-terminal kinase) inhibitory peptide

An improved understanding of the roles of protein kinases in intracellular signalling and disease progression has driven significant advances in protein kinase inhibitor discovery. Peptide inhibitors that target the kinase protein substrate-binding site have continued to attract attention. In the present paper, we describe a novel JNK (c-Jun N-terminal kinase) inhibitory peptide PYC71N, which inhibits JNK activity in vitro towards a range of recombinant protein substrates including the transcription factors c-Jun, ATF2 (activating trancription factor 2) and Elk1, and the microtubule regulatory protein DCX (doublecortin). Analysis of cell culture studies confirmed the actions of a cell-permeable version of PYC71 to inhibit c-Jun phosphorylation during acute hyperosmotic stress. The analysis of the in vitro data for the kinetics of this inhibition indicated a substrate–inhibitor complex-mediated inhibition of JNK by PYC71N. Alanine-scanning replacement studies revealed the importance of two residues (PYC71N Phe9 or Phe11 within an FXF motif) for JNK inhibition. The importance of these residues was confirmed through interaction studies showing that each change decreased interaction of the peptide with c-Jun. Furthermore, PYC71N interacted with both non-phosphorylated (inactive) JNK1 and the substrate c-Jun, but did not recognize active JNK1. In contrast, a previously characterized JNK-inhibitory peptide TIJIP [truncated inhibitory region of JIP (JNK-interacting protein)], showed stronger interaction with active JNK1. Competition binding analysis confirmed that PYC71N inhibited the interaction of c-Jun with JNK1. Taken together, the results of the present study define novel properties of the PYC71N peptide as well as differences from the characterized TIJIP, and highlight the value of these peptides to probe the biochemistry of JNK-mediated substrate interactions and phosphorylation.

Sensitive and selective detection of free FXIII activation peptide: a potential marker of acute thrombotic events

Coagulation factor XIII (FXIII) stabilizes fibrin fibers and is therefore a major player in the maintenance of hemostasis. FXIII is activated by thrombin resulting in cleavage and release of the FXIII activation peptide (AP-FXIII). The objective of this study was to characterize the released AP-FXIII and determine specific features that may be used for its specific detection. We analyzed the structure of bound AP-FXIII within the FXIII A-subunit and interactions of AP-FXIII by hydrogen bonds with both FXIII A-subunit monomers. We optimized our previously developed AP-FXIII ELISA by using 2 monoclonal antibodies. We determined high binding affinities between the antibodies and free AP-FXIII and demonstrated specific binding by epitope mapping analyses with surface plasmon resonance and enzyme-linked immunosorbent assay. Because the structure of free AP-FXIII had been characterized so far by molecular modeling only, we performed structural analysis by nuclear magnetic resonance. Recombinant AP-FXIII was largely flexible both in plasma and water, differing significantly from the rigid structure in the bound state. We suggest that the recognized epitope is either occluded in the noncleaved form or possesses a structure that does not allow binding to the antibodies. On the basis of our findings, we propose AP-FXIII as a possible new marker for acute thrombotic events.

Generation of novel anti-BTLA monoclonal antibodies for in vivo use and their functional testing at near-physiological conditions

We have generated and characterized a panel of monoclonal antibodies recognizing B and T lymphocyte attenuator (BTLA), a transmembrane protein expressed on essentially all lymphoid cells. One of the monoclonal antibodies (MAbs) detects for the first time all BTLA protein variants described for various mouse strains with high sensitivity, both in flow cytometry and immunohistology. Further tests have determined that this MAb recognizes a BTLA epitope independent of the HVEM binding site. Moreover, we identified a number of antibodies capable of efficiently blocking the interaction of BTLA with its ligand herpes virus entry mediator (HVEM). A series of experiments was performed with these MAbs at near-physiological conditions to assess their blocking potential in vivo. These tests, performed with whole MAbs and also their F(ab)(2) formats, revealed that measurements of binding at 37 degrees C to primary cells expressing the target protein on the cell surface offer superior information on their blocking capacity. The generated BTLA-specific MAb will be used for in vivo studies to further elucidate the biological role of BTLA-HVEM interaction and function in vivo.

