This application contains a Sequence Listing which has been submitted electronically in ASCII format concurrently herein and is hereby incorporated by reference in its entirety. Said ASCII copy is named MARKS-47-PTUSCON_Sequence_Listing.txt and is 45,274 bytes in size.
The present invention is directed to novel sensors, particularly sensors useful in the detection of bio-analytes.
Biosensors are analytical devices which convert a biological response into a measurable electrical signal. Biosensors may be used, for example, to determine the concentration of substances or other parameters in biological material. Biosensors find use across a range of industries, predominantly the healthcare industry, but also in other areas such as food quality monitoring, environmental monitoring and the like.
A particular area of focus is the use of biosensors in the health-care industry to analyse biological samples to assist in clinical management. For example, according to the WHO, the global prevalence of diabetes among adults over 18 years of age was 8.5% in 2014, and there is a significant unmet medical need for rapid, accurate and simple glucose monitoring biosensors.
Biosensors should ideally possess some or all of the following attributes: accuracy, preciseness, reproducibility, specificity, stability, and low cost. There remains a significant unmet need for biosensors achieving some or all of these aims.
In a first aspect of the present invention there is provided a sensor B-L-S; wherein: B is a biomolecule comprising one or more surface-exposed thiol moieties, L is a linker comprising a thiol reactive group, and S is a substrate; wherein L is covalently linked to B via the one or more surface-exposed thiol moieties.
By linking the biomolecule to the linking group via a surface-exposed thiol moiety, it is possible to selectively and precisely control conjugation leading to sensors with enhanced properties. The present invention makes use of thiol reactive compounds: surface exposed on the biomolecule and on a linker to enable selective conjugation of the biomolecule and linker.
In a further aspect of the present invention, there is provided a sensor comprising a biomolecule immobilised to a substrate; wherein the biomolecule is immobilised to the substrate via a linker; and wherein the biomolecule has one or more surface accessible thiol moieties and is connected to the linker via said one or more surface accessible thiol moieties.
Preferably, the biomolecule is a modified biomolecule, and the modification introduces said surface accessible thiol moieties. For example, pre-modification, the biomolecule may not contain any surface accessible thiol moieties, but modification introduces linkable surface accessible thiol moieties. The modification may be a mutation.
As such, in a further aspect of the present invention there is provided a sensor comprising a mutated biomolecule immobilised to a substrate; wherein the biomolecule is immobilised to the substrate via a linker; wherein the biomolecule is mutated to introduce one or more surface accessible thiol moieties; and wherein the biomolecule is connected to the linker via said one or more surface accessible thiol moieties.
In a further aspect of the present invention, there is provided a sensor comprising a biomolecule immobilised to a substrate via a linker, wherein the linker is connected to the biomolecule through a thiol linkage, and wherein the substrate is a material having optical or charge carrying properties. In embodiments, the thiol linkage is between one or more surface accessible thiol moieties on the biomolecule and thiol reactive group(s) on the linker.
In a further aspect of the present invention, there is provided a sensor comprising a biomolecule immobilised to a carbon nanomaterial via a linker, wherein the linker is connected to the biomolecule through a thiol linkage.
In a yet further aspect of the present invention, there is provided a method of controlling biomolecules immobilised on a carbon nanomaterial substrate, said method comprising: modifying said biomolecules to create biomolecules having a surface accessible thiol moieties, and immobilising said modifying biomolecules to said substrate using linkers having thiol reactive groups, wherein the biomolecules are connected to the linkers via the surface accessible thiol moieties and the thiol reactive groups.
The method enables controlled immobilisation by controlling where the linker attaches to the biomolecule. This, in turn, controls how the biomolecule immobilises onto the substrate since it is the linker which adheres to the substrate surface. Preferably, a biomolecule will have one surface accessible thiol moiety, and therefore, one linker, but it is possible for a biomolecule to have more than one surface accessible thiol moiety, if desired.
By using a thiol based linking strategy, it is possible to control at which location the linking group will attach to the biomolecule. Thiol groups are not common on protein surfaces, and therefore, providing a surface-exposed thiol moiety allows for consistent placement of the linking group on the protein surface. This can, for example, ensure that the linker is place in a region such that it will not adversely affect the reactive binding site for the biomolecule. The linker may, for example, be located to facilitate charge flow through the sensor to improve sensitivity. Controlled placement may also help ensure consistent protein folding on the sensor. Controlled placement may enable greater stability of the sensor device.
The sensor may contain a plurality of biomolecules adhered to the surface of the substrate. By controlling the linking site on the biomolecule, it is possible to ensure a more consistent orientation of biomolecules on the surface. Such an approach may improve density of biomolecule adherence. Improving biomolecule density and/or orientation consistency may improve the sensitivity and/or reliability of the sensor.
