# Patent

## Title
Biosensing system with extended lifetime via cofactor recycling

## Abstract

The present disclosure relates to biosensing systems and biosensing elements having increased storage capability and increased functional lifetimes through using compositions and methods for recycling cofactors.

## Background
RELATED APPLICATIONS
This application is a continuation of U.S. application Ser. No. 14/236,531 filed Jan. 31, 2014, which is a national phase entry under 35 U.S.C. § 371 of PCT/US2012/049384 filed Aug. 2, 2012, which claims priority under 35 U.S.C. § 119(e) to U.S. Provisional Patent Application No. 61/514,309 filed Aug. 2, 2011. PCT/US2012/049384 is a continuation-in-part of U.S. patent application Ser. No. 13/562,592 filed on Jul. 31, 2012. Each of these applications is specifically incorporated herein by reference to the extent not inconsistent herewith.


GOVERNMENT RIGHTS
This invention was made with Government support under contract number BES-0529048 awarded by the National Science Foundation. The U.S. Government has certain rights in this invention.


BACKGROUND
Biosensors use biological components to detect an analyte of interest. Biosensors have the potential to be excellent alternatives or complements to traditional analytical chemical methods for environmental and process monitoring. A biosensor is capable of real-time analysis with simplicity of operation. Biosensors are often reagentless and can provide continuous, in-situ measurements as a cost effective alternative compared with traditional analytical methods.
SUMMARY
In one aspect, a biosensing system comprising a biocomponent is disclosed wherein the biocomponent comprises a whole cell containing oxygenase enzymes and dehydrogenase enzymes. In an embodiment, the nucleotide coding sequence of the oxygenase enzymes are on a plasmid within the whole cell biocomponent. In an embodiment, the nucleotide coding sequence of the dehydrogenase enzymes are encoded for on a plasmid within the whole cell.
In another aspect, a method for regenerating NADH and NADPH cofactors in a biosensing system is disclosed wherein a whole cell biocomponent comprises an oxygenase enzyme and a dehydrogenase enzyme. In one embodiment, an oxygenase enzyme is selected from the group consisting of monooxygenases and dioxygenases. In another embodiment, the oxygenase enzyme is toluene ortho-monooxygenase. In another embodiment, the oxygenase enzyme is a toluene ortho-monooxygenase variant. In another embodiment, the dehydrogenase enzyme is formate dehydrogenase.
In one aspect, a method for regenerating NADH and NADPH cofactors in a biosensing system is disclosed wherein a whole cell biocomponent comprises an oxygenase enzyme and a dehydrogenase enzyme and wherein a substrate for the dehydrogenase enzyme is delivered to the whole cell biocomponent. In one embodiment, the oxygenase enzyme is toluene ortho-monooxygenase. In one embodiment, the oxygenase enzyme is a toluene ortho-monooxygenase variant. In another embodiment, dehydrogenase enzyme is formate dehydrogenase and the substrate is formate. In one embodiment, the substrate is delivered through a capillary to the whole cell biocomponent. In another embodiment, the substrate is delivered through diffusion to the biocomponent.
In another aspect, a biosensing system that detects an analyte in a solution is disclosed. The system comprises a first biocomponent that catalyzes the reaction of the analyte and oxygen and uses a cofactor selected from the group consisting of NADH, NADPH, FADH, FADH2, FMNH, and FMNH2.
The system also comprises a second biocomponent that catalyzes the reaction of NAD+, NADP+, FAD, FADH, FMN, FMNH and an electron donor. The first biocomponent and the second biocomponent are within a whole cell biocomponent. The whole cell biocomponent is immobilized within a matrix and the matrix is in contact with a transducer layer. The transducer layer is part of an optode. In one embodiment, the whole cell biocomponent is alive. In another embodiment, the whole cell biocomponent is dead. In one embodiment, the transducer layer is a chemical transducer that interacts with oxygen. In another embodiment, the transducer layer is an optical transducer that interacts with oxygen. In one embodiment, the first biocomponent is selected from the group consisting of monooxygenases and dioxygenases. In another embodiment, the second biocomponent is formate dehydrogenase and the electron donor is formate. In one embodiment, the matrix comprises soluble formate. In one embodiment, the biosensing system has an optode comprising a distal tip of a capillary tube wherein the capillary tube contains formate or a salt of formate, and wherein the capillary tube is disposed to deliver the formate through the distal tip to the whole cell biocomponent.
In one aspect, a method for detecting the concentration of an analyte in a solution is disclosed wherein the analyte is a reactant in a reaction catalyzed by an oxygenase enzyme that requires a cofactor selected from the group consisting of NADH, NADPH, FADH, FADH2, FMNH, and FMNH2; and wherein a first biocomponent comprises an oxygenase enzyme; and wherein a second biocomponent comprises a dehydrogenase enzyme that catalyzes the reaction of an oxidized cofactor selected from the group consisting of NAD+, NADP+, FAD, FADH, FMN, and FMNH and an electron donor; and wherein a third biocomponent comprises an enzyme selected from the group consisting of epoxide hydrolase, glutathione synthetase, glutathione S-transferase and gamma-glutamylcysteine sythetase; and wherein the first biocomponent catalyzes the reaction of the analyte and the cofactor selected from the group consisting of NADH, NADPH, FADH, FADH2, FMNH, and FMNH2 while consuming oxygen and producing oxidized cofactor and an epoxide product; and wherein the oxidized cofactor is reduced by the second biocomponent; and wherein the epoxide product is a reactant in a reaction catalyzed by the third biocomponent; and wherein a transducer layer interacts with oxygen; and wherein the photons enter into a fiber optic cable and are transmitted to a photomultiplier; and wherein the photomultiplier produces an output signal that is input to an algorithm that transforms the signal generated by the photomultiplier into an output correlated to the concentration of the analyte in the solution. In one embodiment, the first biocomponent is toluene ortho-monooxygenase. In an embodiment, the first biocomponent is toluene ortho-monooxygenase. In an embodiment, the first biocomponent is a toluene ortho-monooxygenase variant. In one embodiment, the second biocomponent is formate dehydrogenase and the electron donor is formate. In one embodiment, the third biocomponent is selected from the group consisting of epoxide hydrolase, glutathione synthetase, glutathione S-transferase and gamma-glutamylcysteine sythetase.
In one aspect, a biosensing system for detecting the concentration of an analyte in a solution is disclosed wherein the analyte is a reactant in a reaction catalyzed by an oxygenase enzyme from Enzyme Commission numbers 1.13 and 1.14; and wherein the oxygenase enzyme requires a cofactor selected from the group consisting of NADH, NADPH, FADH, FADH2, FMNH, and FMNH2; and wherein a first biocomponent comprises an oxygenase enzyme; and wherein a second biocomponent comprises a dehydrogenase enzyme that catalyzes the reaction of an oxidized cofactor selected from the group consisting of NAD+, NADP+, FAD, FADH, FMN, and FMNH and an electron donor; and wherein a third biocomponent comprises an enzyme selected from the group consisting of epoxide hydrolase, glutathione synthetase, glutathione S-transferase and gamma-glutamylcysteine sythetase; and wherein the first biocomponent catalyzes the reaction of the analyte and the cofactor selected from the group consisting of NADH, NADPH, FADH, FADH2, FMNH, and FMNH2 while consuming oxygen and producing oxidized cofactor and an epoxide product; and wherein the oxidized cofactor is reduced by the second biocomponent; and wherein the epoxide product is a reactant in a reaction catalyzed by the third biocomponent; and wherein a transducer layer reacts interacts with oxygen; and wherein the photons enter into a fiber optic cable and are transmitted to a photomultiplier; and wherein the photomultiplier produces an output signal that is coupled to an algorithm that transforms the signal generated by the photomultiplier into an output correlated to the concentration of the analyte in the solution. In an embodiment, the first biocomponent is toluene ortho-monooxygenase. In an embodiment, the first biocomponent is toluene ortho-monooxygenase. In an embodiment, the first biocomponent is a toluene ortho-monooxygenase variant. In an embodiment, the second biocomponent is formate dehydrogenase and the electron donor is formate. In an embodiment, the first biocomponent, the second biocomponent and the third biocomponent all reside within a whole cell biocomponent that is immobilized within a matrix, and the matrix is adhered to the transducer layer.
