Biosensors research(Chambers et al., Taitt et al., Rogers et al.)

[Sophlei]

Biosensor Recognition Elements James P. Chambers, Bernard P. Arulanandam, Lean

• Selective overview of molecular recognition elements, including receptors, enzymes, antibodies, nucleic acids, molecular imprints and lectins currently impacting biosensor development
• describe the different recognition elements, the advantages and disadvantages of each element
• doesn’t talk about transduction of the biorecognition events

Definition of a receptor: Receptors are transmembrane (plasma and intracellular membranes) and soluble proteins that bind to specific molecules called ligands, the binding event initiating a specific cellular response. Ligand-induced receptor conformational changes give rise to subsequent events such as channel opening, adenyl/guanyl cyclase mediated second messenger generation, and reaction cascades involving a multitude of other proteins, including G proteins, tyrosine kinases, phosphatases, phosphorylases, transcription factors, and antigen processing cell receptor responses

Enzyme-based recognition: Catalytic enzyme based sensor recognition elements are very attractive for biosensor applications due to a variety of measurable reaction products arising from the catalytic process, which include protons, electrons, light, and heat. The enzyme urease has been widely used as a sensor biorecognition element due to a need for urea determination/monitoring for both medical and environmental applications

Importantly, the use of inactive apoenzymes for reversible sensing greatly simplifies the sensing platform as well as expands the range of metabolically important proteins that can be used as sensor biorecognition elements.

Antibody based recognition: The majority of rapid detection systems employ antibodies for recognition, identification and quantitation of target analytes. Antibodies have been used extensively for detection purposes. Antibody recognition elements make use of the sensitivity and specificity of bimolecular antibody–antigen interactions. The major advantage of antibody sensor biorecognition elements is that the immunogen, i.e. target, need not be purified prior to detection.

Aptamer based recognition: Aptamers are nucleic acid ligands (RNA, ssDNA, modified ssDNA, or modified RNA) that are isolated from libraries of oligonucleotides by an in vitro selection process called SELEX (Systematic Evolution of Ligands by EXponential enrichment) These DNA/RNA ligands are thought to recognize their target primarily by shape (i.e. conformation) and not sequence Aptamers bind with high affinity and specificity to a broad range of target molecules, and have proven suitable for analytic and diagnostic applications

Peptide nucleic acid based recognition: Peptide nucleic acids (PNA) are synthetic DNA analogues or mimics with a polyamide backbone instead of a sugar phosphate bone Of significant importance to biosensing, PNAs exhibit superior hybridization characteristics and improved chemical and enzymatic stability compared to nucleic acids The uncharged nature of PNAs is responsible for a better thermal stability of PNA–DNA duplexes compared with DNA–DNA equivalents

Molecular imprint based recognition: Molecular imprinting is a method for making selective binding sites in synthetic polymers using molecular templates. Molecular imprinted polymers offer great promise for development of very stable “solid-state like” artificial biosensing elements → inexpensive, accessible and effective strategy for developing sorbent materials exhibiting high specificity for selected substrate materials

Lectin based recognition: Lectins constitute a broad family of proteins involved in diverse biological processes, occasionally having potent toxic properties. Lectins generally exhibit strong binding to specific carbohydrate moieties known as glycans, and this property has been extensively exploited as a basis for biosensor design Lectins are excellent biorecognition elements due to high affinity for saccharide moieties via multivalent interactions arising from the spatial organization of oligosaccharide ligands. The selective binding of lectins to terminal carbohydrate moieties on cell surfaces and protein aggregates has been widely exploited Due to the high specificity of lectin biorecognition elements, lectin based sensors have been made which take advantage of advanced fluorescence techniques such as FRET

[Sophlei]

[Uploading Biosensor recognition elements.pdf…]()

[research555]

Thats cool, I checked out thew paper and its a pretty broad review. Do you think we can use any of this in our project?

[Sophlei]

I think it can help us to choose the most adapted recognition element for our project and then we can use more specific papers from the references to have more infos

[Sophlei]

Array biosensor for detection of biohazards Chris A Rowe-Taitt, Joel PGolden, Mark JFeldstein, John JCras, Karen EHoffman, Frances SLigler https://doi.org/10.1038/42432

article about the development of rapid assays for potentially hazardous analytes at concentrations similar to competing technologies and the testing of a fully automated system utilizing a computer-controlled fluidics system

A fluorescence-based biosensor has been developed for simultaneous analysis of multiple samples for multiple biohazardous agents. A patterned array of antibodies immobilized on the surface of a planar waveguide is used to capture antigen present in samples; bound analyte is then quantified by means of fluorescent tracer antibodies. This array biosensor has been used to detect toxins, toxoids, and killed or non-pathogenic (vaccine) strains of pathogenic bacteria.