In comparison to directly adhering the biomolecule to the substrate, the biomolecules according to the present invention may be more stably secured to the substrate due to the linking strategy. Thy may also be applied with a higher density. They may also enable the biomolecule to better conform to its natural structure (e.g., better protein folding). Many of the same advantages may be present when compared against biomolecules linked via, say, an amide or carboxylic acid group on the biomolecule. While these linkages are possible, they are less controlled than a thiol linking strategy as there are many more amide sites on the surface of a biomolecule. This leads to less control of the linking strategy and many of the same issues outlined above.
In a yet further aspect of the present invention, there is provided: a glucose oxidase (GOx) polypeptide comprising one or more mutations, a glucose-binding protein (GBP) comprising one or more mutations, a concanavalin A (ConA) comprising one or more mutations, a cholesterol oxidase comprising one or more mutations, a carbohydrate oxidase polypeptide comprising one or more mutations or a lactate oxidase polypeptide comprising one or more mutations; wherein said one or more mutations introduces a site-selective thiol conjugation site selected to permit conjugation of the polypeptide to a linker comprising a thiol reactive group. Such modified polypeptides enable sensors with enhanced properties.
In a yet further aspect of the present invention, there is provided a polynucleotide encoding the glucose oxidase polypeptide, the carbohydrate oxidase polypeptide, or the lactate oxidase polypeptide of the present invention.
In a yet further aspect of the present invention, there is provided a nucleic acid construct comprising the polynucleotides of the present invention operably linked to a regulatory sequence. In a yet further aspect of the present invention there is provided a method of producing a sensor, comprising:
The method may involve modifying the biomolecule to obtain one or more surface-exposed thiol moieties.
Preferably, the method involves a surfactant exchange method.
In a yet further aspect of the present invention, there is provided the use of a sensor according to the present invention in the detection and/or quantification of an analyte in a sample. In a yet further aspect, there is provided a method of detecting and/or quantifying an analyte in a sample comprising the use of a sensor according to the present invention. The method may comprise contacting the sample with a sensor according to the present invention and detecting a change in the sensor properties due to presence of the analyte. The analyte, for example, may be the glucose level in a patient.
In a yet further aspect of the present invention, there is provided a method of attaching a biomolecule to a carbon nanomaterial substrate comprising: modifying the biomolecule to introduce one or more surface-exposed thiol moieties; attaching a linker to the biomolecule wherein the linker comprises a thiol reactive group and a substrate adherence group; wherein the linker attaches to the biomolecule via the thiol group and thiol reactive group; and wherein the biomolecule-linker adheres to the substrate via the substrate adherence group.
In a yet further aspect of the present invention, there is provided a method of obtaining structured immobilisation of biomolecules on a substrate comprising modifying the biomolecules to comprise one or more surface-exposed thiol moieties; attaching linking groups to the biomolecules via the surface-exposed thiol moieties and a thiol reactive group on the linking group; and adhering the biomolecules to the substrate via the linking groups.
The following embodiments apply to all aspects of the present invention.
“Biomolecule” (B) may be any peptide, polypeptide, protein, antibody or the like which is used to bind the target analyte. Suitable biomolecules include, but are not limited to, glucose oxidase, concanavalin A, glucose binding protein, cholesterol oxidase, lactate oxidase and the like. A preferred biomolecule is glucose oxidase (GOx).
The biomolecule comprises one or more surface-exposed thiol moieties.
“Surface-exposed” means that the thiol moiety is accessible to the thiol reactive linking group such that the linker can attach to the biomolecule via the exposed thiol group. The thiol moiety is therefore surface accessible.
“Thiol moiety” means a moiety which contains a thiol group. A suitable thiol moiety is a cysteine residue. Further suitable thiol moieties include non-natural amino acids containing a thiol group.
An example of a non-natural amino acid containing a thiol group is selenocysteine. Since pairs of thiol groups in proteins typically form disulfide bonds either within the same biomolecule or between biomolecules, it may be necessary to reduce the biomolecule to form free thiol groups suitable for linking.
In a preferred embodiment, the biomolecule comprises a single surface accessible thiol moiety.
In an alternative embodiment, the biomolecule comprises a plurality of surface accessible thiol moieties.
Having a single surface accessible moiety ensures each biomolecule orients in the same direction. In some embodiments, however, it may be advantageous to have more than one linking point. Having multiple linkers may increase the binding strength of the biomolecule to the substrate which may, for example, improve resilience of the device. Further, it may be possible to better control orientation of the biomolecule on the surface by having multiple tether points. It could, for example, ensure a particular protein presentation or folding conformation.
In a preferred embodiment, the biomolecule is modified to provide a surface exposed thiol moiety. By this approach, it is possible to fully control the linking position. However, in some instances, the biomolecule may naturally contain one or more surface exposed thiol moieties which are suitable as a linking position for the linker. Thus, in some embodiments, it is not necessary to modify the biomolecule for use in the present invention. However, in a preferred embodiment, the biomolecule is modified.