In one aspect, a biosensing system for detecting the concentration of an analyte in a solution is disclosed wherein the analyte is a reactant in a reaction catalyzed by an oxygenase enzyme from Enzyme Commission numbers 1.13 and 1.14; and wherein the oxygenase enzyme requires a cofactor selected from the group consisting of NADH, NADPH, FADH, FADH2, FMNH, and FMNH2; and wherein a first biocomponent comprises an oxygenase enzyme; and wherein a second biocomponent comprises a dehydrogenase enzyme that catalyzes the reaction of an oxidized cofactor selected from the group consisting of NADH, NADPH, FADH, FADH2, FMNH, and FMNH2, and an electron donor; and wherein a third biocomponent comprises an enzyme selected from the group consisting of epoxide hydrolase, glutathione synthetase, glutathione S-transferase and gamma-glutamylcysteine sythetase; and wherein the first biocomponent catalyzes the reaction of the analyte and the cofactor selected from the group consisting of NADH, NADPH, FADH, FADH2, FMNH, and FMNH2 while consuming oxygen and producing oxidized cofactor and an epoxide product; and wherein the oxidized cofactor is reduced by the second biocomponent; and wherein the epoxide product is a reactant in a reaction catalyzed by the third biocomponent; and wherein a transducer layer reacts interacts with oxygen; and wherein the photons enter into a fiber optic cable and are transmitted to a photomultiplier; and wherein the photomultiplier produces an output signal that is coupled to an algorithm that transforms the signal generated by the photomultiplier into an output correlated to the concentration of the analyte in the solution. In an embodiment, the first biocomponent is toluene ortho-monooxygenase. In an embodiment, the first biocomponent is a toluene ortho-monooxygenase variant. In an embodiment, the second biocomponent is formate dehydrogenase and the electron donor is formate. In an embodiment, the first biocomponent, the second biocomponent and the third biocomponent all reside within a whole cell biocomponent that is immobilized within a matrix, and the matrix is adhered to the transducer layer.
In one aspect, a method for constructing biosensing systems having a linear response to the concentration of an analyte in a solution is disclosed wherein the biosensing system has an optode, and the optode has a fiber optical cable having a first tip and a second tip, and the first tip is covered by a transducer layer, and the transducer layer is covered by a biocomponent layer, and the biocomponent layer is covered by a porous layer, and the second tip is coupled to a photon-detection device, and the photon-detection device is coupled to a signal processing system, and the analyte concentration in the solution, the depth of the biocomponent layer, the depth of the porous layer, the diffusion coefficient of the porous layer, and the Km and Vmax of the reaction of the analyte that is catalyzed by the first biocomponent are selected such that the quotient between Da2 and 4β is from about 10 to about 1000. In one embodiment, the first biocomponent is toluene ortho-monooxygenase. In one embodiment, the first biocomponent is a toluene ortho-monooxygenase variant. In one embodiment, the biocomponent has both a toluene ortho-monooxygenase variant and formate dehydrogenase. In another embodiment, the biocomponent has both a toluene ortho-monooxygenase variant and formate dehydrogenase, and also has at least one enzyme selected from an epoxide hydrolase, a glutathione synthetase, a glutathione S-transferase and a gamma-glutamylcysteine sythetase. In one embodiment, the transducer layer is RuDPP. In one embodiment, the porous layer is track-etched polycarbonate.
In one aspect, a biosensing system for detecting the concentration of an analyte in a solution is disclosed wherein the biosensing system has an optode, and the optode has a fiber optical cable having a first tip and a second tip, and the first tip is covered by a transducer layer, and the transducer layer is covered by a biocomponent layer, and the biocomponent layer is covered by a porous layer, and the second tip is coupled to a photon-detection device, and the photon-detection device is coupled to a signal processing system, and the analyte concentration in the solution, the depth of the biocomponent layer, the depth of the porous layer, the diffusion coefficient of the porous layer, and the Km and Vmax of the reaction of the analyte that is catalyzed by the first biocomponent are selected such that the quotient between Da2 and 4β is from about 10 to about 1000. In one embodiment, the biocomponent is toluene ortho-monooxygenase. In one embodiment, the biocomponent is a toluene ortho-monooxygenase variant. In one embodiment, the biocomponent has both a toluene ortho-monooxygenase variant and formate dehydrogenase. In another embodiment, the biocomponent has both a toluene ortho-monooxygenase variant and formate dehydrogenase, and also has at least one enzyme selected from an epoxide hydrolase, a glutathione synthetase, a glutathione S-transferase and a gamma-glutamylcysteine sythetase. In one embodiment, the transducer layer is RuDPP. In one embodiment, the porous layer is track-etched polycarbonate.
In one aspect, a method for detecting the concentration of an analyte in a solution is disclosed wherein the analyte is a reactant in a reaction catalyzed by an oxygenase enzyme that requires a cofactor selected from the group consisting of NADH, NADPH, FADH, FADH2, FMNH, and FMNH2; and wherein a first biocomponent comprises an oxygenase enzyme; and wherein a second biocomponent comprises a dehydrogenase enzyme that catalyzes the reaction of an oxidized cofactor selected from the group consisting of NAD+, NADP+, FAD, FADH, FMN, and FMNH and an electron donor; and wherein the first biocomponent catalyzes the reaction of the analyte and the cofactor selected from the group consisting of NADH, NADPH, FADH, FADH2, FMNH, and FMNH2 while consuming oxygen and producing oxidized cofactor; and wherein the oxidized cofactor is reduced by the second biocomponent; and wherein a transducer layer interacts with oxygen; and wherein the photons enter into a fiber optic cable and are transmitted to a photomultiplier; and wherein the photomultiplier produces an output signal that is input to an algorithm that transforms the signal generated by the photomultiplier into an output correlated to the concentration of the analyte in the solution. In one embodiment, the first biocomponent is toluene ortho-monooxygenase. In an embodiment, the first biocomponent is toluene ortho-monooxygenase. In an embodiment, the first biocomponent is a toluene ortho-monooxygenase variant. In one embodiment, the second biocomponent is formate dehydrogenase and the electron donor is formate.
In one aspect, a biosensing system for detecting the concentration of an analyte in a solution is disclosed wherein the analyte is a reactant in a reaction catalyzed by an oxygenase enzyme from Enzyme Commission numbers 1.13 and 1.14; and wherein the oxygenase enzyme requires a cofactor selected from the group consisting of NADH, NADPH, FADH, FADH2, FMNH, and FMNH2; and wherein a first biocomponent comprises an oxygenase enzyme; and wherein a second biocomponent comprises a dehydrogenase enzyme that catalyzes the reaction of an oxidized cofactor selected from the group consisting of NAD+, NADP+, FAD, FADH, FMN, and FMNH and an electron donor; and wherein the first biocomponent catalyzes the reaction of the analyte and the cofactor selected from the group consisting of NADH, NADPH, FADH, FADH2, FMNH, and FMNH2 while consuming oxygen and producing oxidized cofactor and an epoxide product; and wherein the oxidized cofactor is reduced by the second biocomponent; and wherein a transducer layer reacts interacts with oxygen; and wherein the photons enter into a fiber optic cable and are transmitted to a photomultiplier; and wherein the photomultiplier produces an output signal that is coupled to an algorithm that transforms the signal generated by the photomultiplier into an output correlated to the concentration of the analyte in the solution. In an embodiment, the first biocomponent is toluene ortho-monooxygenase. In an embodiment, the first biocomponent is toluene ortho-monooxygenase. In an embodiment, the first biocomponent is a toluene ortho-monooxygenase variant. In an embodiment, the second biocomponent is formate dehydrogenase and the electron donor is formate. In an embodiment, the first biocomponent, and the second biocomponent all reside within a whole cell biocomponent that is immobilized within a matrix, and the matrix is adhered to the transducer layer.
In one aspect, a biosensing system for detecting the concentration of an analyte in a solution is disclosed wherein the analyte is a reactant in a reaction catalyzed by an oxygenase enzyme from Enzyme Commission numbers 1.13 and 1.14; and wherein the oxygenase enzyme requires a cofactor selected from the group consisting of NADH, NADPH, FADH, FADH2, FMNH, and FMNH2; and wherein a first biocomponent comprises an oxygenase enzyme; and wherein a second biocomponent comprises a dehydrogenase enzyme that catalyzes the reaction of an oxidized cofactor selected from the group consisting of NADH, NADPH, FADH, FADH2, FMNH, and FMNH2, and an electron donor; and wherein the first biocomponent catalyzes the reaction of the analyte and the cofactor selected from the group consisting of NADH, NADPH, FADH, FADH2, FMNH, and FMNH2 while consuming oxygen and producing oxidized cofactor and an epoxide product; and wherein the oxidized cofactor is reduced by the second biocomponent; and wherein a transducer layer reacts interacts with oxygen; and wherein the photons enter into a fiber optic cable and are transmitted to a photomultiplier; and wherein the photomultiplier produces an output signal that is coupled to an algorithm that transforms the signal generated by the photomultiplier into an output correlated to the concentration of the analyte in the solution. In an embodiment, the first biocomponent is toluene ortho-monooxygenase. In an embodiment, the first biocomponent is a toluene ortho-monooxygenase variant. In an embodiment, the second biocomponent is formate dehydrogenase and the electron donor is formate. In an embodiment, the first biocomponent, the second biocomponent and the third biocomponent all reside within a whole cell biocomponent that is immobilized within a matrix, and the matrix is adhered to the transducer layer.



