Determination of Ribonuclease H Surface Enzyme Kinetics by Surface Plasmon Resonance Imaging and Surface Plasmon Fluorescence Spectroscopy

Deciphering heterogeneous enzymatic surface reactions on xylan using surface plasmon resonance spectroscopy

Xylans' unique properties make it attractive for a variety of industries, including paper, food, and biochemical production. While for some applications the preservation of its natural structure is crucial, for others the degradation into monosaccharides is essential. For the complete breakdown, the use of several enzymes is required, due to its structural complexity. In fact, the specificity of enzymatically-catalyzed reactions is guided by the surface, limiting or regulating accessibility and serving structurally encoded input guiding the actions of the enzymes. Here, we investigate enzymes at surfaces rich in xylan using surface plasmon resonance spectroscopy. The influence of diffusion and changes in substrate morphology is studied via enzyme surface kinetics simulations, yielding reaction rates and constants. We propose kinetic models, which can be applied to the degradation of multilayer biopolymer films. The most advanced model was verified by its successful application to the degradation of a thin film of polyhydroxybutyrate treated with a polyhydroxybutyrate-depolymerase. The herein derived models can be employed to quantify the degradation kinetics of various enzymes on biopolymers in heterogeneous environments, often prevalent in industrial processes. The identification of key factors influencing reaction rates such as inhibition will contribute to the quantification of intricate dynamics in complex systems.

Kinetic Model for the Heterogeneous Biocatalytic Reactions Using Tethered Cofactors

Understanding the mechanism of interfacial enzyme kinetics is critical to the development of synthetic biological systems for the production of value-added chemicals. Here, the interfacial kinetics of the catalysis of β-nicotinamide adenine dinucleotide (NAD+)-dependent enzymes acting on NAD+ tethered to the surface of silica nanoparticles (SiNPs) has been investigated using two complementary and supporting kinetic approaches: enzyme excess and reactant (NAD+) excess. Kinetic models developed for these two approaches characterize several critical reaction steps including reversible enzyme adsorption, complexation, decomplexation, and catalysis of the surface-bound enzyme/NAD+ complex. The analysis reveals a concentrating effect resulting in a very high local concentration of enzyme and cofactor on the particle surface, in which the enzyme is saturated by surface-bound NAD, facilitating a rate enhancement of enzyme/NAD+ complexation and catalysis. This resulted in high enzyme efficiency within the tethered NAD+ system compared to that of the free enzyme/NAD+ system, which increases with decreasing enzyme concentration. The role of enzyme adsorption onto solid substrates with a tethered catalyst (such as NAD+) has potential for creating highly efficient flow biocatalytic systems.

Hydrolysis of Oligodeoxyribonucleotides on the Microarray Surface and in Solution by Catalytic Anti-DNA Antibodies in Systemic Lupus Erythematosus

Anti-DNA antibodies are known to be classical serological hallmarks of systemic lupus erythematosus (SLE). In addition to high-affinity antibodies, the autoantibody pool also contains natural catalytic anti-DNA antibodies that recognize and hydrolyze DNA. However, the specificity of such antibodies is uncertain. In addition, DNA binding to a surface such as the cell membrane, can also affect its recognition by antibodies. Here, we analyzed the hydrolysis of short oligodeoxyribonucleotides (ODNs) immobilized on the microarray surface and in solution by catalytic anti-DNA antibodies from SLE patients. It has been shown that IgG antibodies from SLE patients hydrolyze ODNs more effectively both in solution and on the surface, compared to IgG from healthy individuals. The data obtained indicate a more efficient hydrolysis of ODNs in solution than immobilized ODNs on the surface. In addition, differences in the specificity of recognition and hydrolysis of certain ODNs by anti-DNA antibodies were revealed, indicating the formation of autoantibodies to specific DNA motifs in SLE. The data obtained expand our understanding of the role of anti-DNA antibodies in SLE. Differences in the recognition and hydrolysis of surface-tethered and dissolved ODNs need to be considered in DNA microarray applications.