“Linker” or “linking group” means a group which attaches to the biomolecule and enables the biomolecule-linker to adhere to the substrate. Suitable linkers comprise a group which enables attachment to the biomolecule and a group which enables attachment to the substrate. The linker is preferably covalently attached to the biomolecule via a thiol reactive group. The linker is preferably non-covalently adhered to the surface of the biomolecule. The linker, therefore, comprises a thiol reactive group and a substrate adherence group. In an embodiment, the linker is a hydrophobic linker. In an embodiment, the linker does not comprise DNA. In an embodiment, the linker comprises monomeric molecules. In a preferred embodiment, the linker is a hydrophobic linker with thiol reactive group(s) and is not DNA.
“Thiol reactive group” means a group which can form bonds with a thiol group. Suitable groups include maleimides, aziridines, acryloyl derivatives, arylating agents, pyridyl disulfides, disulfide reagents, vinylsulfone derivatives, haloacetyl and alkyl halide derivatives (including iodoacetyl and bromoacetyl and the like). A preferred thiol reactive group is maleimides.
“Substrate adherence group” means a group which is configured to adhere to the substrate. This may be via non-covalent bonds (e.g., π-π stacking). Suitable substrate adherence groups include, but are not limited to, pyrenyl, porphyrin, triphenylene, anthracene, dibenzocyclooctyne, pentacene, naphthalene. In an embodiment, the substrate adherence group comprises at least one aromatic ring. In a further embodiment, the substrate adherence group comprises at least two, at least three or at least four aromatic rings.
As such, the linker comprises a moiety which can form bonds with a thiol group on the biomolecule, and a moiety which enables adherence to the substrate. A particular linker according to the present invention comprises a maleimide group as thiol reactive group, and a pyrenyl group as substrate adherence group. A particular linker is N-(1-pyrenyl)-maleimide (PM).
The size of the linker will depend on the requirements of sensor. In embodiments, the linker length will be selected to allow the biomolecule to adopt the correct conformational structure on the surface of the substrate. In further embodiments, the linker length will be selected to facilitate charge transfer from the reactive site on the biomolecule to the substrate.
In an embodiment, the linker length is selected to immobilise the biomolecule within about 50 Angstrom from the substrate surface, preferably below about 25 Angstrom, below about 15 Angstrom, below about 10 Angstrom, below about 7 Angstrom, or below about 5 Angstrom. Particularly preferred is below about 15 Angstrom to facilitate direct electron transfer. In an embodiment, the linker length is selected to immobilise the reactive site of the biomolecule within the aforesaid distance from the substrate surface.
The linker may comprise the thiol reactive group directly linked to the substrate adherence group. Alternatively, the linker may include a spacer between the thiol reactive group and the substrate adherence group. Suitable spacers include alkyl, alkenyl or alkynyl groups, cycloalkyls, cycloalkenyls, or heterocyclic groups, which may optionally be substituted by one or more suitable substituents. Suitable spacers also include polymer chains, for example polyethylene glycol, polypropylene glycol, polytetramethylene glycol or the like. Short polymer chains are preferred. “Substrate” means a material upon which the biomolecule is immobilised. Suitable substrates include carbon nanomaterial, including nanocarriers, single-walled carbon nanotubes (SWCNTs), multi-walled carbon nanotubes (MWCNTs), single-walled carbon nanohorns, fullerene, graphene, graphene oxide and the like.
In an embodiment, the substrate is a material which has optical properties. Such a substrate may be used in an optical sensor. An example of a material with optical properties is SWCNTs which fluoresce.
In an embodiment, the substrate is a material which has charge carrying properties. Such a material can allow electron transfer onto the material. Materials with charge carrying properties can be used in electrochemical sensors. An example of a material with charge carrying properties is MWCNTs.
“Sensor” means a device which is able to detect a target condition (for example, the presence of an analyte) and to provide a detectible signal which can be used to determine whether the condition is present (for example, to determine the presence or concentration of said analyte). In an embodiment, the sensor is an optical sensor. In a further embodiment, the sensor is an electrochemical sensor. In a preferred embodiment, the sensor is an optical sensor.
The present invention provides biomolecules immobilised on a substrate. In a preferred embodiment, the biomolecules are aligned on the substrate due to the positioning of the linking group. Such a conformance can increase packing density and/or sensitivity. The degree of alignment will depend on the substrate and the linking strategy.
The present invention provides a mutated biomolecule; wherein said mutation introduces one or more site-selective thiol conjugation site selected to permit conjugation of the polypeptide to linker comprising a thiol reactive group. Preferably, the one or more mutations are not in the analyte-binding cavity of the polypeptide. According to the present invention, the term “mutation” or “mutated” does not include a C-terminus modification to the biomolecule. Said another way, a biomolecule including a C-terminus modification to introduce a thiol reactive group would not fall within the scope of the present invention.
The present invention provides: a glucose oxidase polypeptide comprising one or more mutations, a carbohydrate oxidase polypeptide comprising one or more mutations or a lactate oxidase polypeptide comprising one or more mutations; wherein said one or more mutations introduces a site-selective thiol conjugation site selected to permit conjugation of the polypeptide to linker comprising a thiol reactive group. Preferably, the one or more mutations are not in the analyte-binding cavity of the polypeptide.