A monomeric chicken IgY receptor binds IgY with 2:1 stoichiometry

IgY is the principal serum antibody in birds and reptiles, and an IgY-like molecule was the evolutionary precursor of both mammalian IgG and IgE. A receptor for IgY on chicken monocytes, chicken leukocyte receptor AB1 (CHIR-AB1), lies in the avian leukocyte receptor cluster rather than the classical Fc receptor cluster where the genes for mammalian IgE and IgG receptors are found. IgG and IgE receptors bind to the lower hinge region of their respective antibodies with 1:1 stoichiometry, whereas the myeloid receptor for IgA, FcalphaRI, and the IgG homeostasis receptor, FcRn, which are found in the mammalian leukocyte receptor cluster, bind with 2:1 stoichiometry between the heavy chain constant domains 2 and 3 of each heavy chain. In this paper, the extracellular domain of CHIR-AB1 was expressed in a soluble form and shown to be a monomer that binds to IgY-Fc with 2:1 stoichiometry. The two binding sites have similar affinities: K(a)(1) = 7.22 +/- 0.22 x 10(5) m(-1) and K(a)(2) = 3.63 +/- 1.03 x 10(6) m(-1) (comparable with the values reported for IgA binding to its receptor). The affinity constants for IgY and IgY-Fc binding to immobilized CHIR-AB1 are 9.07 +/- 0.07 x 10(7) and 6.11 +/- 0.02 x 10(8) m(-1), respectively, in agreement with values obtained for IgY binding to chicken monocyte cells and comparable with reported values for human IgA binding to neutrophils. Although the binding site for CHIR-AB1 on IgY is not known, the data reported here with a monomeric receptor binding to IgY at two sites with low affinity suggest an IgA-like interaction.

Computational investigation of nanohole array based SPR sensing using phase shift

We present a new high spatial resolution sensor for monitoring refractive index variations caused by binding of organic and biological molecules to the metallic surface containing arrays of nanoholes. Signal transduction is provided through detecting the optical phase change in the extraordinary optical transmission (EOT) effected by surface plasmon resonance (SPR). These 2D nanoholes are well suited for the sensor chip format in which high dense integration is readily achievable. While the sensor operates at normal illumination, practical implementation of the sensor is much easier in comparison to the traditional Kretschmann arrangement for SPR sensing. Various design parameters of the device have been studied by simulation. Our results indicate that the scheme has a shot-noise limited sensitivity threshold of 4.37 x 10(-9) refractive index units (RIU) and a dynamic range of 0.17 RIU, which compare favorably with typical SPR sensors, particularly in terms of achieving high resolution and wide dynamic range sensor attributes. The phase change is also quite linear over the entire refractive index detection range.

A truncated soluble epidermal growth factor receptor-Fc fusion ligand trap displays anti-tumour activity in vivo

A number of therapeutic strategies including small molecule tyrosine kinase inhibitors and monoclonal antibodies have been developed to target the epidermal growth factor receptor (EGFR) signalling axis for the treatment of cancer. To date, the focus of therapeutic intervention has been the EGFR itself. In the current study, we have assembled and expressed in mammalian cells a soluble, EGFR ligand trap comprising the first 501 amino acids of the mature EGFR sequence fused in-frame with a human IgG Fc domain. The fusion protein, designated sEGFR501.Fc, was secreted as a 220 kDa disulphide-linked homodimer that exhibited high affinity (0.4-8 nM) in competition assays for a number of EGFR ligands including EGF and transforming growth factor-alpha (TGF-alpha). sEGFR501.Fc inhibited EGF-stimulated tyrosine phosphorylation of the EGFR of the lung cancer cell lines A549 and H1437, and inhibited and blocked the proliferation of H1437 cells. Administration of sEGFR501.Fc to mice bearing human tumour xenografts derived from A431 (epidermoid carcinoma) and DU145 (androgen-independent prostate cancer) tumour cell lines resulted in modest retardation of tumour growth. These results provide proof-in-principle that using high affinity soluble receptors is a viable method for inhibiting multi-ligand systems, and the impetus to optimize this approach and develop reagents with greater affinity and broader specificity.