Surface Plasmon-Assisted Fluorescence Enhancing and Quenching: From Theory to Application

The integration of surface plasmon resonance and fluorescence yields a multiaspect improvement in surface fluorescence sensing and imaging, leading to a paradigm shift of surface plasmon-assisted fluorescence techniques, for example, surface plasmon enhanced field fluorescence spectroscopy, surface plasmon coupled emission (SPCE), and SPCE imaging. This Review aims to characterize the unique optical property with a common physical interpretation and diverse surface architecture-based measurements. The fundamental electromagnetic theory is employed to comprehensively unveil the fluorophore-surface plasmon interaction, and the associated surface-modification design is liberally highlighted to balance the surface plasmon-induced fluorescence-enhancement efforts and the surface plasmon-caused fluorescence-quenching effects. In particular, all types of surface structures, for example, silicon, carbon, protein, DNA, polymer, and multilayer, are systematically interrogated in terms of component, thickness, stiffness, and functionality. As a highly interdisciplinary and expanding field in physics, optics, chemistry, and surface chemistry, this Review could be of great interest to a broad readership, in particular, among physical chemists, analytical chemists, and in surface-based sensing and imaging studies.

How Influenza's Spike Motor Works

While often believed to be a passive agent that merely exploits its host's metabolism, the influenza virus has recently been shown to actively move across glycan-coated surfaces. This form of enzymatically driven surface motility is currently not well understood and has been loosely linked to burnt-bridge Brownian ratchet mechanisms. Starting from known properties of influenza's spike proteins, we develop a physical model that quantitatively describes the observed motility. It predicts a collectively emerging dynamics of spike proteins and surface-bound ligands that combined with the virus' geometry give rise to a self-organized rolling propulsion. We show that in contrast to a Brownian ratchet, the rotary spike drive is not fluctuation driven but operates optimally as a macroscopic engine in the deterministic regime. The mechanism also applies to relatives of influenza and to man-made analogs like DNA monowheels and should give guidelines for their optimization.

Real-Time Interferometric Refractive Index Change Measurement for the Direct Detection of Enzymatic Reactions and the Determination of Enzyme Kinetics

Back scatter interferometry (BSI) is a sensitive method for detecting changes in the bulk refractive index of a solution in a microfluidic system. Here we demonstrate that BSI can be used to directly detect enzymatic reactions and, for the first time, derive kinetic parameters. While many methods in biomedical assays rely on detectable biproducts to produce a signal, direct detection is possible if the substrate or the product exert distinct differences in their specific refractive index so that the total refractive index changes during the enzymatic reaction. In this study, both the conversion of glucose to glucose-6-phosphate, catalyzed by hexokinase, and the conversion of adenosine-triphosphate to adenosine di-phosphate and mono-phosphate, catalyzed by apyrase, were monitored by BSI. When adding hexokinase to glucose solutions containing adenosine-triphosphate, the conversion can be directly followed by BSI, which shows the increasing refractive index and a final plateau corresponding to the particular concentration. From the initial reaction velocities, K_M was found to be 0.33 mM using Michaelis–Menten kinetics. The experiments with apyrase indicate that the refractive index also depends on the presence of various ions that must be taken into account when using this technique. This study clearly demonstrates that measuring changes in the refractive index can be used for the direct determination of substrate concentrations and enzyme kinetics.

High-speed DNA-based rolling motors powered by RNase H

DNA-based machines that walk by converting chemical energy into controlled motion could be of use in applications such as next-generation sensors, drug-delivery platforms and biological computing. Despite their exquisite programmability, DNA-based walkers are challenging to work with because of their low fidelity and slow rates (∼1 nm min(-1)). Here we report DNA-based machines that roll rather than walk, and consequently have a maximum speed and processivity that is three orders of magnitude greater than the maximum for conventional DNA motors. The motors are made from DNA-coated spherical particles that hybridize to a surface modified with complementary RNA; the motion is achieved through the addition of RNase H, which selectively hydrolyses the hybridized RNA. The spherical motors can move in a self-avoiding manner, and anisotropic particles, such as dimerized or rod-shaped particles, can travel linearly without a track or external force. We also show that the motors can be used to detect single nucleotide polymorphism by measuring particle displacement using a smartphone camera.