When determining suitable mutation positions, a number of considerations may be taken into account. First, the mutated residue must be surface-exposed. Second, to facilitate charge transfer, if the biomolecule is an enzyme, the distance between the mutated residue and the active site of the protein should be short to facilitate charge transfer onto the substrate. Third, the mutated residue should not adversely interfere with the active site of the biomolecule. Fourth, if the protein activity is based on an allosteric effect, e.g., a conformational change in the biomolecule (for example, glucose binding protein), then the mutation should ideally be implemented at the flexible domain (or domains).
Preferably the mutation is a substitution. Preferably the substitution is a substitution of the wild type residue for a residue that is suitable for conjugation. Preferably said residue is cysteine, but alternatively the residue is a non-natural amino acid including a thiol or selenol group. An example of an alternative amino acid is selenocysteine.
In one embodiment, the polypeptide is glucose oxidase (GOx). In an embodiment, the wild type (i.e., non-mutated) sequence of GOx comprises or consists of SEQ ID NO: 1 or a functional variant thereof. The present invention relates to one or more substitutions in the wild type sequence. In one embodiment, the substitution is at one or more of the following positions in SEQ ID NO: 1: 13, 70, 418, and 446 or any combination thereof. In a further preferred embodiment, the substitution is one or more of the following: K13C, D70C, A4180 and H446C or any combination thereof.
In one embodiment, the sequence of the GOx polypeptide is selected from SEQ ID NO: 2, 3, 4, 5 or 6 or a functional variant thereof wherein X is selected from a cysteine or an amino acid including a thiol or selenol group, for example selenocysteine.
The term “functional variant” as used herein with reference to any of SEQ ID NOs: 1 to 6 refers to a variant sequence or part of the sequence which retains the biological function of the full non-variant sequence. In the context of SEQ ID Nos 1 to 6, this may mean that the variant sequence is able to catalyse the oxidation of glucose to hydrogen peroxide and D-glucono-delta-lactone. A functional variant also comprises a variant which has sequence alterations that do not affect function, for example in non-conserved residues. Also encompassed is a variant that is substantially identical, i.e., has only some sequence variations, for example, in non-conserved residues, compared to the wild type sequences as shown herein and is biologically active. Each of the proposed modifications is well within the routine skill in the art, as is determination of retention of biological activity of the encoded products.
As used in any aspect of the invention described herein a “variant” or a “functional variant” has at least 25%, 26%, 27%, 28%, 29%, 30%, 31%, 32%, 33%, 34%, 35%, 36%, 37%, 38%, 39%, 40%, 41%, 42%, 43%, 44%, 45%, 46%, 47%, 48%, 49%, 50%, 51%, 52%, 53%, 54%, 55%, 56%, 57%, 58%, 59%, 60%, 61%, 62%, 63%, 64%, 65%, 66%, 67%, 68%, 69%, 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or at least 99% overall sequence identity to the non-variant amino acid sequence.
Two nucleic acid sequences are said to be “identical” if the sequence of amino acids in the two sequences is the same when aligned for maximum correspondence as described below. The terms “identical” or percent “identity,” in the context of two or more amino acids, refer to two or more sequences or subsequences that are the same or have a specified percentage of amino acids that are the same, when compared and aligned for maximum correspondence over a comparison window, as measured using one of the following sequence comparison algorithms or by manual alignment and visual inspection. For sequence comparison, typically one sequence acts as a reference sequence, to which test sequences are compared. When using a sequence comparison algorithm, test and reference sequences are entered into a computer, subsequence coordinates are designated, if necessary, and sequence algorithm program parameters are designated. Default program parameters can be used, or alternative parameters can be designated. The sequence comparison algorithm then calculates the percent sequence identities for the test sequences relative to the reference sequence, based on the program parameters. Non-limiting examples of algorithms that are suitable for determining percent sequence identity and sequence similarity are the EMBOSS Stretcher algorithms.
In another aspect of the invention, there is provided an isolated polynucleotide encoding a GOx polypeptide of the present invention. In one embodiment, the polynucleotide encodes a modified GOx polypeptide as defined in any one of SEQ ID NO: 2 to 5 or a functional variant thereof. In a further embodiment, the GOx polypeptide comprises or consists of a sequence selected from SEQ ID NO: 8 to 11 or a functional variant thereof.
In another aspect of the invention there is provided a nucleic acid construct comprising a polynucleotide of the present invention operably linked to a regulatory sequence. Preferably, the nucleic acid construct is an expression vector, for example, pBSYA3Z. Also provided is a host cell comprising the nucleic acid construct.
The term “operably linked” as used herein refers to a functional linkage between the regulatory sequence and the polynucleotide of the present invention, such that the regulatory sequence is able to initiate transcription of the polynucleotide. In one embodiment, the regulatory sequence is a promoter, such as a constitutive promoter. Suitable promoters would be well known to the skilled person.