DESCRIPTION OF FIGURES
FIG. 1. Results of repeated measurements using two different toluene biosensing systems, both containing TOM and FDH.
FIG. 2. Storage tests of toluene biosensing systems, comparing those without NADH recycling (TOM) to those with NADH recycling via formate/FDH.
FIG. 3. Graphical representation of Michaelis-Menten equation relationships between enzyme reaction rate and substrate concentration.
FIG. 4. Representation of optical enzymatic biosensing element portion of a biosensing system for measuring analytes in high concentrations.
FIG. 5. Response curve for biosensing system A. Biosensing system A is a lactose biosensing system with a thin film of enzyme immobilized on the surface.
FIG. 6. Response curve for biosensing system B. Biosenor system B is a lactose biosensing system with a porous diffusive barrier.
FIG. 7. Response curve for biosensing system C. Biosensing system C is a lactose biosensing system having a less porous diffusive barrier compared to the porous diffusive barrier used in biosensing system B.
FIG. 8. System for providing design parameters used for constructing biosensing elements.
FIG. 9. Schematic representation of a biosensing system.
FIG. 10. Schematic representation of exemplary method for using a biosensing system to measure the concentration of an analyte in a solution.



DETAILED DESCRIPTION
Biosensing systems offer the potential of measurements of analytes or other molecules that are specific, continuous, rapid, and reagentless. Biosensing systems combine a biocomponent which is coupled to a transducer to yield a device capable of measuring chemical concentrations in a solution. A biocomponent may be any biological detection agent. Examples of biocomponents include enzymes, whole cells, microorganisms, RNA, DNA, viruses and antibodies.
Disclosed herein is a method of regenerating oxidation-reduction (redox) cofactors in enzymatic biosensing systems. Enzymatic biosensing systems that require cofactors usually stop working when the cofactor is depleted. The cofactor is often the reduced form of nicotine adenine dinucleotide (NADH), the reduced form of phosphorylated NADH (NADPH), and/or the reduced form of flavin adenine nucleotide (FADH2, FAD), and/or the reduced form of flavin mononucleotide (FMNH2, FMNH); after these reduced cofactors participate in an enzyme-catalyzed reaction, they are converted to a less energetic form, NAD+, NADP+, FADH, FAD, FMNH, FMN, respectively.
In living cells, the higher energy form of the cofactor (e.g., NAD(P)H) is regenerated as part of metabolism. Biosensing systems that have biocomponents that require these cofactors can work longer if there is a way to regenerate the higher energy form of the cofactor.
In one embodiment, biosensing systems have one biocomponent that catalyzes the reaction of an analyte of interest and a second biocomponent that regenerates NAD(P)H. The recycling of NAD(P)H with the second biocomponent requires the addition of an electron-donating molecule. The enzymes responsible for this recycling reaction are generally dehydrogenases of the Enzyme Commission number (EC number) EC 1, oxidoreductases, such as formate dehydrogenases (FDH), EC 1.2.1, for example.
Biosensing systems that use oxygenase enzymes as biocomponents typically require energy input in the form of a NAD(P)H cofactor. In one embodiment, oxygenases are monooxygenases EC 1.13 and/or dioxygenases EC 1.14. Genes for the enzymes toluene ortho-monooxygenase (TOM) and/or toluene ortho-monooxygenase-green (TOM-Green, a toluene ortho-monooxygenase variant) and formate dehydrogenase (FDH) may be cloned into plasmids and then introduced into Escherichia coli (E. coli) or may also be cloned directly into the chromosomal DNA of E. coli. TOM, TOM-Green and FDH may also be used as biocomponents exclusive of microorganisms and/or whole cells. The E. coli containing plasmids with genes encoding TOM and FDH may be used as biocomponents in a system that uses oxygenases while recycling cofactor NAD(P)H through FDH. These genes may also be encoded naturally on plasmid or chromosomal DNA in certain microorganisms that are useful as biocomponents.
The cofactors used in the biosensing systems may be pegylated by derivatizing with polyethylene oxide or otherwise modified to alter the diffisuvity of the cofactor.
Definitions
Amperometric: Amperometric pertains to measurement of an electrical current.
Halogenated hydrocarbon: A halogenated hydrocarbon is a hydrocarbon chemical in which one or more halogen atoms are substituted for hydrogen atoms. The halogen atoms may be fluorine, chlorine, bromine, and/or iodine. Non-limiting examples of halogenated hydrocarbons include tetrachloroethene, trichloroethene, dichloroethene and monochloroethene and isomers thereof.
Toluene ortho-monooxygenase: Toluene ortho-monooxygenase (TOM) is an enzyme that belongs to the family of oxidoreductases. TOM oxidizes many substrates, including o-xylene, m-xylene, p-xylene, toluene, benzene, ethyl benzene, styrene, naphthalene, trichloroethene as well as tetrachloroethene. TOM uses oxygen and NADH as a cofactor to oxidize its substrate.
Toluene ortho-monooxygenase variant: Toluene ortho-monooxygenase (TOM) variants refer generally to any variant of TOM that has improved substrate binding kinetics, a faster turnover rate or other improved enzymological parameters over native TOM. One example of a TOM variant is TOM-Green which has a valine to alanine substitution (V106A) in the hydroxylase alpha-subunit of TOM from Burkholderia cepacia G4. NAD: NAD (nicotinamide adenine dinucleotide) used herein includes the oxidized form NAD+ and the reduced form NADH. NAD is a cofactor.
NAD: NAD (nicotinamide adenine dinucleotide) used herein includes the oxidized form NAD+ and the reduced form NADH. NAD is a cofactor.
NADP: NADP (nicotinamide adenine dinucleotide phosphate) used herein includes the oxidized form NADP+ and the reduced form NADPH. NADP is a cofactor.
NAD(P)H: NAD(P)H is an inclusive term that embodies both the reduced form of nicotine adenine dinucleotide, NADH, and the reduced form of phosphorylated NADH, NADPH. NAD(P)H is a cofactor.
FAD: FAD (Flavin Adenine Dinucleotide) used herein includes FAD (fully oxidized form, or quinone form) that accepts two electrons and two protons to become FADH2 (hydroquinone form). FADH2 can then be oxidized to the semireduced form (semiquinone) FADH by donating one electron and one proton. The semiquinone is then oxidized once more by losing an electron and a proton and is returned to the initial quinone form, FAD. FAD is a cofactor.
FMN: FMN (Flavin Mononucleotide) used herein includes FMN (fully oxidized form), or FMNH (semiquinone form), and FMNH2 (fully reduced form). FMN is a cofactor. In one embodiment, FMN is a prosthetic group for oxidoreductases.
Cofactor: A cofactor used herein is a non-protein chemical compound that is bound to a protein and is required for the protein's biological activity. Non-limiting examples of cofactors include: thiamine pyrophosphate, reduced and oxidized forms of flavin adenine mononucleotide (FAD), reduced and oxidized forms of flavin adenine mononucleotide (FMN), reduced and oxidized forms of nicotinamide adenine dinucleotide (NAD), reduced and oxidized forms of nicotinamide adenine dinucleotide phosphate (NADP), pyridoxal phosphate, lipoamide, methylcobalamin, cobalamine, biotin, coenzyme A, tetrahydrofolic acid, menaquinone, ascorbic acid, flavin adenine dinucleotide, coenzyme F420, adenosine triphosphate, S-adenosyl methionine, coenzyme B, coenzyme M, coenzyme Q, cytidine triphosphate, glutathione, heme, methanofuran, molybdopterin, nucleotide sugars, 3′-phosphoadenosine-5′-phosphosulfate, pyrroloquinoline, quinine, tetrahydrobiopterin, and tetrahydromethanopterin. Cofactors may also include metal ions such as Ca2+, Zn2+, Fe2+, Fe3+, Mg2+, Ni2+, Cu+, Cu2+, Mn2+, and iron-sulfur clusters, for example.
Dehydrogenase: A dehydrogenase is an enzyme that oxidizes a substrate by transferring one or more hydrides (H) to an acceptor, usually NAD+/NADP+ or a flavin coenzyme such as FAD or FMN.
Measurement solution: A measurement solution is a solution in which an analyte may be dissolved to make a biosensor measurement. A non-limiting example of a measurement solution is 0.15 M NaCl and 0.025 M CaCl2 at pH 7.0
Biocomponent: A biocomponent binds, catalyzes the reaction of or otherwise interacts with analytes, compounds, atoms or molecules thereby generating an atom, molecule or compound. Non-limiting examples of biocomponents include aptamers, DNA, RNA, proteins, enzymes, antibodies, cells, whole cells, tissues, single-celled microorganisms, and multicellular microorganisms. A biocomponent may be a cell, microorganism, cell organelle or any other membrane bound container that contains biocomponent enzymes within. A biocomponent may be purified or otherwise substantially isolated biocomponent enzymes. A biocomponent may be an unpurified extract of cells containing biocomponent enzymes.
Analyte: An analyte is the substance or chemical constituent that is desired to be detected or measured, such as the analyte concentration. With enzymatic biosensing systems, the analyte itself is not measured. Rather, a reaction of the analyte that is catalyzed by an enzymatic biocomponent causes a change in the concentration of a reactant or product that is measurable by the biosensing system. An analyte may also be a substrate of an enzyme.
Transducer: A transducer is a substance that interacts with the atoms, compounds, or molecules produced or used by the biocomponent. The interaction of the transducer with the atoms, compounds, or molecules produced or used by the biocomponent causes a signal to be generated by the transducer layer. The transducer layer may also generate a signal as an inherent property of the transducer. The signal may be an electrical current, a photon, a luminescence, or a switch in a physical configuration. In one embodiment, the signal produced by the transducer is quenched by a reactant or product of the biocomponent or may also be quenched by a molecule such as oxygen.
Chemical transducer: A chemical transducer is a chemical that catalyzes the reaction of an atom, molecule or compound and that reaction causes the production of a proton, oxygen molecule, luminescent event, photon or other atoms and molecules.
Optical transducer: An optical transducer is a material that luminesces. An optical transducer interacts with an atom, molecule, photon or compound and that interaction causes a change in the intensity and/or lifetime of the fluorescence of the optical transducer.
Physical transducer: A physical transducer is a material that interacts with an atom, molecule, photon or compound and that interaction causes a shift in its physical properties.
Biosensor: A biosensor measures the concentration of compounds, atoms or molecules using a biocomponent. A biosensor may also detect compounds, atoms or molecules using a biocomponent. A biosensor may also measure the toxicity of compounds, atoms or molecules using a biocomponent. A biosensor may alternatively be referred to as a biosensing system and/or a biosensing element.
Biosensing system: A biosensing system contains a biosensing element, a transducer, and a signal processing system. A biosensing system may alternatively be referred to as a biosensor system. Biosensing system may alternatively refer to various parts of the biosensing system such as the biosensing element, for example. A biosensing system may also contain a biosensing element, an optode, and a signal processing system.
Biosensing element: A biosensing element detects analytes. A biosensing element comprises one or more biocomponents and a transducer. In certain embodiments, a biosensing element comprises one or more biocomponents, a transducer and/or an optode.
Crosslinking: Crosslinking is the process of linking a biocomponent to a matrix. Crosslinking may be through chemical bonds, ionic interactions, physical entrapment or other modes and methods of linking a biocomponent to a matrix.
Matrix: A matrix is an interlacing, repeating cell, net-like or other structure that embodies the biocomponents. The immobilization material is an example of a matrix. A matrix may be a polymer.
Immobilization material: Immobilization material is the substance, compound or other material used to immobilize the biocomponent onto the biosensing element transducer layer. The immobilization material may be a matrix or may be less ordered than a matrix. The immobilization material may be a polymer such as cellulose acetate, polycarbonate, collage, acrylate copolymers, poly(ethylene glycol), polytetrafluroethylene (PTFE), agarose, alginate, polylysine, alginate-polylysine-alginate microcapsule, algal polysaccharides, agar, agarose, alginate, and carrageenan, polyacrylamide, polystyrene, polyurethane and other naturally occurring and synthetic polymers.
Polymer: Polymers as used herein include any natural or synthetic polymer including cellulose acetate, polycarbonate, collage, acrylate copolymers, poly(ethylene glycol), polytetrafluroethylene (PTFE), agarose, alginate, polylysine, alginate-polylysine-alginate microcapsule, algal polysaccharides, agar, agarose, alginate, and carrageenan, polyacrylamide, polystyrene, polyurethane and other naturally occurring and synthetic polymers. Polymers may be used to create a diffusivity barrier between the bulk solution and a biocomponent of a biosensing system. A polymer may be a porous layer.
Optode: An optode is a sensor device that measures the concentration of a specific substance usually with the aid of a transducer. An optode can be an optical sensor device that optically measures the concentration of a specific substance usually with the aid of a transducer. In one embodiment, for example, an optode requires a transducer, a polymer to immobilize the transducer and instrumentation such as optical fiber, a light source, detectors and other electronics. Optodes can apply various optical measurement schemes such as reflection, absorption, an evanescent wave, luminescence (for example fluorescence and phosphorescence), chemiluminescence, and surface plasmon resonance. Optodes may be fiber optical cable, planar wave guides or other surfaces conducive to the propagation of total internally reflecting light waves. An optode may be an optical transducer such as a photon detector.
pH sensor: A pH sensor measures the concentration of hydrogen ions in a solution.
pH optode: A pH optode is an optode that has a detection element that interacts with hydrogen ions. An example of a detection element that interacts with hydrogen ions is fluorescein, fluoresceinamine or other fluorescein-containing compounds. In an embodiment, for example, a pH optode based on luminescence has a luminescent reagent that is pH responsive.
Luminescence: Luminescence is a general term which describes any process in which energy is emitted from a material at a different wavelength from that at which it is absorbed. Luminescence may be measured by intensity and/or by lifetime decay. Luminescence is an umbrella term covering fluorescence, phosphorescence, bioluminescence, chemoluminescence, electrochemiluminescence, crystalloluminescence, electroluminescence, cathodoluminescence, mechanoluminescence, triboluminescence, fractoluminescence, piezoluminescence, photoluminescence, radioluminescence, sonoluminescence, and thermoluminescence.