Comparison of static and microfluidic protease assays using modified bioluminescence resonance energy transfer chemistry

Background

Fluorescence and bioluminescence resonance energy transfer (F/BRET) are two forms of Förster resonance energy transfer, which can be used for optical transduction of biosensors. BRET has several advantages over fluorescence-based technologies because it does not require an external light source. There would be benefits in combining BRET transduction with microfluidics but the low luminance of BRET has made this challenging until now.

Methodology

We used a thrombin bioprobe based on a form of BRET (BRET^H), which uses the BRET¹ substrate, native coelenterazine, with the typical BRET² donor and acceptor proteins linked by a thrombin target peptide. The microfluidic assay was carried out in a Y-shaped microfluidic network. The dependence of the BRET^H ratio on the measurement location, flow rate and bioprobe concentration was quantified. Results were compared with the same bioprobe in a static microwell plate assay.

Principal Findings

The BRET^H thrombin bioprobe has a lower limit of detection (LOD) than previously reported for the equivalent BRET¹–based version but it is substantially brighter than the BRET² version. The normalised BRET^H ratio of the bioprobe changed 32% following complete cleavage by thrombin and 31% in the microfluidic format. The LOD for thrombin in the microfluidic format was 27 pM, compared with an LOD of 310 pM, using the same bioprobe in a static microwell assay, and two orders of magnitude lower than reported for other microfluidic chip-based protease assays.

Conclusions

These data demonstrate that BRET based microfluidic assays are feasible and that BRET^H provides a useful test bed for optimising BRET-based microfluidics. This approach may be convenient for a wide range of applications requiring sensitive detection and/or quantification of chemical or biological analytes.

Surface plasmon resonance sensing of nucleic acids: a review

Biosensors based on surface plasmon resonance (SPR) have become a central tool for the investigation and quantification of biomolecules and their interactions. Nucleic acids (NAs) play a vital role in numerous biological processes and therefore have been one of the major groups of biomolecules targeted by the SPR biosensors. This paper discusses the advances of NA SPR biosensor technology and reviews its applications both in the research of molecular interactions involving NAs (NA-NA, NA-protein, NA-small molecule), as well as for the field of bioanalytics in the areas of food safety, medical diagnosis and environmental monitoring.

Kinetics of enzyme action on surface-attached substrates: a practical guide to progress curve analysis in any kinetic situation

In the present work, exact kinetic equations describing the action of an enzyme in solution on a substrate attached to a surface have been derived in the framework of the Michaelis-Menten mechanism but without resorting to the often-used steady-state approximation. The here-derived kinetic equations are cast in a workable format, allowing us to introduce a simple and universal procedure for the quantitative analysis of enzyme surface kinetics that is valid for any kinetic situation. The results presented here should allow experimentalists studying the kinetics of enzyme action on immobilized substrates to analyze their data in a perfectly rigorous way.

Enzyme responsive materials: design strategies and future developments

Enzyme responsive materials (ERMs) are a class of stimuli responsive materials with broad application potential in biological settings. This review highlights current and potential future design strategies for ERMs and provides an overview of the present state of the art in the area.

Surface plasmon resonance based biosensor technique: a review

Optical Surface plasmon resonance (SPR) biosensors represent the most advanced and developed optical label-free biosensor technology. Optical SPR biosensors are a powerful detection and analysis tool that has vast applications in environmental protection, biotechnology, medical diagnostics, drug screening, food safety and security. This article reviews the recent development of SPR biosensor techniques, including bulk SPR and localized SPR (LSPR) biosensors, for detecting interactions between an analyte of interest in solution and a biomolecular recognition. The concepts of bulk and localized SPs and the working principles of both sensing techniques are introduced. Major sensing advances on biorecognition elements, measurement formats, and sensing platforms are presented. Finally, the discussions on both biosensor techniques as well as comparison of both SPR sensing techniques are made.