New assay to detect low-affinity interactions and characterization of leukocyte receptors for collagen including leukocyte-associated Ig-like receptor-1 (LAIR-1)

Leukocyte activity is controlled by numerous interactions between membrane receptors and ligands on the cell surface. These interactions are of low affinity making detection difficult. We developed a sensitive assay that could readily detect extremely weak interactions such as that between CD200 and the activating receptor CD200RLa (K(d)>500 microM) at the protein level. We used the new technology to screen for interactions of inhibitory receptors for collagens. We confirmed that both human and mouse leukocyte-associated Ig-like receptor-1, and in addition the related inhibitory leukocyte Ig-like receptor subfamily B member 4 (CD85K, Gp49B), bound collagen specifically, whereas other cell surface proteins gave no binding. The monomeric affinities of the interactions were then determined to allow comparison with other leukocyte interactions and indicate conditions when these interactions might lead to inhibitory signals.

High sensitivity detection of 16s rRNA using peptide nucleic acid probes and a surface plasmon resonance biosensor

A signal enhancing method allowing highly sensitive detection of E. coli 16s rRNA was developed using peptide nucleic acid (PNA) as a capture probe and a surface plasmon resonance (SPR) sensor as a detector. 16s rRNA has been used as a genetic marker for identification of organisms, and can be analyzed directly without PCR amplification due to the relatively high number of copies. PNA has a neutral backbone structure, therefore hybridization with 16s rRNA results in the ionic condition being changed from neutral to negative. A cationic Au nanoparticle was synthesized and used for signal amplification by ionic interaction with 16s rRNA hybridized on the PNA probe-immobilized SPR sensor chip. This method resulted in a detection limit of E. coli rRNA of 58.2+/-1.37 pg mL(-1). Using this analytical method, Staphylococcus aureus was detected without purification of rRNA.

Use of multidimensional separation protocols for the purification of trace components in complex biological samples for proteomics analysis

The routine detection of low abundance components in complex samples for detailed proteomics analysis continues to be a challenge. Whilst the potential of multidimensional chromatographic fractionation for this purpose has been proposed for some years, and was used effectively for the purification to homogeneity of trace components in bulk biological samples for N-terminal sequence analysis, its practical application in the proteomics arena is still limited. This article reviews some of the recent data using these approaches, including the use of microaffinity purification as part of multidimensional protocols for downstream proteomics analysis.

Isolation and affinity maturation of hapten-specific antibodies

More and more recombinant antibodies specific for haptens such as drugs of abuse, dyes and pesticides are being isolated from antibody libraries. Thereby isolated antibodies tend to possess lower affinity than their parental, full-size counterparts, and therefore the isolation techniques must be optimized or the antibody genes must be affinity-matured in order to reach high affinities and specificities required for practical applications. Several strategies have been explored to obtain high-affinity recombinant antibodies from antibody libraries: At the selection level, biopanning optimization can be performed through elution with free hapten, analogue pre-incubation and subtractive panning. At the mutagenesis level, techniques such as random mutagenesis, bacterial mutator strains passaging, site-directed mutagenesis, mutational hotspots targeting, parsimonious mutagenesis, antibody shuffling (chain, DNA and staggered extension process) have been used with various degrees of success to affinity mature or modify hapten-specific antibodies. These techniques are reviewed, illustrated and compared.

Preparing a highly specific inert immunomolecular-magnetic beads for rapid detection and separation of S. aureus and group G Streptococcus

The rapid detection and separation of Staphylococcus aureus and group G Streptococcus was based on the affinity chromatography interactions between Fc fragment of human IgG and protein A/G (located on the cell wall of S. aureus and group G Streptococcus). In this case, immobilization of antibodies had to take place in a different and complementary way than in the case of conventional immunosensors. In this study, three different kinds of immunomolecular-magnetic beads (IMB) were prepared for rapid detection and separation of S. aureus and group G Streptococcus (GGS). The Fc regions of the immobilized antibodies were fully accessible to adsorb protein A or protein G. On the contrary, conventional immunosensors had to have fully accessible Fab regions to facilitate the antigen-antibody recognition. It was suggested that the worse method of immobilization of the antibodies for conventional use would yield the better results for this specific use. In this study, we also perfectly solved the nonspecific adsorptions and interaction problems, which were the most serious critical problems for all kinds of sensors. It was achieved by blocking the excess surface groups of aldehyde IMB and the Fab region of the immobilized antibodies with aldehyde-dextran.