Fluorescence: Fluorescence is a luminescence phenomenon in which electron de-excitation occurs almost spontaneously, and in which emission from a luminescent substance ceases when the exciting source is removed. Fluorescence may be measured by intensity and/or by lifetime of the decay.
Phosphorescence: Phosphorescence is a luminescence phenomenon in which light is emitted by an atom or molecule that persists after the exciting source is removed. It is similar to fluorescence, but the species is excited to a metastable state from which a transition to the initial state is forbidden. Emission occurs when thermal energy raises the electron to a state from which it can de-excite. Phosphorescence may be measured by intensity and/or by lifetime of the decay.
Oxygen sensor: An oxygen sensor measures, or is responsive to, the concentration of oxygen in a solution.
Oxygen optode: An oxygen optode is an optode that has a transducer layer that interacts with oxygen. An example of a transducer layer that interacts with oxygen is tris(4,7-diphenyl-1,10-phenanthroline)Ru(II) chloride, also known as RuDPP.
Photon-detection device: A photon-detection device is a class of detectors that multiply the current produced by incident light by as much as 100 million times in multiple dynode stages, enabling, for example, individual photons to be detected when the incident flux of light is very low. Photon-detection devices may be vacuum tubes, solid state photomultipliers or other devices that interact with incident light, and amplify or otherwise process the signal and/or photons produced by that interaction. Alternative embodiments of a photon-detection device include an image sensor, CCD sensors, CMOS sensors, photomultiplier tubes, charge coupled devices, photodiodes and avalanche photodiodes.
Signal processing system: A signal processing system processes the signal from a biosensing system into information that can be displayed to an end user. An example of a signal processing system is a photon-detection device that detects the photons from the output of a photo optical cable of the optode of the biosensing system. The output of the photon-detection device is coupled to the input of a converter or sampler device such as a signal processor or a transimpedance amplifier. The output of the converter or sampler device is coupled to the input of a microprocessor that processes the output of the converter or sampler device into an output corresponding to the concentration of an analyte within the solution that was measured by the biosensing system. The output of the microprocessor is then communicated to an end user, for example by displaying the concentration on a screen.
Image sensor: An image sensor is a device that converts an optical image to an electric signal. Examples of image sensors include charge-coupled devices (CCD) or complementary metal-oxide-semiconductor (CMOS) active pixel sensors.
Sampler device: A sampler device reduces a continuous signal to a discrete signal. A common example is the conversion of a sound wave or light wave (a continuous signal) to a sequence of samples (a discrete-time signal).
Avalanche photodiode: An avalanche photodiode (APD) is a highly sensitive semiconductor electronic device that exploits the photoelectric effect to convert light to electricity. APDs can be thought of as photodetectors that provide a built-in first stage of gain through avalanche multiplication.
Converter: A converter is a current-to-voltage converter, and is alternatively referred to as a transimpedance amplifier. A converter is an electrical device that takes an electric current as an input signal and produces a corresponding voltage as an output signal. In another embodiment a converter may be a voltage-to-current converter.
Advantages
Advantages in using biosensing systems for measuring analytes include fast measurement, generally on the order of minutes. This is a big advantage over traditional methods like GC or HPLC in which a lot of time is spent in collection of the sample and extraction of analytes from the sample.
Small size is another advantage of using biosensing systems. Biosensing systems of the present disclosure have a compact design and are therefore capable of measurements in confined places such as needles and catheters in vivo and in conditions where weight is critical like spacecraft or airplanes.
Another advantage of using biosensing systems is that they can be used to measure the concentration of multiple analytes in a small sample in a continuous real-time measurement in a reversible manner with extremely low signal loss in an optical fiber as compared to electronic sensors such as amperometric assays. Furthermore, biosensing systems are capable of measuring at depths for applications such as groundwater monitoring.
An important advantage is the ability of biosensing systems to analyze complex samples with no prior preparation of samples. Biosensing systems can provide direct measurements in blood, food, and waste water, for example. This is important as removal of the sample from its environment (as in case of analyses by GC or HPLC) can change its chemistry and can thereby lead to inaccurate results. Also, this eliminates and simplifies sample separation steps and reduces the cost of the process. Measurements using biosensing systems can be made with minimum perturbations of the sample.
Biosensing systems have high specificity and sensitivity for measuring analytes of interest. Although most of the traditional methods (GC or HPLC) are very sensitive, they require expensive, laboratory-based hardware and trained operators. Other methods such as solid-phase enzyme-linked immunoassay (ELISA) may have good sensitivity but are generally not highly specific and cannot provide continuous measurements.
Another advantage for using biosensing systems of the present disclosure is the low cost of mass production compared to most of the traditional methods like GC or HPLC. Biosensing systems of the present disclosure are easy to use compared to traditional monitoring techniques such as gas chromatography, ion chromatography and high-pressure liquid chromatography. Biosensing systems using the proper biocomponents can also measure the toxicity of chemicals whereas analytical methods such as GC and HPLC can only measure concentration.
Biocomponents
Biocomponents react with, bind to or otherwise interact with an analyte. Reactive biocomponents produce or react with atoms, molecules or compounds that interact with the transducer.
Enzymes are proteins that can serve as biocomponents that catalyze reactions with their substrates. Substrates may be analytes. The products or reactants of the enzymatic reactions are usually measured by the biosensing system. In one embodiment, the products of the substrates that react with the analyte may themselves be acted upon and thereby produce additional products which may be measured by the biosensing system. Therefore, a biosensing system may measure primary, secondary or even higher orders of products caused by an initial reaction or binding of the analyte with the biocomponent.
Generally, enzymes for use in biosensing systems may be disposed within whole cells or extracted from cells and purified. Whole cells and microorganisms are also biocomponents. The cells and organisms used as biocomponents may or may not be living (able to replicate). Whether or not the cells are living, diffusion mechanisms and membrane-bound pumps may still be active that allow for the exchange of analytes and other compounds with the environment of the cell. It is often advantageous to use a dead cell or microorganism as a biocomponent at least because the proteolytic enzymes and pathways operating in a living cell may cease to function and the enzymes, for example, that are responsible for binding or reacting with the analytes therefore last longer than they would in a living cell. Another advantage of using dead cells or microorganisms is that if the biosensing system is used in-situ, such as in-line testing of milk being produced at a factory, there can be no contamination of the sample with cells or microorganisms that may infect or adulterate the sample.
Purified enzymes may be used as a biocomponent in biosensing systems. One benefit of using purified enzymes is that side reactions occurring within cells that result in the loss of enzyme activity may be avoided.
Enzymes isolated from extremophilic organisms such as hyperthermophiles, halophiles, and acidophiles may be used as biocomponents. They are often more resistant to losing their catalytic activity when compared to mesophilic enzymes.
An enzyme's resistance to becoming inactivated due to environmental factors, or even by the nature of the reaction that they catalyze, may be increased through mutagenic techniques. Such techniques are well known in the art and include various incarnations of changing the coding nucleotide sequence for the protein through various techniques. The proteins produced by expressing the mutagenic nucleotide sequences may then be tested for resistance to environmental factors and/or increased reactivity with substrates. Such an increase in reactivity may be due to advantageous binding specificity and/or increased kinetics of the binding and/or reaction catalyzed by the enzyme.
Methods of choosing cells and microorganisms that increase the response of the biosensing system may also be used to create biosensing systems that possess increased sensitivity, have quicker response times and last longer. Such techniques include directed evolution and using micro-assays to determine an increase in the production amount and/or rate of production of the molecules and/or atoms that react with the transducer layer.
Transducers
A transducer is a device that produces a measurable signal, or change in signal, upon a change in its chemical or physical environment. Transducers suited for biosensing systems that use enzymes as the biocomponent are those that interact with the reactants and/or products of the biocomponent and send a signal that is processed into a measurement reading. The nature of the interaction of the biological element with the analyte has a major impact on the choice of transduction technology. The intended use of the biosensing system imposes constraints on the choice of suitable transduction technique.
Amperometric transducers work by maintaining a constant potential on the working electrode with respect to a reference electrode, and the current generated by the oxidation or reduction of an electroactive species at the surface of the working electrode is measured. This transduction method has the advantage of having a linear response with a relatively simple and flexible design. Also, the reference electrode need not be drift-free to have a stable response. Since the signal generated is highly dependent on the mass transfer of the electroactive species to the electrode surface there can be a loss in sensitivity due to fouling by species that adsorb to the electrode surface. As a result of fouling, use of amperometric transducers is restricted where continuous monitoring is required. Enzymes, particularly oxidoreductases, are well suited to amperometric transduction as their catalytic activity is concerned with electron transfer.
Electroactive species that can be monitored at the electrode surface include substrates of a biological reaction (e.g., O2, NADH), final products (e.g., hydrogen peroxide for oxidase reactions, benzoquinone for phenol oxidation) and also electrochemical mediators that can directly transfer electrons from the enzyme to the working electrode surface (e.g. hexacyanoferrate, ferrocene, methylene blue).
Potentiometric transducers work by having a potential difference between an active and a reference electrode that is measured under the zero current flow condition. The three most commonly used potentiometric devices are ion-selective electrodes (ISEs), gas-sensing electrodes and field-effect transistors (FETs). All these devices obey a logarithmic relationship between the potential difference and the activity of the ion of interest. This makes the sensors have a wide dynamic range. One disadvantage of this transducer is the requirement of an extremely stable reference electrode. Ion selective electrodes are commonly used in areas such as water monitoring. FETs are commercially attractive as they can be used to make miniaturized sensors, but manufacturing cost of FETs are high. Examples of potentiometric sensors are for acetaldehyde and cephalosporins, where the sensing electrode measures pH. Other examples are sensors used to measure creatinine, glutamine and nitrate with the sensing electrode detecting NH3 gas.
Conductimetric transducers are often used to measure the salinity of marine environments. Conductance is measured by the application of an alternating current between two noble metal electrodes immersed in the solution. Due to specific enzyme reactions, they convert neutral substrates into charged products, causing a change in the conductance of the medium. This method can be used to make more selective and informative sensors by using multi-frequency techniques.
Optical transducers use optical phenomena to report the interaction of the biocomponent and the analyte. The main types of photometric behavior which have been exploited are ultraviolet and visible absorption, luminescence such as fluorescence and phosphorescence emission, bioluminescence, chemiluminescence, internal reflection spectroscopy using evanescent wave technology and laser light scattering methods.
One embodiment of an optical transducer uses luminescent reagents. In optical transducers that use luminescent reagents, a luminescent substance is excited by incident light, and as a result it emits light of a longer wavelength. The intensity and/or lifetime decay of emitted light changes when an atom, molecule or compound binds or otherwise interacts with the luminescent substance. The atom, molecule or compound may be a reactant or product of the biocomponent. Thus, if a reactant or product of the biocomponent catalyzes the reaction of the luminescent transducer and affects the intensity and/or lifetime decay of the light emitted by the transducer layer, the change in the measurement of the intensity and/or lifetime decay can be measured as a response to a particular analyte. There are several luminescent reagents that may be useful as optical transducers. Examples include Tris(4,7-diphenyl-1,10-phenanthroline)Ru(II) chloride, also known as RuDPP, for oxygen sensors, trisodium 8-hydroxy-1,3,6-trisulphonate fluorescein, fluoresceinamine and other compounds containing fluorescein for pH sensors, fluoro (8-anilino-1-naphthalene sulphonate) for Na+ ion sensor and acridinium- and quinidinium-based reagents for halides.
Chemiluminescent and bioluminescent sensors work on principles similar to fluorescent sensors. Chemiluminescence occurs by the oxidation of certain substances, usually with oxygen or hydrogen peroxide, to produce visible light. Bioluminescence is, for example, the mechanism by which light is produced by certain enzymes, such as luciferase.