In a further aspect of the invention, there is provided a method of making the GOx polypeptide of the invention, the method comprising introducing and expressing the nucleic acid construct of the present invention in a host cell.
The present invention provides methods to manufacture sensors according to the present invention. In an embodiment, the method comprises a number of steps:
The invention will now be described with reference to the following non-limiting examples.
Construction of Recombinant Plasmids for GOx Expression
Positions for non-conserved amino acids were identified using ConSurf software (Ashkenazy, H., et al. ConSurf 2010: calculating evolutionary conservation in sequence and structure of proteins and nucleic acids. Nucleic Acids Res. 38, 529-533 (2010)). GOx expression plasmids were constructed as using a puC57 vector harbouring a synthetic gene of Aspergillus niger GOx (GenBank® X16061; SEQ ID NO: 6) that lacks the signal peptide.
Site directed mutagenesis for the amino-acid exchanges was performed by two single primer reactions according to a protocol by Oded et al. (Edelheit, O., et al. Simple and efficient site-directed mutagenesis using two single-primer reactions in parallel to generate mutants for protein structure-function studies. BMC Biotechnol. 9, 1-8 (2009)) with the exception of Pwo polymerase, which was substituted by Q5 polymerase. The wild type and variants of the synthetic gox gene were amplified using primer pairs from Table 1 that add a Sapl restriction site, and the gene was ligated into the Sapl digested expression vector, pBSYA3S1Z. The ligation fused the coding sequence to an α-factor secretion signal. The resulting vectors were subcloned into E. coli and verified by sequencing (GATC, Germany). The PCR was performed in 0.2 mL MicroAmp™ reaction tubes (applied Biosystems, Life Technologies) in a SimpliAmp™ Thermal Cycler (Thermo Fisher Scientific). Briefly, the 50 μL reaction mix included 5 μl of a 4 μM primer, 4 μL (or 500 ng) of the plasmid DNA, 2 μL of 0.2 mM dNTPs, 1 μl (or 1.5 U) of Q5® Polymerase, 10 μL 5×Q5® buffer from a cloning kit (M0491S, New England Biolabs), and 28 μL of ddH2O water. The PCR protocol included denaturation for 15 s at 98° C., annealing for 15 s at 60° C., elongation for 2 h 30 min at 72° C. This procedure was repeated over 33 cycles. Next, the 40 μL of two single-primer PCR products with forward and reversed primers were combined in a PCR tube and denatured for 5 min at 98° C. to separate the synthesized DNA from the plasmid template DNA. The tubes were gradually cooled from 98° C. to 16° C. The non-mutated DNAs were digested by 1 μL of 20 U Dpnl in 2.5 μL of FD Buffer for 3 h at 37° C. and incubated overnight at 10° C. The digested PCR products were analysed by agarose gel electrophoresis (
P. pastoris Transformation
Prior to transformation, P. pastoris BG11 competent cells were prepared according to a protocol reported by J. Lin-Cereghino et al. (Lin-Cereghino, J. et al. Condensed protocol for competent cell preparation and transformation of the methylotrophic yeast P. pastoris. Biotechniques 38, 44-48 (2005)). 100 μL competent P. pastoris cells were mixed with 3 μg of pBSYA3-GOx-K13C, pBSYA3-GOx-D700, pBSYA3-GOx-A4180, pBSYA3-GOx-H4460 plasmids and wild type pBSYA3-GOx plasmid. Backbone plasmid pBSYA3S1Z was obtained from Bisy e. U. Competent P. pastoris BG11 cells were transformed with 3 μg plasmid DNA by electroporation at 1.25 kV (Eppendorf Eporator®) and transformed colonies were selected on YPD agar plates with 100 μg mL−1 Zeocin®. 12 randomly selected clones from each strain were transferred inoculated in 250 μL of BMD 1% growth medium in a sterile 96-deep well plate covered with a gas-permeable 114 μm Rayon film (VWR International) at 30° C. while shaking at 300 rpm. After three days, 250 μL of BMM2 medium was added to the wells. After 12 additional hours, 50 μL of BMM10 medium were added, and this step was repeated two times after an additional 12 and 24 h of incubation. The media preparation protocols are shown in Table 2. After four days, the optical densities of the cultures were measured at 600 nm, and the cultures were centrifugated at 3220×g for 10 minutes. The supernatants collected to test for GOx activity, and the cell pellets stored at 4° C.
Enzymatic activity was measured colorimetrically using ABTS (BioChemica, ITW Reagents) (Bateman, R. C., et al. Using the Glucose Oxidase/Peroxidase System in Enzyme Kinetics. J. Chem. Educ. 72, 240-241 (1995)). Briefly, 119.8 μL of 50 mM sodium citrate buffer at pH 5.75 was mixed with 80 μL of 1 M glucose (β-D-glucose, AB 136302, ABCR GmbH & CO. KG). Also, 40 μL of 20 mM ABTS prepared in the sodium citrate buffer. 0.2 μL of 2 mg mL−1 horseradish peroxidase type VI (P6782, Sigma) was added before transferring the mixture to 15 μL of the cell culture supernatant. Absorbance at 414 nm was continuously measured in a plate reader Varioskan™ LUX. Changes in absorbance were normalized to the optical density of the original expression cultures.