Proprotein convertases promote processing of VEGF-D, a critical step for binding the angiogenic receptor VEGFR-2

Vascular endothelial growth factor (VEGF)-D is a secreted glycoprotein that induces angiogenesis and lymphangiogenesis. It consists of a central domain, containing binding sites for VEGF receptor-2 (VEGFR-2) and VEGFR-3, and N- and C-terminal propeptides. It is secreted from the cell as homodimers of the full-length form that can be proteolytically processed to remove the propeptides. It was recently shown, using adenoviral gene delivery, that fully processed VEGF-D induces angiogenesis in vivo, whereas full-length VEGF-D does not. To better understand these observations, we monitored the effect of VEGF-D processing on receptor binding using a full-length VEGF-D mutant that cannot be processed. This mutant binds VEGFR-2, the receptor signaling for angiogenesis, with approximately 17,000-fold lower affinity than mature VEGF-D, indicating the importance of processing for interaction with this receptor. Further, we show that members of the proprotein convertase (PC) family of proteases promote VEGF-D processing, which facilitates the VEGF-D/VEGFR-2 interaction. The PCs furin and PC5 promote cleavage of both propeptides, whereas PC7 promotes cleavage of the C-terminal propeptide only. The finding that PCs promote activation of VEGF-D and other proteins with roles in cancer such as matrix metalloproteinases, emphasizes the importance of these enzymes as potential regulators of tumor progression and metastasis.

Human ribosomal protein L7 displays an ER binding property and is involved in ribosome-ER association

Human ribosomal protein L7 incorporates an ER-binding characteristic. It is evident from the in vivo ER co-localization of the transiently expressed recombinant L7 in mycophenolic acid treated HeLa cells, the in situ detection of the fluorescent L7 at the ER in digitonin-permeablized HeLa cells, and the expression of a similar K(D) value to ribosomes binding to the ER. However, no ER co-localization and a lower K(D) was observed if the last 50 amino acid residues at the carboxyl end of L7 were removed, implying that the carboxyl region embodies the ER-binding specificity. Based on the inhibitory effect of an anti L7 antibody during ribosome rebinding to the microsome, we suggest that the L7-ER-binding nature could be one of multiple factors that allow a nascent peptide-less ribosome to remain at the ER.

The unfolded protein response transducer Ire1p contains a nuclear localization sequence recognized by multiple beta importins

The Ire1p transmembrane receptor kinase/endonuclease transduces the unfolded protein response (UPR) from the endoplasmic reticulum (ER) to the nucleus in Saccharomyces cerevisiae. In this study, we analyzed the capacity of a highly basic sequence in the linker region of Ire1p to function as a nuclear localization sequence (NLS) both in vivo and in vitro. This 18-residue sequence is capable of targeting green fluorescent protein to the nucleus of yeast cells in a process requiring proteins involved in the Ran GTPase cycle that facilitates nuclear import. Mutagenic analysis and importin binding studies demonstrate that the Ire1p linker region contains overlapping potential NLSs: at least one classical NLS (within sequences 642KKKRKR647 and/or 653KKGR656) that is recognized by yeast importin alpha (Kap60p) and a novel betaNLS (646KRGSRGGKKGRK657) that is recognized by several yeast importin beta homologues. Kinetic binding data suggest that binding to importin beta proteins would predominate in vivo. The UPR, and in particular ER stress-induced HAC1 mRNA splicing, is inhibited by point mutations in the Ire1p NLS that inhibit nuclear localization and also requires functional RanGAP and Ran GEF proteins. The NLS-dependent nuclear localization of Ire1p would thus seem to be central to its role in UPR signaling.

In situ phosphorylation of immobilized receptors on biosensor surfaces: application to E-cadherin/beta-catenin interactions

Phosphorylation is a key posttranslational modification for modulating biological interactions. Biosensor technology is ideally suited for examining in real time the role of phosphorylation on protein-protein interactions in signaling pathways. We have developed processes for on-chip phosphorylation of immobilized receptors on biosensor surfaces. These processes have been used to analyze E-cadherin/beta-catenin interactions. Phosphorylation of the intracellular domain (ICD) of E-cadherin modulates its affinity to beta-catenin and consequently the strength of cell-cell adhesion. We have phosphorylated immobilized E-cadherin ICD in situ using casein kinase 1 (CK1), casein kinase 2 (CK2), and src. On-chip phosphorylation of E-cadherin was confirmed using anti-phosphoserine and anti-phosphotyrosine antibodies. The binding of beta-catenin to E-cadherin was analyzed quantitatively. CK1 phosphorylation of E-cadherin increased the binding affinity to beta-catenin from approximately 230 to 4 nM. A similar increase in affinity, from 260 to 4 nM, was obtained with CK2 phosphorylation of E-cadherin. However, phosphorylation by src kinase decreased the affinity constant from approximately 260 nM to 4 microM. Interestingly, phosphorylation of E-cadherin by CK1 or CK2 prevented the inhibition of beta-catenin binding by src phosphorylation.