Calorimetric transducers use the heat generated from biological reactions and correlate it with the reaction conditions. In order to measure such small amounts of heat liberated during the reaction, a very sensitive device is required. In the calorimetric technique a very sensitive, electrical resistance thermometer is used to detect temperature changes down to 0.001° C. This method is advantageous, as it is independent of the chemical properties of the sample. Calorimetric transduction has been used in a wide range of areas, including clinical chemistry, determination of enzyme activity, monitoring gel filtration, chromatography, process control and fermentation.
An acoustic transducer uses materials such as piezoelectrics as a sensor transducer due to their ability to generate and transmit acoustic waves in a frequency-dependent manner. The optimal resonant frequency for acoustic-wave transmission is highly dependent on the physical dimensions and properties of the piezoelectric crystal. Any change in the mass of the material at the surface of the crystal will cause quantifiable changes in the resonant frequency of the crystal. There are two types of mass-balance acoustic transducers: bulk wave and surface acoustic wave. Acoustic transduction is a relatively cheap technique but it has the disadvantage of having low sensitivity with non-specific binding. This technique is commonly used to measure the concentration of volatile gases and vapors. A piezoelectric immunobiosensor for measuring an analyte of interest in drinking water may use a piezoelectric crystal coated with polyclonal antibodies that bind to that analyte. When the analyte molecules come into contact with the antibodies, they bond with the antibodies causing a change in the crystal mass, which in turn leads to a shift in the oscillation frequency and produces a measurable signal that can be measured and correlated to the concentration of the analyte of interest within the sample.
Optical and Signal Processing Systems
In an embodiment, biosensing systems of the present disclosure have a biocomponent, a transducer, a photon-detection device, and a signal-processing system. A signal processing system processes the signal from a photon-detection device into information that can be displayed to an end user. An example of a signal processing system is a microprocessor that accepts an input signal from a photon-detection device that is coupled to a biosensing element. The signal processing system then uses a software program that encodes an algorithm. The algorithm used by the software transforms the data provided by the input signal and provides an output signal that correlates to a numerical display of the concentration of an analyte that the biosensing system detected.
In an embodiment of the present disclosure, a biosensing system comprises biocomponent attached to a fiber optic pH optode, lens focusing system, photomultiplier (PMT), analog/digital (A/D) converter and a microprocessor. The biosensing element may be coupled to a polymethylmethacrylate (PMMA) optical fiber optic. The length of this connecting optical fiber may vary from 1 mm to well over 1 km. In an embodiment, the other end of this cable is attached to a light emitting diode (LED). In another embodiment, the other end of this cable is attached to a metal casing containing a 5 W halogen lamp or other light source and a lens focusing system. The light source should be able to operate at high temperatures, having a very short warm-up time in order to reach a constant power output. In one embodiment, light from the halogen lamp is first passed through a bandpass filter such as a 480-nm bandpass filter, for example. The light is then collected, paralleled and focused to the tip of fiber optic cable using a lens focusing system. An embodiment of the lens focusing system comprises spheric, aspheric, and convex lenses, and a dichroic mirror. Light from the lamp that radiates in opposite directions to the lens system may be refocused by the spheric lens and paralleled by the aspheric lens.
When light, for example light at 480 nm, is incident on a sensing tip coated with PVA/fluoresceinamine dye, fluorescence occurs. In an embodiment, this light is then passed back through a 520 nm bandpass filter or other bandpass filter having a frequency of light that is either blue or red shifted in comparison to the incident light wavelength, paralleled by focusing lens and then directed by the dichroic mirror onto the window of a single channel photo-detection device. The change in intensity and/or lifetime decay properties of the light can be measured. The photon detection device processes this light and the output potentiometric signal is sent to a computer interface using a connector block where it was converted into a digital signal by a data acquisition card. The final output is observed on a computer using software such as LabView software or other algorithmic software that interprets the signals from the sensing tip and processes them into correlating concentration measurements of the atom, compound, molecule or analyte of interest.
Immobilization of the Biocomponent
In order to construct a biosensing system, the biocomponent of the biosensing element of the biosensing system needs to be bound to or otherwise in contact with the transducer. This can be achieved by immobilizing the biocomponent on to the transducer. The viability of a biosensing system depends on the processing and type of material used for immobilizing the biocomponent. The material used for immobilizing the biocomponent may be referred to as a matrix, matrix material or as an immobilizing material.
Biocomponents may be very sensitive to the immobilizing process as well as the material that is used for immobilization. The pH, ionic strength, and any other latent chemistries of the gel matrix should be compatible with the biocomponent. The reactants and products of the reaction carried by the biocomponent should not affect the material used for immobilization. The biocomponent should be effectively immobilized and there should not be any leakage of the biocomponent from the matrix during the active lifetime of the biosensing system. The immobilization material should be non-toxic and non-polluting. The material should have proper permeability to allow sufficient diffusion of substrates, products and gases. The matrix material should allow for sufficient cell activity and cell density. The immobilization material should protect the biocomponent from biotic and abiotic environmental stresses that would lower biocomponent activity or lifetime.
Techniques of Immobilization
In one embodiment, adsorption is used to immobilize the biocomponent. Many substances adsorb enzymes, cells, microorganisms and other biocomponents on their surfaces, e.g., alumina, charcoal, clay, cellulose, kaolin, silica gel and collagen. Adsorption can be classified as physical adsorption (physisorption) and chemical adsorption (chemisorption). Physisorption is usually weak and occurs via the formation of van der Waals bonds or hydrogen bonds between the substrate and the enzyme molecules. Chemisorption is much stronger and involves the formation of covalent bonds. Adsorption of the biocomponent may be specific through the interaction of some moiety, link or other reactive component of the biocomponent or may be non-specific.
In another embodiment, microencapsulation is used to immobilize the biocomponent. In this method, a thin microporous semipermeable membrane or layer is used to surround the biocomponent. In one embodiment whole cell biocomponents may be microencapsulated. In another embodiment, purified or otherwise substantially isolated enzyme biocomponents may be microencapsulated. Because of the proximity between the biocomponent and the transducer and the very small thickness of the membrane, the biosensing element response is fast and accurate, and there is always an option of bonding the biocomponent to the fiber optical portion of the biosensing system via molecules that conduct electrons, such as polypyrrole, for example. The membrane used for microencapsulation may also serve additional functions such as selective ion permeability, enhanced electrochemical conductivity, mediation of electron transfer processes, or controlling the sensitivity of the response of the biosensing system. Examples of membranes that may be used for microencapsulation immobilization of biocomponents are cellulose acetate, polycarbonate, collage, acrylate copolymers, poly(ethylene glycol) and polytetrafluroethylene (PTFE). Additional materials that may be used are agarose, and alginate and polylysine, which together form an alginate-polylysine-alginate microcapsule.
In another embodiment, entrapment is used to immobilize the biocomponent. In this method, cells are physically constrained (entrapped) to stay inside a three-dimensional matrix. The materials used for entrapment must allow uniform cell distribution, biocompatibility and good transport of substrates, cofactors and products. Both natural and synthetic materials (like alginate, agarose and collagen) may be used for entrapment.
In another embodiment, hydrogels are used to immobilize the biocomponent. Hydrogels provide a hydrophilic environment for the biocomponent and they require only mild conditions to polymerize. Hydrogels are capable of absorbing large quantities of water which can facilitate enzymatic biocomponent reactions such as hydrolysis. Both natural and synthetic hydrogels may be used such as algal polysaccharides, agar, agarose, alginate, and carrageenan, polyacrylamide, polystyrene and polyurethane.
Alginate, a hydrogel, provides a good, biocompatible microenvironment for the biocomponent and has a gentle encapsulation process. It is a naturally occurring linear polymer composed of β-(1,4) linked D-mannuronic acid and a-(1,4)-L-guluronic acid monomers. Commercially, alginate is obtained from kelp, but bacteria such as Azotobacter vinelandii, several Pseudomonas species and various algae also produce it. When alginate is exposed to Ca2+ ions, a cross-linking network is formed by the bonding of Ca2+ ions and polyguluronic portions of the polymer strand by a process known as ionic gelation. The gelation process is temperature-independent. Complete gelling time without biocomponents may be from about 1 minute to greater than about 30 minutes. Gelling time usually increases with an increase in biocomponent density and decreases with an increase in CaCl2 concentration.
In another embodiment, sol-gels may be used to entrap biocomponents into silicate networks. Sol-gels may require milder polymerization processes and create matrices that exhibit good mass transport and molecular access properties particularly for electrochemical and optical transduction modes.
In another embodiment, cross-linking is used to immobilize the biocomponent. Cross-linking chemically bonds the biocomponent to solid supports or to other supporting materials such as a gel. Bifunctional agents such as glutaraldehyde, hexamethylene diisocyanate and 1,5-dinitro-2,4-difluorobenzene may be used to bind the biocomponent to the solid support such as a matrix, for example. Cross-linking produces long-term stability under more strenuous experimental conditions, such as exposure to flowing samples, stirring, washing, etc.
In another embodiment, covalent bonding is used to immobilize the biocomponent. Covalent bonding uses a particular group present in the biocomponent, which is not involved in catalytic action, and attaches it to the matrix, transducer layer, membrane, porous layer, or fiber optical surface through a covalent bond. The radicals that take part in this reaction are generally nucleophilic in nature (e.g., —NH2, —COOH, —OH, —SH and imidazole groups).
Stabilization
Biosensing systems of the present disclosure are stable and long-lived, can stand prolonged storage and can also perform consistently when used for extended periods. Biocomponents may be stabilized through various means, depending upon the type of biocomponent and transducer used.
In one embodiment, the biocomponent may be stabilized through molecular modification. Molecular modification improves the stability of enzymes, and other biocomponents, through changing certain amino acids or nucleotides in the peptide or nucleic acid sequence, respectively. Molecular modifications may increase the temperature stability of various enzymes by modifying the amino acids at the catalytically active enzyme reaction site or at structurally sensitive amino acid sequences, through site-directed mutagenesis.
Another method for improving the stability of biocomponents, such as enzymes, is through glycosylation. Since glycosylated proteins are very stable, grafting or otherwise bonding polysaccharides or short chains of sugar molecules onto protein molecules usually improves the stability of the biocomponent.
In one embodiment, the biocomponent may be stabilized through cross-linking Cross-linking of the biocomponent may occur through covalent bonding, entrapment, encapsulation and other immobilization techniques or processes. These immobilization processes can improve enzyme stability by reducing the biocomponent's mobility and thereby reducing degradation of its three-dimensional structure. In addition, cross-linking prevents the loss of biocomponents from the matrix in which they are immobilized. Using the entrapment method discussed above, the loss of biocomponents may further be reduced by the addition of certain gel-hardening agents such as glutaraldehyde, polyethyleneimine, hexamethylenediamine and formaldehyde.
In another embodiment for stabilizing the biocomponent, freeze drying, also known as lyophilization, may be used. Freeze drying is a method for long-term preservation of microorganisms and enzymes. It involves removal of water from frozen bacterial suspensions by sublimation under reduced pressure. The lyophillization is performed in the presence of cryoprotective agents such as glycerol and DMSO which reduce the damage caused during freezing and during thawing. Lyophillized biocomponents, for example dried cells, are stable to degradation by keeping the lyophilized biocomponents below 4° C., and away from oxygen, moisture and light. Even after prolonged periods of storage, such as about 10 years, lyophillized biocomponents may then be rehydrated and restored to an active state. Two examples of lyophilizing techniques used on biocomponents include centrifugal freeze-drying and prefreezing.
In another embodiment, the biocomponents by be stabilized through heat shocking Heat shocking involves heating vacuum-dried cells at a high temperature (about 300° C., for example) for a very short time (about 2-3 minutes, for example). With the proper combination of temperature and heating time, biocomponents such as whole cells and microorganisms can be killed but still retain an active enzyme system that may be used to detect a compound of interest. These dead cells and microorganisms can be kept for a long time away from moisture without any requirement of nutrients.
In another embodiment, the addition of carbohydrates and other polymers will stabilize the biocomponents. Carbohydrates used to stabilize biocomponents include polyalcohols and various sugars such as trehalose, maltose, lactose, sucrose, glucose and galactose, for example. This stabilization may occur due to the interaction of polyhydroxyl moieties from the polyalcohols and/or sugars with water with the biocomponents, thus increasing hydrophobic interactions and keeping the biocomponents in a stable conformation.