Optimizing electrode-attached redox-peptide systems for kinetic characterization of protease action on immobilized substrates. Observation of dissimilar behavior of trypsin and thrombin enzymes

In this work, we experimentally address the issue of optimizing gold electrode attached ferrocene (Fc)-peptide systems for kinetic measurements of protease action. Considering human α-thrombin and bovine trypsin as proteases of interest, we show that the recurring problem of incomplete cleavage of the peptide layer by these enzymes can be solved by using ultraflat template-stripped gold, instead of polished polycrystalline gold, as the Fc-peptide bearing electrode material. We describe how these fragile surfaces can be mounted in a rotating disk configuration so that enzyme mass transfer no longer limits the overall measured cleavage kinetics. Finally, we demonstrate that, once the system has been optimized, in situ real-time cyclic voltammetry monitoring of the protease action can yield high-quality kinetic data, showing no sign of interfering effects. The cleavage progress curves then closely match the Langmuirian variation expected for a kinetically controlled surface process. Global fit of the progress curves yield accurate values of the peptide cleavage rate for both trypsin and thrombin. It is shown that, whereas trypsin action on the surface-attached peptide closely follows Michaelis-Menten kinetics, thrombin displays a specific and unexpected behavior characterized by a nearly enzyme-concentration-independent cleavage rate in the subnanomolar enzyme concentration range. The reason for this behavior has still to be clarified, but its occurrence may limit the sensitivity of thrombin sensors based on Fc-peptide layers.

Enhanced fluorescence in a nanoporous waveguide and its quantitative analysis

Fluorescence behavior was examined for fluorophore-labeled protein (BSA-AF) adsorbed on the nanopore surface of a nanoporous waveguiding film. The waveguiding film has a bilayer structure of a porous anodic alumina (PAA) layer on a metallic aluminum (Al) layer, and this structure allows efficient interaction of fluorophores entrapped in the nanoporous waveguiding film with a hotspot of the enhanced electromagnetic field of the waveguide modes. Fluorescence response of BSA-AF depends on the enhanced field within the waveguiding film and the enlarged adsorbed amount in the PAA layer where most of the light is confined. Enhancement of the field in the waveguiding film can be controlled by the refractive index of the PAA layer and enlargement of the pore size efficiently affects the enhancement of the fluorescence response. Compared to the film without a PAA layer, the PAA/Al film exhibits more than 140-fold larger fluorescence response due to the large adsorption capacity of the PAA nanopores and the enhanced field formed by the waveguide modes in the PAA layer with a low refractive index.

Real-Time Analysis of Specific Protein-DNA Interactions with Surface Plasmon Resonance

Several proteins, like transcription factors, bind to certain DNA sequences, thereby regulating biochemical pathways that determine the fate of the corresponding cell. Due to these key positions, it is indispensable to analyze protein-DNA interactions and to identify their mode of action. Surface plasmon resonance is a label-free method that facilitates the elucidation of real-time kinetics of biomolecular interactions. In this article, we focus on this biosensor-based method and provide a detailed guide how SPR can be utilized to study binding of proteins to oligonucleotides. After a description of the physical phenomenon and the instrumental realization including fiber-optic-based SPR and SPR imaging, we will continue with a survey of immobilization methods. Subsequently, we will focus on the optimization of the experiment, expose pitfalls, and introduce how data should be analyzed and published. Finally, we summarize several interesting publications of the last decades dealing with protein-DNA and RNA interaction analysis by SPR.

Line-monitoring, hyperspectral fluorescence setup for simultaneous multi-analyte biosensing

Conventional fluorescence scanners utilize multiple filters to distinguish different fluorescent labels, and problems arise because of this filter-based mechanism. In this work we propose a line-monitoring, hyperspectral fluorescence technique which is designed and optimized for applications in multi-channel microfluidic systems. In contrast to the filter-based mechanism, which only records fluorescent intensities, the hyperspectral technique records the full spectrum for every point on the sample plane. Multivariate data exploitation is then applied to spectra analysis to determine ratios of different fluorescent labels and eliminate unwanted artifacts. This sensor is designed to monitor multiple fluidic channels simultaneously, providing the potential for multi-analyte biosensing. The detection sensitivity is approximately 0.81 fluors/μm², and this sensor is proved to act with a good homogeneity. Finally, a model experiment of detecting short oligonucleotides has demonstrated the biomedical application of this hyperspectral fluorescence biosensor.