Composition of this antibody array biosensor: an array of immobilized capture antibodies acting as molecular recognition elements an image capture and processing system an automated fluidics unit

Antibodies specific for hazardous analytes are immobilized in discrete regions on an avidin-coated waveguide by flowing solutions of biotinylated antibodies through a network of polymer channels that confine the solutions to separate regions Unknown sample is subsequently flowed over the substrate in an orientation perpendicular to the stripes of immobilized antibodies and any antigens present in the sample bind to the appropriate analyte-specific loci in the array.

work performed using the array biosensor has demonstrated that mixtures of fluorescent tracer antibodies can be used in rapid assays for protein, bacterial, and viral analytes with sensitivities similar to standard ELISAs

Methods of study: Assays were developed for six analytes potentially capable of causing illness or disease. These assays consisted of simple sandwich immunoassays performed on the surface of planar waveguides using biotinylated capture antibodies for antigen recognition; these platforms were prepared in advance of the assays and incubation of sample with the prepared substrates required only 7 min. Bound antigens were then detected by a 3 min incubation with fluorescent tracer molecules. Following this 14-min assay procedure, the location and intensity of evanescently excited fluorescent sandwiches were determined using a CCD and an automated analysis program to extract data from captured images. The total time required to perform the biochemical assay and extract data was less than 20 min.

→ detection of bacteria and toxins

Possible application: routine monitoring of environmental samples

The sandwich immunoassay format described here is designed to allow reuse of sensor substrates when negative results are obtained; competitive immunoassays require regeneration of substrates and removal of bound analyte before subsequent analyses. The key strength of the array sensor is its ability to analyze multiple samples for multiple analytes simultaneously. Only planar waveguide systems have demonstrated the ability to detect multiple analytes on a single sensor substrate

Automated tests: The automated fluidics protocol significantly streamlines the manipulations involved with running the assays; the user simply adds sample to appropriate vials, attaches buffer and reagent reservoirs, attaches the input and output manifolds to the pre-patterned waveguide, and starts the pre-programmed protocol. Following the assay, the automated data analysis program extracts data from the imaged slide and presents it to the user in both a tabular format and in an easy-to-read bubble-chart, clearly indicating the absence or presence of analyte in each sample lane.

Conclusion: The array biosensor assays multiple samples simultaneously for multiple analytes. Not only does it exhibit sensitivity comparable with other antibody-based methods that require sample aliquots to be assayed individually for different agents, but the multianalyte assays have been automated.

[Sophlei]

Array biosensor for detection of biohazards.pdf

[Sophlei]

Recent advances in biosensor techniques for environmental monitoring KR Rogers https://doi.org/10.1016/j.aca.2005.12.067

Sophie 23/03/2021

Review about recent advances in biosensors for environmental applications In addition to detecting and measuring specific compounds or compound classes such as pesticides, hazardous industrial chemicals, toxic metals, and pathogenic bacteria, biosensors and bioanalytical assays have been designed to measure biological effects such as cytotoxicity, genotoxicity, biological oxygen demand, pathogenic bacteria, and endocrine disruption effects.

Interest: Monitoring of contaminants in the air, water and soil is an instrumental component in understanding and managing risks to human health and the environment. → agricultural monitoring, ground water screening, ocean monitoring and global environmental monitoring

Enzyme-based biosensors: Advantages: a stable source of material (primarily through biorenewable sources), the ability to modify the catalytic properties or substrate specificity by means of genetic engineering, and catalytic amplification of the biosensor response by modulation of the enzyme activity with respect to the target analyte. Limits: the limited number of substrates for which enzymes have been evolved, the limited interaction between environmental pollutants and specific enzymes, and in the case of inhibitor formats, the lack of specificity in differentiating among compounds of similar classes such as nerve agents as well as organophosphate (OP) and carbamate pesticides Immobilization: One important step in biosensor development is immobilization of the biological recognition element to the sensor surface. A number of innovative immobilization techniques have been reported using enzymes. Approaches for these techniques include the use of new materials and incorporation of oxidation–reduction (redox) mediators into the immobilization process. Another innovation for immobilization of enzymes to biosensors involves the use of sol–gel. Advantages for this strategy include thermal stability, pH buffering and physical ruggedness typically required for environmental applications. Other approaches for immobilization of enzymes to environmental biosensors include combinations of covalent and non-covalent binding. Advances in processes and particularly in the area of electrochemistry have yielded improvements in operational characteristics of biosensors. For example, the sonochemical ablation of a non-conducting polymer-coated electrode produced microelectrode arrays Nanomaterials have also been used to improve the operational characteristics of enzyme-based biosensors. This improvement results from both increased surface area and increased catalytic activity.

Antibody-based biosensors: Advantages: Antibody-based biosensors (immunosensors) are inherently more versatile than enzyme-based biosensors in that antibodies have been generated which specifically bind to individual compounds or groups of structurally related compounds with a wide range of affinities. Limits: the complexity of assay formats and the number of specialized reagents (e.g., antibodies, antigens, tracers, etc.) that must be developed and characterized for each compound and the limited number of compounds typically determined in an individual assay as compared to the multiple compounds that contaminate environmental samples.