GOx Expression in P. pastoris
Recombinant GOx was produced in P. pastoris. Selected GOx clones (K13C, D70C, A418C, H446C) and wild type GOx were used for protein expression in 2 L Erlenmeyer flasks with cotton tissue plugs. The cells were added to the flasks to 75 mL of BMD 1% medium, and they were incubated at 30° C. while shaking at 300 rpm for two days. On the third day, 75 mL of BMM2 medium was added to induce the protein expression. After 12 h, 15 mL of BMM10 medium was added to the flask, and this step was repeated two times. The cell cultures were then centrifuged at 3220×g for 10 minutes, and the supernatants were filtered through a 0.2 μm porous filter. The supernatants were kept on ice and concentrated down to ˜30 mL using a Vivaflow® 50R 30 kDa MWCO crossflow dialysis device (Sartorius). The solutions were further concentrated in an Amicon® Ultra centrifugal filter unit (Merck Millipore) with a 10 kDa MWCO, and the buffer was exchanged to PBS (pH 7.4). Finally, ˜6 mL of each solution was filtered through a 0.2 μm porous filter and stored at 4° C.
Purification and extraction of GOx from the protein mixture were performed using the ÄKTA start setup (GE Healthcare) at 5° C. A HiPrep™ 16/60 Sephacryl® S-300 high-resolution column (GE Healthcare) was used for size-exclusion protein purification. 5.5 mL of the protein mixtures were loaded onto the column and eluted using a 10 mM PBS at pH 7.4 with 140 mM NaCl. The protein presence in each collection tube was confirmed using the colorimetric GOx enzymatic activity assay, and GOx-containing fractions were collected and concentrated to 1-1.5 mL in a 10 kDa MWCO Amicon® Ultra centrifugal unit. During concentration, the buffer was changed with 10 mM PBS (pH 7.0) with 10 mM EDTA (Sigma) and 150 mM NaCl. The concentration of GOx in the stock solutions were measured in a NanoDrop™ 2000 (flavin extinction coefficient at 450 nm is 1.4×104 M−1 cm−1) (Bateman, R. C., et al. Purification and Properties of the Glucose Oxidase from Aspergillus niger. J. Biol. Chem. 240, 2209-2215 (1965)), and adjusted to 3 mg mL−1 (molecular weight of GOx was determined in SDS-PAGE analysis to be ˜85 kDa). The final protein yields ranged between 8 to 15 mg L−1 of cell culture media. GOx solutions were stored at 4° C. in PBS (pH 7.0) with the addition of EDTA as an antimicrobial agent.
1 μL of each protein solution was diluted in 9 μL of PBS (pH 7.4) and combined solution was added to 10 μL of a 2×BlueJuice™ loading buffer (Invitrogen™) containing SDS and 20 mM 1,4-dithiothreitol (DTT, Carl Roth GmbH). A commercial wild type GOx solution was prepared in PBS (pH 7.4) commercially available GOx from A. niger (Type II, 19 440 U g−1, Sigma Aldrich). The solution was also mixed with the loading buffer. The proteins were heated to 95° C. for 6 minutes while shaking at 500 rpm in 1.5 mL tubes. After, 15 μL of each solution was loaded in a gel. Gel electrophoresis was performed in a Mini-PROTEAN® Tetra Cell system (Bio-Rad Laboratories) at 100 V for 10 minutes and 250 V for 50 minutes. The gel was stained with a 0.25% Coomassie brilliant blue R-250 (ITW Reagents) solution in 40% ethanol and 10% acetic acid for 2 h at room temperature. The gel was then distained for 4 h in ethanol:acetic acid:water solution prepared in a 4:1:5 ratio. The gel was imaged in a Fusion Solo S gel imager (Vilber Loumat).
UV-CD spectra of GOx was measured between 195 and 250 nm using a J-810 CD spectropolarimeter (Jasco). A reference cuvette was filled with PBS (pH 7.0) with EDTA. Spectra were smoothed using a convolution filter kernel from “convolve” function. The spectra were analysed using BeStSel software to identify differences in the folding of the proteins (Micsonai, A., et al. Accurate secondary structure prediction and fold recognition for circular dichroism spectroscopy. Proceedings of the National Academy of Sciences. 112, E3095-E3103 (2015); Micsonai, A., et al. BeStSel: A web server for accurate protein secondary structure prediction and fold recognition from the circular dichroism spectra. Nucleic Acids Research. 46, W315-W322 (2018)).