A dual surface plasmon resonance assay for the determination of ribonuclease H activity

There is a demand for efficient tools for the monitoring of RNase H activity. We report on a new assay which allows for simultaneous (1) real-time monitoring of RNase H activity and (2) detection of cleavage reaction products. The dual assay is implemented using a multichannel surface plasmon resonance (SPR) biosensor with two independently functionalized sensing areas in a single fluidic path. In the first sensing area the RNA cleavage by RNase H is monitored, while the products of the cleavage reaction are captured in the second sensing area with specific DNA probes. The assay was optimized with respect to AON concentration and temperature. A significant improvement was obtained with special chimeric probes, which contain RNA substrate for RNase H and a longer deoxyribonucleotide tail, which enhances the SPR signal. It has been shown that RNase H stabilizes the RNA:DNA hybrid duplex before the cleavage. The potential of the assay is demonstrated in the study in which the ability of natural and modified oligonucleotides to activate RNase H is examined.

Imaging of surfaces by concurrent surface plasmon resonance and surface plasmon resonance-enhanced fluorescence

Surface plasmon resonance imaging and surface plasmon induced fluorescent are sensitive tools for surface analysis. However, existing instruments in this area have provided limited capability for concurrent detection, and may be large and expensive. We demonstrate a highly cost-effective system capable of concurrent surface plasmon resonance microscopy (SPRM) and surface plasmon resonance-enhanced fluorescence (SPRF) imaging, allowing for simultaneous monitoring of reflectivity and fluorescence from discrete spatial regions. The instrument allows for high performance imaging and quantitative measurements with surface plasmon resonance, and surface plasmon induced fluorescence, with inexpensive off-the-shelf components.

Surface plasmon resonance imaging for biosensing

Surface plasmon resonance imaging (SPRI) is a useful tool for the study of surface biomolecular interactions allowing for label-free detection and elegant instrumentation. SPRI imaging system is described in this review with an emphasis on recent applications with examples of different biological interactions and high throughput analysis. Signal amplification in SPRI using nanoparticle and waveguide-based optical coupling is introduced. Finally the detection sensitivity of the SPRI system is examined in terms of other competitive methods.

Quantitative serum proteomics from surface plasmon resonance imaging

The detection and quantification of specific proteins in complex mixtures is a major challenge for proteomics. For example, the development of disease-related biomarker panels will require fast and efficient methods for obtaining multiparameter protein profiles. We established a high throughput, label-free method for analyzing serum using surface plasmon resonance imaging of antibody microarrays. Microarrays were fabricated using standard pin spotting on bare gold substrates, and samples were applied for binding analysis using a camera-based surface plasmon resonance system. We validated the system by measuring the concentrations of four serum proteins using part of a 792-feature microarray. Transferrin concentrations were measured to be 2.1 mg/ml in human serum and 1.2 mg/ml in murine serum, which closely matched ELISA determinations of 2.6 and 1.2 mg/ml, respectively. In agreement with expected values, human and mouse albumin levels were measured to be 24.3 and 23.6 mg/ml, respectively. The lower limits of detection for the four measurements ranged from 14 to 58 ng/ml or 175 to 755 pm. Where purified target proteins are not available for calibration, the microarrays can be used for relative protein quantification. We used the antibody microarray to compare the serum protein profiles from three liver cancer patients and three non-liver cancer patients. Hierarchical clustering of the serum protein levels clearly distinguished two distinct profiles. Thirty-nine significant protein changes were detected (p < 0.05), 10 of which have been observed previously in serum. alpha-Fetoprotein, a known liver cancer marker, was observed to increase. These results demonstrate the feasibility of this high throughput approach for both absolute and relative protein expression profiling.

Detection of single-nucleotide polymorphisms using gold nanoparticles and single-strand-specific nucleases

The current study reports an assay approach that can detect single-nucleotide polymorphisms (SNPs) and identify the position of the point mutation through a single-strand-specific nuclease reaction and a gold nanoparticle assembly. The assay can be implemented via three steps: a single-strand-specific nuclease reaction that allows the enzyme to truncate the mutant DNA; a purification step that uses capture probe-gold nanoparticles and centrifugation; and a hybridization reaction that induces detector probe-gold nanoparticles, capture probe-gold nanoparticles, and the target DNA to form large DNA-linked three-dimensional aggregates of gold nanoparticles. At high temperature (63 degrees C in the current case), the purple color of the perfect match solution would not change to red, whereas a mismatched solution becomes red as the assembled gold nanoparticles separate. Using melting analysis, the position of the point mutation could be identified. This assay provides a convenient colorimetric detection that enables point mutation identification without the need for expensive mass spectrometry. To our knowledge, this is the first report concerning SNP detection based on a single-strand-specific nuclease reaction and a gold nanoparticle assembly.