Indispensable, Functionally Complementing N and C-terminal Domains Constitute Site-specific Topoisomerase I

Mycobacterium smegmatis topoisomerase I differs from the typical type IA topoisomerase in many properties. The enzyme recognizes both single and double-stranded DNA with high affinity and makes sequence-specific contacts during DNA relaxation reaction. The enzyme has a conserved N-terminal domain and a highly varied C-terminal domain, which lacks the characteristic zinc binding motifs found in most of the type I eubacterial enzymes. The roles of the individual domains of the enzyme in the topoisomerase I catalyzed reactions were examined by comparing the properties of full-length topoisomerase I with those of truncated polypeptides lacking the conserved N-terminal or the divergent C-terminal region. The N-terminal larger fragment retained the site-specific binding, DNA cleavage and religation properties, hallmark characteristics of the full-length M.smegmatis topoisomerase I. In contrast, the non-conserved C-terminal fragment lacking the typical DNA binding motif, exhibited non-specific DNA binding behaviour. The two polypeptide fragments, on their own do not catalyze DNA relaxation reaction. The relaxation activity is restored when both the fragments are mixed in vitro reconstituting the enzyme function. These results along with the DNA interaction pattern of the proteins implicate an essential role for the C-terminal region in single-strand DNA passage between the two transesterification reactions catalyzed by the N-terminal domain.

Serodiagnostic Comparison between Two Methods, ELISA and Surface Plasmon Resonance for the Detection of Antibodies of Classical Swine Fever

A protein chip based on surface plasmon resonance (SPR) was developed to measure the antibody (Ab) titers of classical swine fever virus (CSFV) using the recombinant gp55 protein as an antigen. The diagnostic potential of this SPR assay for detecting the Ab titers to CSFV gp55 was compared that of the enzyme-linked immunosorbent assay (ELISA) using 170 serum samples from 14 pig farms. The SPR assay was highly specific and sensitive, and there were no cross-reactions detected. There was a strong positive correlation between the SPR and ELISA titers (n=170, r=0.869, p<0.01). Therefore, the SPR label-free method is a valuable tool in the serodiagnosis of CSFV infection and determining Ab titers after vaccination.

Fiber-optic nanosensors for single-cell monitoring

This article is an overview of the fabrication, operating principles, and applications of fiber-optic nanobiosensors with the capability of in-vivo analysis at the single-cell level. Recently, the cross-disciplinary integration of nanotechnology, biology, and photonics has been revolutionizing important areas in molecular biology, especially diagnostics and therapy at the molecular and cellular level. Fiber-optic nanobiosensors are a unique class of biosensor that enable analytical measurements in individual living cells and the probing of individual chemical species in specific locations within a cell. This article provides a review of the research performed in our laboratory and discusses the usefulness and potential of this nanotechnology-based biosensor system in biological research and its applications to biomonitoring of individual cells.

Development of an assay for the quantification of type I collagen synthesis in the guinea pig

There is a need for a reliable assay for the quantification of collagen type I synthesis in the guinea pig, an important model for many connective tissue diseases. Procollagen type I C-terminal propeptide (PICP) is the established marker of type I collagen synthesis but, to date, no assay has been developed to measure PICP in guinea pig tissue extracts. A monoclonal antibody, known to cross-react with intact guinea pig procollagen type I (anti-PICP), was tested for its ability to bind soluble guinea pig PICP in crude skin extracts using a biosensor. Anti-PICP was immobilised to the surface of a sensor chip and antibody-antigen binding was detected using the phenomenon of surface plasmon resonance (SPR). The binding component in the SPR-immunoassay was identified as PICP by purification and N-terminal sequencing. Guinea pig PICP was purified from skin by gel filtration, ion exchange chromatography and lectin affinity chromatography. Purified PICP was then biotinylated and used with anti-PICP to develop a competition ELISA that was able to selectively and sensitively measure PICP in extracts of guinea pig connective tissue.