In an additional embodiment, stabilization of the biocomponents may occur through freezing the biocomponents. When a biocomponent is frozen, the metabolic activities may be reduced considerably. Storage of the biosensing system, and/or biosensing element at temperatures at which the biocomponents remain frozen may increase the stability and life-time of the biosensing system.
Biosensing Elements
Several biosensing system designs are disclosed herein including biosensing elements on the tip of a fiber optical cable, and biosensing elements displaced upon a surface, for example. The biosensing system may be based on an optical pH or optical oxygen sensor. Oxygenases may be used alone as the biocomponent or in conjunction with other biocomponents. The biosensing elements may be separate from one another or combined into the same tip or biosensing element.
Some biosensing systems are made using food-grade enzymes and materials. These biosensing systems are advantageously used for measuring analytes in food products.
In an embodiment, the disclosures presented herein are a set of biosensing system designs based on optical transduction. Optical enzymatic biosensing system designs using an optical signal transaction are more robust and less susceptible to chemical interference than electrochemical (e.g., amperometric) methods. In one embodiment, optical pH and optical oxygen sensors (optodes) employ fluorophores that are sensitive to either protons (H+ ions) or molecular oxygen. Optical enzymatic biosensing elements are formed by combining a transducer and/or optode with a biocomponent that catalyzes a reaction with the analyte and results in altered pH or oxygen.
Biosensing System Detection at High Analyte Concentrations
Some biosensing system applications may require the measurement of relatively high analyte concentrations. These concentrations are high enough to saturate the response of the biocomponent, meaning that all of the binding sites of an antibody or all of the enzymatic reaction sites are occupied. Under these saturating conditions, the biosensing system response is no longer dependent upon the analyte concentration and no measurement can be made.
One embodiment of the present disclosure is for optical enzymatic biosensing systems for the measurement of analytes at high concentrations. Optical enzymatic biosensing systems for the measurement of analytes at high concentrations and the concepts disclosed herein are broadly applicable for the measurement of many different kinds of analytes in solutions such as the measurement of halogenated hydrocarbons, for example.
Optical enzymatic biosensing systems may use biosensing elements that may be constructed as thin enzyme-containing films deposited or placed over an optical transducer layer. The response of these biosensing systems (signal as a function of analyte concentration) is governed by the rate of the enzymatic reaction and the manner in which that rate depends on the analyte concentration. For most enzymes, this relationship is the saturation type shown in FIG. 3 in which the rate depends nearly linearly on analyte concentration at low concentrations but becomes independent of concentration at high concentrations. For a biosensing system that has a biosensing element with a thin-layer biocomponent, this means that the biosensing system response becomes saturated and consequently it is not possible to distinguish one high concentration value from another.
To describe this high concentration range more accurately, it is convenient to use the Michaelis-Menten equation, which relates the enzymatic reaction rate Renz to the concentration of the analyte (CA) as Renz=kCECA/(KM+CA) in which k and KM are parameters of the enzymatic reaction rate (depending on the enzyme and the analyte) and CE is the concentration of enzyme. The combined term kCE is frequently presented as Vmax, the maximum reaction rate (“velocity”). The Michaelis-Menten equation has been found to accurately describe many different enzyme-catalyzed reactions.
When analyte concentrations are low enough that CA is much less than KM, the MichaelisMenten equation approximately reduces to a first-order (linear) dependence of the reaction rate on the analyte concentration, Renz=(Vmax/KM)CA This linear response is the desired operating condition for a biosensing system. However, for thin-film enzymatic biocomponent biosensing systems, this range extends only to values of CA that are small relative to KM; “small” can be interpreted as 10% or less. At higher analyte concentrations, the relationship of the enzymatic reaction rate to the analyte concentration, and thus the relationship of the biosensing system response to the analyte concentration, becomes increasingly nonlinear. Once the analyte concentration becomes much larger than KM such that CA+KM=CA, the enzymatic reaction rate and the biosensing system response become essentially independent of CA. Modifying the Michaelis-Menten equation for this case of CA>>KM yields Renz=Vmax 
The analysis above is based on the assumption that the analyte concentration in the vicinity of the biocomponent enzyme molecules (“local” concentration) is the same as in the solution in which the biosensing element is placed (“bulk solution” concentration). However, this situation can be manipulated such that the local concentration is lowered such that it falls within the linear measurement range. The local concentration can be related to the bulk solution concentration by either calculating the reaction-diffusion behavior of the system or through experimental calibration procedures.
A solution to extend the linear (useful) measurement range of optical enzymatic biosensing systems beyond that available with thin-film designs is to add a mass transfer (diffusion) barrier. This diffusion barrier may take the form of a polymer coating, a membrane, a porous layer, or any other material through which the analyte passes more slowly than through the measurement medium. In an embodiment, the mass transfer barrier is a layer of a polymer coating whose thickness is varied to correspond to the linear measurement range of a biosensing system for a given bulk solution. An effective diffusion barrier could also be created by increasing the thickness of the enzyme layer. Biosensing systems that have an increased thickness of the enzyme layer are generally referred to as thick-film biosensing systems. Linear measurement ranges can be extended through the use of thick-film biosensing system designs. The rates of analyte mass transfer and reaction remain coupled in thick-film biosensing system designs. Thus, at some analyte concentration, the rate of mass transfer is high enough that the analyte concentration near the enzymes exceeds the linear reaction rate range and the biosensing system no longer has a direct, linear response to the analyte concentration.
In one embodiment, biosensing systems of the present disclosure use a design scheme for the construction of optical enzymatic biosensing systems capable of measurements at high analyte concentrations. This is based on the combination of a high mass transfer resistance and a high enzyme concentration, so that the analyte concentration near the transducer/fluorophore layer always remains in the linear reaction rate (and biosensing system response) range.
For any given concentration of any particular analyte, the appropriate ranges of the mass transfer coefficient of the analyte or substrate from the bulk solution to the enzyme layer, and the reaction rate parameters of the enzyme layer can be determined according to Equation 1: (((Da+1−β)2)/4β)>>1. Where β=the substrate concentration in the bulk solution divided by the KM of the enzyme for the substrate; and where Da is (heVmaxhp)/(DpKM) where he is the thickness of the enzyme layer which is embedded within a matrix; hp is the thickness of a porous polymeric or ceramic material which sits atop the enzyme layer; where Dp is the diffusion coefficient of the polymer coating, see FIG. 4.
Therefore, by using Equation 1, the calculations provide specific design parameters such as the thickness of the enzymatic (detection) and mass transfer resistance layers such that a linear biosensing system response is obtained for a given concentration, see FIG. 4.
As an example of different embodiments of biosensing systems of the present disclosure, a series of biosensing systems were constructed with different membranes/porous layers or no membrane/porous layer covering the enzyme layer. The analyte concentration that was measured was lactose, but this series of biosensing systems is representative for any analyte or substrate, such as halogenated hydrocarbons, for example. In one embodiment, biosensing system A, the biosensing system has only a thin film of enzyme that is immobilized on the surface of the biosensing system that is exposed to the solution. In another embodiment, biosensing system B, the biosensing system has a porous layer placed over the same thickness of enzyme layer as was used in biosensing system A. In another embodiment, biosensing system C, the same thickness of enzyme layer as biosensing systems A and B has a membrane layer/porous layer placed over it that is less porous than the porous layer of biosensing system B.
Biosensing systems B and C have a membrane material consisting of track-etched polycarbonate with a pore size of 0.015 μm. Additional mass transfer resistance was provided for biosensing system C by casting a polyurethane coating on top of the porous layer material.
The response of biosensing system A to a series of lactose standards is shown in FIG. 5. From FIG. 5 it is seen that the biosensing system response begins to saturate at concentrations above 1.01 mM lactose. Signal saturation is due to the presence of analyte at concentrations that exceed the KM of the enzyme.
Biosensing system B has the addition of a diffusive barrier on top of the enzyme layer. This diffusive barrier extended the linear range of biosensing system B into higher concentration ranges, see FIG. 6. For biosensing system B, a porous polycarbonate membrane was immobilized on top of the enzyme layer to act as barrier to analyte mass transfer, which resulted in a lower analyte concentration in the enzyme layer compared to that in bulk solution.
Biosensing system C used a less porous polycarbonate membrane relative to the membrane of biosensing system B. This decrease in the porosity of the diffusive barrier resulted in the ability to measure lactose at even higher concentrations relative to biosensing system B, see FIG. 7. The linear range of biosensing system C was extended into this higher concentration regime as a direct result of the increased mass transfer resistance of the less porous diffusive barrier.
FIG. 8 shows one exemplary embodiment of a system 100 that is used to provide the appropriate design parameters for constructing biosensing elements used in biosensing systems that have a linear response in a given range of an analyte concentration in a solution. System 100 uses a computer 110 that has a microprocessor 120 that contains software 130 that processes input data 140 to provide output data 150 that contains the appropriate design parameters used for constructing biosensing elements used in biosensing systems that have a linear response in a given range of an analyte concentration in a solution. Output data 150 is displayed upon a screen or saved in a memory storage device or may be transmitted to another memory device or display device.
Constructing the Biosensing System and/or Biosensing Element
In an embodiment, the biosensing element is constructed by putting an immobilized biocomponent within a matrix and coupling that biocomponent-containing matrix onto a transducer. In another embodiment, a biosensing system is created by bonding, affixing or otherwise causing the biocomponent to be in contact with an optode.
An embodiment of biosensing system of the present disclosure is depicted in FIG. 9. FIG. 9 depicts a biosensing system 10. Biosensing system 10 includes a biocomponent 20 that is displaced within a matrix 22. Matrix 22 is in direct contact with a transducer 30. Transducer 30 is in direct contact with an end of a bifurcated optical cable 50. Biocomponent 20 and transducer 30 comprise a biosensing element 40. Bifurcated optical cable 50 transmits light from a light source 70 through a filter 80. The light that is transmitted through filter 80 is transmitted through bifurcated optical cable 50 at a first light wavelength 82. Transducer 30 interacts with first light wavelength 82 and luminesces at a second light wavelength 90. Second light wavelength 90 is transmitted through bifurcated optical cable 50 and is detected by a photon-detection device 60 that produces a signal that is sent to a signal processing system 62. Signal processing system 62 contains software 64 that uses an algorithm for determining the concentration of an analyte in a solution based on the luminescence of transducer 30 at second wavelength 90.
Method of Using the Biosensing System and/or Biosensing Element
FIG. 10 shows one exemplary method 200 for using a biosensing system to measure the concentration of an analyte in a solution. In step 202, method 200 is implemented by generating light of a first wavelength 82 by light source 70 as it passes through filter 80 and travels down bifurcated optical cable 50 to interact with transducer 30 of biosensing element 40. In step 204, method 200 is further implemented by placing biosensing element 40 at the end of a bifurcated optical cable 50 into a solution. In step 206, an analyte diffuses into matrix 22 and catalyzes the reaction of biocomponent 20. In step 208, the product of the reaction of the analyte with biocomponent 20 produces or uses oxygen and/or hydrogen ions that interact with transducer 30 to affect the amount of fluorescence at a second light wavelength 90 of transducer 30. In step 210, the second light wavelength 90 is transmitted through bifurcated optical cable 50 and detected by photon-detection device 60. In step 212, photon-detection device 60 detects and multiplies the signal of second light wavelength 90 and sends a signal to signal processing system 62. In step 214, signal processing system 62 has software 64 that uses an algorithm that transforms the signal from photon-detection device 60 into an output that can be read as a numerical representation of the concentration of the analyte in the solution that biosensing element 40 was placed into in step 204.
NAD(P)H Regenerating TOM Biosensing System
One embodiment of the regeneration of NADH using formate dehydrogenase is exemplified in Scheme 1. Scheme 1 depicts reactions within a NADH regeneration system comprising TOM and FDH. TOM catalyzes the reaction of toluene and oxygen while using NADH to generate 2-hydroxy toluene. FDH catalyzes the reaction of formate and NAD+ to generate CO2 and NADH which is then used in the TOM catalyzed reaction. Thus, scheme 1 depicts one embodiment of a cofactor regeneration system for use in biosensing systems.