The wild type and mutant GOx were reduced by 10 mM tris(2-carboxyethyl)phosphine (TCEP, abcr) for 1 hour at 5° C. while shaking at 500 rpm. The TCEP was removed using a PD midiTrap™ G-25 desalting column (GE Healthcare) and eluted with PBS (pH 7.0) with EDTA to minimize the formation of GOx oligomers. The concentrations of GOx were adjusted to 0.87±0.04 mg mL−1 using a NanoDrop™ 2000 spectrometer. 195 μL from each protein solution was transferred in a 96-well plate and absorption spectra were measured in the plate reader. Next, 5 μL of freshly prepared 20 mM (SPDP) (abcam) in dimethyl sulfoxide (DMSO, Sigma) was mixed with the solutions. The absorbance spectra were repeatedly measured 1, 8, 30, 60, and 120 minutes after addition of SPDP. Difference between the final absorbance and absorbance before addition of SPDP at 343 nm was compared between the proteins and a control in the absence of proteins. The number of moles of SPDP per mole of GOx was calculated according to the equation, (ΔA×MVV)/(CGOx×ε343 nm). Where ΔA is absorbance difference at 343 nm, MW is molecular weight of GOx, CGOx is concentration of GOx in mg mL−1, and an extinction coefficient for pyridine-2-thione at 343 nm is ε343 nm=8.08×103 M−1 cm−1 (Hermanson, G. T. Bioconjugate techniques 3rd edition. Elsevier Inc. (2013)).
GOx Crosslinking with PM
The GOx D70C stock solution was reduced with TCEP (as described before) and removed using the desalting column. Next, 5 μL of freshly prepared 30 mM PM in DMSO (abcr) was added to 995 μL of the freshly reduced protein solution (˜1 mg mL−1), PM was added proximately in 10 times excess. The reaction was performed at pH 7.0 that makes maleimide predominantly reacting to free thiols (Mukhortava, A., et al. Efficient Formation of Site-Specific Protein-DNA Hybrids Using Copper-Free Click Chemistry. Bioconjugate Chemistry. 27, 1559-1563 (2016)). The sample was incubated overnight at 4° C. and shaken at 500 rpm. The free PM was removed from the PM-GOx solution using a PD midiTrap™ G-25 desalting column with PBS (pH 7.4) (gibco, Life Technologies). The samples were stored at 4° C.
GOx and GOx-PM fluorescence spectra were measured in a Varioskan™ LUX plate reader (Thermo Scientific™) in bottom-scanning plate reading mode. The samples were excited at 345±2.5 nm.
50 mg of SWCNTs (CoMoCAT® (7,6) enriched carbon nanotubes, Sigma Aldrich) were mixed with 50 mL of 2 wt % sodium cholate (SC) (Sigma Aldrich) and sonicated for 60 minutes using a tip sonicator (¼ in. tip, QSonica Q700) at 1% amplitude in an ice bath. The SC-SWCNT suspension was ultracentrifuged at 164 000×g for 3 h (Beckman Optima™ XPN-80). Approximately 80% of the supernatant was collected and stored at room temperature. 0.5 mL of the 25 mg L−1 SC-SWCNT stock solution was mixed with 0.5 mL of ˜3 mg mL−1 GOx-PM (or GOx). The suspension was subsequently dialysed at 5° C. in a 14 kDa MWCO dialysis tube (D9777, Sigma Aldrich) in 2 L of PBS (pH 7.4) for 4 h. The dialyzed mixture was transferred to a 300 kDa MWCO dialysis device (Spectra/Por™ Float-A-Lyzer™, Spectrum™ Laboratories) and dialysed against 2 L PBS buffer for two days (during which, the buffer was replaced four times) at 5° C. The GOx-PM-SWCNTs were stored at 4° C.
Solutions of GOx in PBS were prepared using a commercial enzyme from A. niger (Type II, 19 440 U g−1, Sigma Aldrich) and spectroscopically measured protein concentrations 0.69, 1.9, and 5.6 mg mL−1 (ε450 nm=1.4×104 M−1 cm−1, GOx molar weight 80 kDa) (Bateman, R., et al. Using the Glucose Oxidase/Peroxidase System in Enzyme Kinetics. Journal of Chemical Education. 12, A240-A241 (1995)). Next, 0.5 mL the solutions were mixed with a SC-SWCNT (25 mg L−1) in the 1:1 ratio, and in this way the samples were diluted by half. The mixtures were dialysed in separate beakers in 300 kDa MWCO dialysis tubes (Spectrum™ Laboratories) against 2 L of PBS and the buffer in beakers were changed every 4 h. Fresh dialysis tubes were used on the second day of dialysis because in some of the samples were seen aggregation of SWCNT on the membranes after 24 h of the dialysis. Colorimetric ABTS GOx activity assay was performed after 24 and 48 h of dialysis according to the procedure which described above (15 μL from each suspension was used for the assay). A control dialysis experiment was performed with 1 mL of 12 mg L−1 SC-SWCNTs, as well as the GOx-SWCNT enzymatic activity was compared to the GOx-PM-SWCNT sample.