Cell-based biosensors: Bacteria have been genetically engineered to construct gene fusions typically composed of a regulatory system (i.e., native promoter) linked to a reporter(s) genes. For these genetically modified microorganisms often referred to as ’biosensors’ or ’bioreporters’, the presence of an effector (nonspecific stressor or biochemically active compound or toxin) results in a cascade of events that produces some measurable response. Effectors for which bioreporters have been constructed include: non-specific stressors such as DNA damage, gamma radiation, heat shock, and oxidative stress; toxic metals such as cadmium, chromate, cobalt, copper, iron, lead, mercury, nickel and zinc; organic environmental pollutants such as chlorinated aromatics, benzene derivatives, organic peroxides, trichloroethylene and PCBs; and compounds of biological importance such as nitrate, ammonia and antibiotics Advantages: Microorganisms are in some ways quite robust sensing elements in that they are continually synthesizing complex systems of enzymes, cofactors and nucleic acids. Once constructed, they are self replicating and many require only the effector to elicit a response. Bioreporter microorganisms also show the potential to be interfaced to a wide range of transducers including optical, electrochemical, piezoelectric and surface plasmon resonance. Limits: the maintenance of their environment (i.e., nutrients, O2, pH, ionic strength, etc.) and the time required for a response

Recent advances in reporter microorganisms have involved novel fusions of a wide range of promoters with conveniently measured reporters, as well as the construction of unique sensing platforms that can be used to study individual organisms as well as population responses. One of the classes of environmental pollutants that are well suited to bioreporter microorganisms are the volatile organic compounds (VOCs). microorganisms have also been engineered to respond to cytotoxic and genotoxic compounds using a variety of mechanisms. One of the challenges in measuring genotoxicity using GEM bioreceptors involves the threshold for cytotoxicity which is often slightly above the concentration required for a genotoxic response. Recent advances in bacterial luminescence assays for cytotoxicity primarily involve linking them to specific environmental applications. One example of this type of application is an automated continuous toxicity monitoring system using the genetically engineered fresh water bacterium Janthinobactrium Ividum YH9-RC that is sensitive to heavy metals as well as a number of toxic organic compounds Unmodified bacteria have also been used as biomarkers and bioindicators of generalized or compound-specific toxicity. Algae have also been used in cell-based biosensors and bioassays to measure several classes of environmental pollutants. In one example, the cyanobacterium Spirulina subsalsa was immobilized to an oxygen probe and placed in a flow cell configuration. This algal biosensor was reversibly responsive to heavy metals, triazine herbicides and carbamate insecticides A wide range of cell-based biosensor and bioanalytical assay systems have been employed for general characterization of ground water and waste water toxicity as well as for use as biological early warning systems (BEWS) in water treatment facilities. Three basic analyses where biosensors have made contributions include biological oxygen demand, toxicity analysis and detection of pathogenic organisms

DNA biosensors: Due to their wide range of physical, chemical and biological activities, nucleic acids have been incorporated into a wide range of biosensors and bioanalytical assays, many of which show the potential for adaptation to environmental applications. DNA has been used to measure Pb2+ by virtue of its catalytic activity. DNA and PNA have also been used to link immunochemicals to specific locations in DNA chip arrays by means of hybridization of complementary oligonucleotides several biosensors and bioassays have been reported for the detection of chemically-induced DNA damage. There is also an ongoing effort in the area of biosensor technology for measuring DNA hybridization prerequisite for genetic identification of pathogenic microorganisms. Advances in the development of hybridization biosensors have also included a visual DNA chip for detection of hepatitis virus, hybridization using lead labeled oligonucleotides detected by anodic stripping voltammetry , optical detection of hybridization using gold nanoparticles, and electrochemical detection of DNA hybridization using silver precipitation on gold nanoparticle-labeled oligonucleotides.

Receptor-based biosensors: Advantages: any detrimental environmental pollutant that will bind to the receptor at physiologically relevant concentrations can potentially be measured. Thus, these systems can be used to screen for a wide range structurally divers pollutants with a similar mechanism of toxicity.

Conclusion: Biosensors for potential environmental applications continue to show advances in areas such as genetic modification of enzymes and microorganisms, improvement of recognition element immobilization and sensor interfaces, and introduction of improved operational formats and unique environmental applications. Novel gene fusions have resulted in more sensitive and versatile reporters such as GFP and show the potential for construction of a battery of organisms that respond to a wide range of physical and chemical stressors using a single detection platform. A biosensor approach toward measuring genetic damage has involved the detection of chemically-induced damage to surrogate DNA. One of the challenges for this area will be the development of environmental applications related to ecosystem and human exposure to genotoxins. This would require the isolation and analysis of DNA after a suspected exposure of the organism to the genotoxic substance. This type of application would also require both high sensitivity to the extent of DNA damage and to the amount of DNA required for the analysis.

[Sophlei]

Recent advances in biosensor techniques for environmental monitoring.pdf

[nathaliaraquelx]

This biosensor approach to quantify genetic damage seems really cool.