Biosensing systems made with E. coli cells expressing TOM only, or TOM and FDH, were constructed and tested three times each for their response to 92 μM toluene. After each test, the biosensing elements of the biosensing systems were placed in fresh measurement solution with formate (a solution of 0.15 M NaCl, 0.025 M CaCl2, and 0.1 M sodium formate at pH 7.0) for 24 h. The control experiments were performed with three fresh TOM biosensing systems (n=3) that were only tested once each. The data in Table 1 demonstrate that the signal from biosensing systems made from cells containing both TOM and FDH was retained consistently over three consecutive measurements of toluene, whereas the signal from TOM only biosensing systems declined rapidly from one measurement to the next and was essentially at noise levels for the third measurement.







TABLE 1







Results of repeated measurements using toluene biosensing


systems with and without FDH to enable NADH regeneration.










TOM
TOM + FDH














Initial
Post-time
Signal
Initial
Post-time
Signal

















Test 1
8750
9840
1090
9620
9940
320


Test2
11020
11470
450
9610
9910
300


Test 3
9210
9230
20
9610
9900
290








Control
Avg of signal = 1066, Std dev of signal = 29, n = 3









Biosensing systems made with E. coli cells expressing TOM and FDH were constructed and tested at various time points and then stored in buffer with formate. This cycle was repeated. The results demonstrate that the biosensing systems with TOM and FDH retained activity when used over 2 weeks and had essentially the same activity after being used on and off over 2 weeks as cells that had been stored but not used, see FIG. 1.
Storage Lifetime
Biosensing systems made with E. coli cells expressing TOM only, or TOM and FDH, were constructed. Each biosensing system was used only once, and all biosensing elements of the biosensing systems were stored at room temperature in a buffer solution with formate until they were tested. The results demonstrate that the biosensing systems made from cells with both TOM and FDH did not lose any activity over two weeks of storage, see FIG. 2.
Examples
The following examples are prophetic and are included as non-limiting illustrations of potential embodiments of the present disclosure.
Bacterial Strains and Growth Conditions
In one prophetic example, biosensing systems use various biocomponent enzymes such as toluene ortho monooxygenase, toluene ortho monooxygenase variants, formate dehydrogenase, epoxide hydrolase (EchA), γ-glutamylcysteine synthetase (GSHI). Combinations of the biocomponent enzymes include: TOM-Green/FDH, TOM/FDH, TOM-Green/FDH/EchA and TOM-Green/GSHI/FDH, all of which may be expressed in E. coli strain TG1. E. coli cultures can be grown aerobically on agar plates made from Luria-Bertani (LB) medium with 20 g/L Bacto-agar (Difco) and 100 mg/L kanamycin (and an additional selective antibiotic if required) at 30° C. for 24 h. A culture tube containing 2 mL LB medium supplemented with the same concentrations of antibiotics is then inoculated from an individual colony on an agar plate and shaken overnight at 30° C. and 200 rpm, then transferred to a flask containing 200 mL of the same LB-Kan medium and shaken at 30° C. and 200 rpm. The cell concentration is measured as culture absorbance at 600 nm (optical density at 600 nm, OD600) with a spectrophotometer Spectronic® 20 GenesysTM, Thermo Electron Corporation. IPTG solution is prepared with deionized water and added to the culture with a final concentration of 1 mM in the early exponential growth phase (OD600 of 0.6) to induce cellular expression of plasmids. The culture is then harvested 4 h after IPTG is added, centrifuged, and resuspended in 20 mL of a solution containing 10 mM phosphate-buffered saline at pH 7.4 and stored at 4° C. until further use.
Exemplary Biosensing System
In one prophetic example, a biosensing system consisting of a layer of whole cells immobilized over an oxygen optode may be constructed from a 25-cm section of PMMA optical fiber terminated with an ST connector. The fiber jacket is detached from 1 mm of the distal end (non-connector terminated) and then polished with 2000-grit and 3 μm polishing film (part of a fiber optic tool kit, IF-TK4-RP2, Industrial Fiber Optics) to minimize potential signal loss due to scattering. One mg of the oxygen-sensitive RuDPP is then dissolved into 1 mL chloroform and mixed with 200 mg silicone gel (clear RTV silicone, Permatex, Inc.). A 1 μL aliquot of this mixture is then added to the polished fiber tip. The RuDPP gel layer is affixed to the optical fiber end as soon as the chloroform evaporated. Previously stored E. coli whole cells containing plasmids encoding enzymes TOM, TOM-Green, epoxide hydrolase, glutathione synthetase, glutathione S-transferase, and/or γ-glutamylcysteine sythetase, and FDH may then be centrifuged and mixed with sodium alginate solution (2.5% w/w) in a cell-to-alginate ratio (wet cell mass:alginate solution) of 1:1 w/w. A 2-μL aliquot of the cell-alginate mixture is then placed on the tip of each oxygen optode and immobilized after immersing the optode in 0.47 M calcium chloride solution for 30 min at 0° C. All biosensing elements can then be stored at 0° C. in a solution of 0.15 M NaCl and 0.025 M CaCl2 at pH 7.0, the measurement solution.
Biosensing System Measurement Protocols
In one prophetic example, all biosensing system experiments are performed in 5 mL glass vials containing 4 mL of measurement solution saturated with air at room temperature with a small magnetic stir bar for rapid mixing. The biosensing element is then immersed in this solution, sealed in the glass vial with a rubber septum, and shielded from external light sources. Aliquots of 0.1 mL of a TCE solution of 0.1 to 4 mg/L are injected into the measurement solution after the biosensing system has produced a steady output. A steady output is defined as the time when the variation in the output is no larger than the peak-to-peak noise for a period of at least 5 min. All measurements are performed at room temperature unless temperature effects are to be studied. Each measurement is performed with a fresh biosensing element to distinguish the effect in question (e.g., temperature, pH, cell/alginate mass ratio). Biosensing elements should not be reused unless it is necessary.
Preparation of Biosensing Element Using Dry-Heated Cells
In another prophetic example, biocomponents of the biosensing element of the present disclosure are prepared by using dry-heated cells. In order to prepare dry heated cells, cells stored at 4° C. in phosphate-buffered saline solution may then be centrifuged at 15,000×g for 3 minutes and washed twice with distilled water. These cells may then be suspended in a small quantity of water (3 mL of stored cell suspension were washed and then suspended in 0.5 mL of water). This suspension is put in a 10-mL beaker and water is completely removed by vacuum drying at 35° C. It takes about an hour to dry these cells. The dried cells are then scratched off from the surface of beaker using a spatula. The beaker is then covered with aluminum foil and left in the oven at a constant temperature of 270° C. and for a given period of time (30 sec, 60 sec, etc.). These dry heated cells may look like a highly porous solid and have a light orange color. These dry-heated cells ( ̃0.003-0.004 g) may also be immobilized using the same entrapment method. These cells are then directly mixed with 4% (w/v) of alginate, thus forming small bubbles in the cell-alginate mixture. Since it is important to eliminate these bubbles in order to obtain a stable response, these cells are first suspended in 10 μL of NaOH (pH 7.0) in a 1.5 mL-vial and then 8% (w/v) of alginate is added (from about 0.3 to about 0.5 g/g of dry wt. of cells to wt. of alginate). This mixture is used to make the biosensing element that is incorporated into the biosensing system.
Preparation of Biosensing Element Using Chloramphenicol Treated Cells
In one prophetic example, cells stored at 4° C. in phosphate-buffered saline are centrifuged at 15,000×g for 2 min and the pellet is then washed twice with saline (9 g/L of NaCl [pH 7.1]) containing 50 μg/mL of chloramphenicol. Next, sodium alginate (4% w/v in water) containing either 50 or 200 μg/mL of chloramphenicol is added and mixed well with the cell pellet. This cell and alginate mixture is kept for 5 minutes at room temperature before it is used to make the biosensing element.
Preparation of Biosensing Element Using Protease Inhibitor Treated Cells
In another prophetic example, cells stored at 4° C. in phosphate-buffered saline are centrifuged at 15,000×g for 2 min and the pellet is then washed twice with saline (9 g/L of NaCl [pH 7.1]) containing 5 μL of protease inhibitor cocktail in 1 mL of saline solution. This cocktail is prepared by adding 215 mg of lyophilized protease inhibitor in a solution containing 1 mL of DMSO (Dimethyl sulfoxide) and 4 mL of deionized water. The cocktail has a broad specificity for the inhibition of serine, cysteine, aspartic and metalloproteases, and aminopeptidases. It is stored at −20° C. in the freezer. These cells are then mixed with Na-alginate solution (4% w/v) containing 200 μL of cocktail per mL of alginate solution. The cell-alginate mixture is left for about 5 minutes at room temperature before it is used for making the biosensing element. The ratio of the weight of wet cells to the weight of alginate used in the experiment is 0.72 g/g.
In another prophetic example, purified enzymes may be used to prepare a biosensing element by substituting purified enzymes for whole cells in the prophetic example above.
Preparation of Biosensing Element with a Poly-L-Lysine Coating
In another prophetic example, the alginate bead is coated with poly-L-lysine (PLL) by preparing the biosensing element with a biocomponent as described above. The Ca-alginate bead on the biosensing element is then washed twice with saline solution (9 g/L of NaCl in water). Then the biosensing element is immersed in 10 mL of 0.4% (w/v) of poly-L-lysine.HCl solution, stored at 4° C. inside the refrigerator) in saline for 30 minutes at 30° C.
In one prophetic example, the PLL layer's thickness can be varied through multiple rounds of application of PLL in to create a diffusivity barrier to enable the biosensing element to respond linearly to the concentration of an analyte in a solution being measured by the biosensing system.
Construction of Biosensing System with Oxygen Sensitive Transducer Layer
In one prophetic example, a general method for constructing a biosensing element having an oxygen sensitive transducer layer is presented as follows. The optode used in the biosensing system is an oxygen optode. An oxygen optode is a biosensing system based on optical measurement of the oxygen concentration in a solution. In one embodiment, a chemical film is adhered to the tip of an optical cable and the fluorescent properties of this film depend on the oxygen concentration. Fluorescence is at a maximum when there is no oxygen present. When an O2 molecule diffuses into the film it quenches the photoluminescence of the chemical film (transducer layer). For a given oxygen concentration there will be a specific number of O2 molecules in the film at any given time, and the fluorescence properties will be stable.
In one prophetic example of a biosensing system that uses an oxygen optode, a biosensing system for measuring the concentration of an analyte consists of a layer of immobilized whole cells over an oxygen optode, which is constructed from a 25-cm section of PMMA optical fiber terminated with an ST connector. The fiber jacket is detached from 1 mm of the distal end (non-connector terminated) and then polished with 2000-grit and 3 μm polishing film (part of a fiber optic tool kit, IF-TK4-RP2, Industrial Fiber Optics) to minimize potential signal loss due to scattering. One mg of the oxygen-sensitive phosphorophore RuDPP, which may classified as a phosphorophore since it has longer decay lifetime than typical fluorophores, is dissolved into 1 mL chloroform and mixed with 200 mg silicone gel (clear RTV silicone, Permatex, Inc.). A 1-μL aliquot of this mixture is then added to the polished fiber tip. The RuDPP gel layer is affixed to the optical fiber end as soon as the chloroform evaporated. Previously stored E. coli whole cells (with plasmids which may encode for TOM, TOM-Green, epoxide hydrolase, glutathione synthetase, glutathione S-transferase, γ-glutamylcysteine sythetase, and/or FDH, for example) were centrifuged and mixed with sodium alginate solution (2.5%) in a cell-to-alginate ratio (wet cell mass:alginate solution) of 1:1 w/w unless otherwise specified. A 2 μL aliquot of the cell-alginate mixture is placed on the tip of each oxygen optode and immobilized after immersing the optode in 0.47 M calcium chloride solution for 30 min at 0° C. All biosensing elements are stored at 0° C. in a measurement solution of 0.15 M NaCl and 0.025 M CaCl2 at pH 7.0.
Oxygen Based Biosensing System Instrumentation
In another prophetic example, an oxygen based biosensing system instrumentation consists of two separate optoelectronic modules: a 470 nm LED and a 450/60 nm optical bandpass filter (Chroma Technologies) as the excitation light source, and a computer-controlled Ocean Optics USB4000-FL spectrometer with 10 nm resolution for detection. The 470 nm excitation light is delivered through one leg of a bifurcated optical fiber assembly that has two 1 mm fibers side-by-side in the common end (Ocean Optics, Inc.), which is connected with the biosensing system via a ST connector. The phosphorescent emission light (peak at 620 nm) from the biosensing element is directed back into the detector through the other leg of the bifurcated optical fiber and measured by a spectrometer having a sensitivity of approximately 60 photons/count at 600 nm. The spectrometer output from 615 nm to 625 nm is integrated over 200 ms and five such values are averaged to yield one measurement value per second. The change in the intensity of the emission light over time correlates to the oxygen concentration change in the RuDPP layer of the biosensing element of the biosensing system.
Mitigation of Epoxide Toxicity and Cofactor Recycling
In one prophetic example, epoxide toxicity to the biocomponents is mitigated. During the reaction of oxygenases with their substrate molecules, highly reactive epoxide intermediates may be generated. These epoxide intermediates may react with active site residues of the biocomponent oxygenase enzyme or the dehydrogenase enzyme and thus cause the biocomponents to lose activity. In one example, the epoxide intermediate TCE epoxide is generated from the activity of TOM acting on TCE. E. coli cells with genes for TOM and/or TOM-Green, and genes for GSHI and/or EchA are developed and used to mitigate the damage created by TCE epoxide or other epoxides.
In one embodiment of the prophetic example, the combination of genes for TOM, GSHI, and FDH in E. coli enables retention of activity of the TOM biocomponent through both epoxide toxicity reduction (by GSHI) and cofactor recycling through the recycling of NADH using FDH as another biocomponent in the biosensing system. NADH recycling via an external supply of formate can replenish biocomponent TOM activity since intracellular FDH and/or FDH expressed from plasmids within the E. coli can reduce the NAD+ to NADH by the oxidation of formate.
In one prophetic example, formate is supplied to the FDH biocomponent via diffusion from a capillary tube containing a concentrated solution of formate. The capillary is positioned such that it delivers the formate at a constant rate within the matrix that the biocomponent is disposed within. In another embodiment, the formate is part of the matrix, immobilizing structure or other membrane or porous layer associated with the biosensing element and diffuses into the immobilized FDH where the formate is used as an electron donor in order to recycle NADP to NADPH. For example, a formate salt could be ionically associated with a matrix within which the biocomponents are immobilized such that when the biosensing element is exposed to the solution containing the analyte of interest, the formate salt would diffuse into the biocomponent containing FDH. The rate at which the formate salt dissolves and then diffuses into the biocomponent could be controlled through modifying the type of formate salt, the concentration of the formate salt, the amount of the formate salt, and the availability of the formate salt to water molecules from the solution and the size of the matrix cells in which the formate salt is associated with. In an additional embodiment of the prophetic example, an amount of formate salt could be encapsulated within a semi-permeable membrane or other porous layer that is itself immobilized within the same matrix that the biocomponents are immobilized within on the biosensing element portion of the biosensing system. The diffusion of the formate salt through the semi-permeable membrane or other porous layer could be controlled by selected an appropriate volume/surface area ratio of the formate salt to semi-permeable membrane/porous layer as well as controlling what the semi-permeable membrane or porous layer is made from.
The above examples, embodiments, definitions and explanations should not be taken as limiting the full metes and bounds of the invention.
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## Claims