Recent advances in surface plasmon resonance based techniques for bioanalysis

Surface plasmon resonance (SPR) is a powerful and versatile spectroscopic method for biomolecular interaction analysis (BIA) and has been well reviewed in previous years. This updated 2006 review of SPR, SPR spectroscopy, and SPR imaging explores cutting-edge technology with a focus on material, method, and instrument development. A number of recent SPR developments and interesting applications for bioanalysis are provided. Three focus topics are discussed in more detail to exemplify recent progress. They include surface plasmon fluorescence spectroscopy, nanoscale glassification of SPR substrates, and enzymatic amplification in SPR imaging. Through these examples it is clear to us that the development of SPR-based methods continues to grow, while the applications continue to diversify. Major trends appear to be present in the development of combined techniques, use of new materials, and development of new methodologies. Together, these works constitute a major thrust that could eventually make SPR a common tool for surface interaction analysis and biosensing. The future outlook for SPR and SPR-associated BIA studies, in our opinion, is very bright. Surface plasmon resonance (SPR) is a powerful and versatile spectroscopic method for biomolecular interaction analysis (BIA) and has been well reviewed in previous years. This updated 2006 review of SPR, SPR spectroscopy, and SPR imaging explores cutting-edge technology with a focus on material, method, and instrument development. A number of recent SPR developments and interesting applications for bioanalysis are provided. Three focus topics are discussed in more detail to exemplify recent progress. They include surface plasmon fluorescence spectroscopy, nanoscale glassification of SPR substrates, and enzymatic amplification in SPR imaging. Through these examples it is clear to us that the development of SPR-based methods continues to grow, while the applications continue to diversify. Major trends appear to be present in the development of combined techniques, use of new materials, and development of new methodologies. Together, these works constitute a major thrust that could eventually make SPR a common tool for surface interaction analysis and biosensing. The future outlook for SPR and SPR-associated BIA studies, in our opinion, is very bright.

Single-nucleotide polymorphism genotyping by nanoparticle-enhanced surface plasmon resonance imaging measurements of surface ligation reactions

A sensitive method for the analysis of single nucleotide polymorphisms (SNPs) in genomic DNA that utilizes nanoparticle-enhanced surface plasmon resonance imaging (SPRI) measurements of surface enzymatic ligation reactions on DNA microarrays is demonstrated. SNP identification was achieved by using sequence-specific surface reactions of the enzyme Taq DNA ligase, and the presence of ligation products on the DNA microarray elements was detected using SPRI through the hybridization adsorption of complementary oligonucleotides attached to gold nanoparticles. The use of gold nanoparticles increases the sensitivity of the SPRI so that single bases in oligonucleotides can be successfully identified at a concentration of 1 pM. This sensitivity is amply sufficient for performing multiplexed SNP genotyping by using multiple PCR amplicons and should also allow for the direct detection and identification of SNP sequences from 1 pM unamplified genomic DNA samples with this array-based and label-free SPRI methodology. As a first example of SNP genotyping, three different human genomic DNA samples were screened for a possible point mutation in the BRCA1 gene that is associated with breast cancer.

Survey of the year 2005 commercial optical biosensor literature

We identified 1113 articles (103 reviews, 1010 primary research articles) published in 2005 that describe experiments performed using commercially available optical biosensors. While this number of publications is impressive, we find that the quality of the biosensor work in these articles is often pretty poor. It is a little disappointing that there appears to be only a small set of researchers who know how to properly perform, analyze, and present biosensor data. To help focus the field, we spotlight work published by 10 research groups that exemplify the quality of data one should expect to see from a biosensor experiment. Also, in an effort to raise awareness of the common problems in the biosensor field, we provide side-by-side examples of good and bad data sets from the 2005 literature.