1. A method for measuring the concentration of an analyte in a solution, the method comprising:
immersing a biosensing element comprising a first biocomponent, a second biocomponent, a third biocomponent, and a transducer layer in said solution, wherein:
said analyte is a reactant in a reaction catalyzed by an oxygenase enzyme that requires a cofactor selected from the group consisting of NADH, NADPH, FADH, FADH2, FMNH, FMNH2; said first biocomponent comprises said oxygenase enzyme;
said second biocomponent comprises a dehydrogenase enzyme that catalyzes a reaction of an oxidized cofactor selected from the group consisting of NAD+, NADP+, FADH, FMNH, FAD and FMN, and an electron donor;
said first biocomponent catalyzes the reaction of said analyte and said cofactor, while consuming oxygen and producing oxidized cofactor and an epoxide product;
said oxidized cofactor is reduced by said second biocomponent and said electron donor; and
wherein said epoxide product is a reactant in a reaction catalyzed by said third biocomponent, causing said transducer layer to fluoresce photons, and

determining the concentration of said analyte in said solution, wherein:
oxygen quenches at least some of the fluorescent photons;
remaining unquenched photons enter into a fiber optic cable and are transmitted to a photomultiplier; and
said photomultiplier produces an output signal that is coupled to an algorithm that transforms the signal generated by said photomultiplier into an output correlated to the concentration of said analyte in said solution.

2. The method of claim 1 wherein said first biocomponent is toluene ortho-monooxygenase.

3. The method of claim 1 wherein said first biocomponent is a toluene ortho-monooxygenase green.

4. The method of claim 1 wherein said second biocomponent is formate dehydrogenase and said electron donor is formate.

5. The method of claim 1 wherein said third biocomponent is selected from the group consisting of epoxide hydrolase, glutathione synthetase, glutathione S-transferase and gamma-glutamylcysteine synthetase.

6. A method of manufacturing a biosensing system having a linear response to the concentration of an analyte in a bulk solution, the method comprising:
covering a first tip of an optical fiber of an optode with a luminescent reagent layer;
covering said luminescent reagent layer with a biocomponent layer having a preselected thickness;
covering said biocomponent layer with a porous layer having a preselected thickness and a preselected diffusion coefficient;

coupling a second tip of said optical fiber to a photon-detection device, and
coupling said photon-detection device to a signal processing system, wherein
said preselected thickness of said biocomponent layer, said preselected thickness of said porous layer, and
said preselected diffusion coefficient of said porous layer, are selected such that Da is greater than the value of 1−β and a quotient between Da2 and 4β is from about 10 to at least 1000.

7. The method of claim 6 wherein said biocomponent layer comprises toluene ortho-monooxygenase.

8. The method of claim 6 wherein said biocomponent layer comprises a toluene ortho-monooxygenase green.

9. The method of claim 6 wherein said biocomponent layer comprises a toluene ortho-monooxygenase green and formate dehydrogenase.

10. The method of claim 6 wherein said biocomponent layer comprises a toluene ortho-monooxygenase green, formate dehydrogenase and at least one enzyme selected from the group consisting of epoxide hydrolase, glutathione synthetase, glutathione S-transferase and gamma-glutamylcysteine sythetase.

11. The method of claim 6 wherein said transducer layer comprises RuDPP.

12. The method of claim 6 wherein said porous layer is track-etched polycarbonate.

13. The method of claim 6 wherein said porous layer is a polymer.

14. The method of claim 6 wherein said biocomponent layer comprises toluene ortho-monooxygenase and formate dehydrogenase.

15. The method of claim 6 wherein said biocomponent layer comprises toluene ortho-monooxygenase, formate dehydrogenase and at least one enzyme selected from the group consisting of epoxide hydrolase, glutathione synthetase, glutathione S-transferase and gamma-glutamylcysteine sythetase.

16. A method for measuring the concentration of an analyte in a solution, the method comprising:
immersing a biosensing element comprising a first biocomponent, a second biocomponent, and a transducer layer in said solution, wherein:
said analyte is a reactant in a reaction catalyzed by an oxygenase enzyme that requires a cofactor selected from the group consisting of NADH and NADPH;
said first biocomponent comprises said oxygenase enzyme;
said second biocomponent comprises a dehydrogenase enzyme that catalyzes a reaction of an oxidized cofactor selected from the group consisting of NAD+ and NADP+ and an electron donor;
said first biocomponent catalyzes the reaction of said analyte and said cofactor, while consuming oxygen and producing oxidized cofactor; and
said oxidized cofactor is reduced by said second biocomponent and said electron donor, causing said transducer layer to fluoresce photons, and

determining the concentration of said analyte in said solution, wherein:
oxygen quenches at least some of the fluorescent photons;
remaining unquenched photons enter into a fiber optic cable and are transmitted to a photomultiplier; and
said photomultiplier produces an output signal that is coupled to an algorithm that transforms the signal generated by said photomultiplier into an output correlated to the concentration of said analyte in said solution.

17. The method of claim 16 wherein said first biocomponent is toluene ortho-monooxygenase.

18. The method of claim 16 wherein said first biocomponent is a toluene ortho-monooxygenase green.

19. The method of claim 16 wherein said second biocomponent is formate dehydrogenase and said electron donor is formate.