Spectra were acquired between 200 and 1350 nm using a UV-vis-NIR spectrophotometer (UV-3600 Plus, SHIMADZU). All measurements were performed in a quartz cuvette (10 mm, Quartz Suprasil®, Hellma® Analytics). SWCNT concentration was calculated using the extinction coefficient at 739 nm (ε739 nm=25.3 mL mg−1 cm−1) (Yang, J., et al. Quantitative analysis of the (n,m) abundance of single-walled carbon nanotubes dispersed in ionic liquids by optical absorption spectra. Materials Chemistry and Physics. 139, 233-240 (2013)).
A 96-well plate (Costar® 3590, Corning® Incorporated) was filed 49 μL of GOx-PM-SWCNT and GOx-SWCNT suspensions in PBS. NIR fluorescence spectra were taken between 950 and 1400 nm (75 I mm−1 grating) using the NIR micro-spectrometer described previously. The samples were illuminated at 660±5 nm laser (SuperK EXTREME EXR-15 and SuperK VARIA, NKT Photonics). Fluorescence spectra were continuously acquired while 1 μL of 1 M glucose in PBS (pH 7.4) was added to the well. The fluorescence of the GOx-PM-SWCNT sensor in response to the addition and removal of a 20 mM glucose solution in PBS was performed in a glass-bottom device with a 14 kDa MWCO cellulose membrane (Sigma Aldrich) on top.
GOx variants with cysteine residues, available for a crosslinker attachment to specific surface areas were designed.
To identify non-conserved surface exposed amino acids, GOx homologues were analysed and sequence conservation was mapped to the crystal structure of GOx from Aspergillus niger (PDB: 3QVP (Kommoju, P., et al. Probing oxygen activation sites in two flavoprotein oxidases. Biochemistry 50, 5521-5534 (2011))).
From all residues amenable for mutagenesis to a cysteine, four positions (D70, H446, A418, and K13) at different distances from the glucose-binding cavity of the enzyme were selected.
Without wishing to be bound by theory, mutation points were selected to give the shortest distance between the active site to the sensor surface to promote the direct electron transfer from the active site of GOx to the substrate.
Wild type GOx and K13C, D70C, A418C, H446C variants were expressed in an optimized P. pastoris production yeast strain (Looser, V., et al. Cultivation strategies to enhance productivity of Pichia pastoris: A review. Biotechnology Advances. 33, 1177-1193 (2014)), which contains a protein N-glycosylation pathway that is similar to that found in human cells (Brooks, S. A. Appropriate glycosylation of recombinant proteins for human use: Implications of choice of expression system. Molecular Biotechnology. 28, 241-256 (2004)). The proteins were purified using size-exclusion chromatography and stored in PBS (pH 7.0) with addition of EDTA. The SDS-PAGE results shown in
The expressed GOx variants were concentrated and purified by size-exclusion chromatography and were achieving yields of 8 to 15 mg L−1 of a cell culture media. The results of the chromatograph are shown in
GOx solutions were stored in sodium phosphate buffer saline (PBS) at pH 7.0 with addition of an antimicrobial agent (ethylenediaminetetraacetic acid, EDTA) (Finnegan, S. et al. EDTA: An Antimicrobial and Antibiofilm Agent for Use in Wound Care. Advances in Wound Care. 4, 415-412 (2015)).
The proteins were analysed by a sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) shown in
The secondary structure of the enzymes was characterised with the circular dichroism (CD) measurements shown in
The preservation of enzymatic activity was also confirmed by comparing activities measured with the colorimetric ABTS assay (
The accessibility of the targeted residues were compared based on their reactivity towards succinimidyl 3-(2-pyridyldithio)propionate (SPDP), which releases conjugation reaction product, pyridine-2-thione, that absorbs at 343 nm30. Absorption spectProteins were prepared for crosslinking by reducing thiols using tris(2-cra were measured over 120 minutes (
A418C was identified as the most reactive cysteine mutant, with ˜0.4 moles of SPDP reacted per mole of GOx, followed by the D70C (˜0.3 moles of SPDP reacted per mole of GOx). As expected, the reduced wild type GOx did not react with SPDP.
The D70C variant was selected to demonstrate a thiol-maleimide “click” chemistry with a PM crosslinker to immobilise the proteins onto SWCNTs.
The D70C variant was selected for immobilisation onto the SWCNT using the conjugation strategy shown in
Protein conjugation to the SWCNT surface was confirmed through both absorbance and NIR fluorescence spectroscopy (
As such, it has been shown that the thiol linked modified biomolecules according to the present invention can cover the SWCNT surface more densely than prior techniques. Achieving tighter SWCNT surface coverage for the GOx-PM-SWCNT suspension may positively impact sensor stability and/or analyte sensitivity. Either effect is valuable for a sensor.
The present invention enables the orientation of proteins on the SWCNT surface. The present invention also significantly improves the SWCNT surface coverage with the proteins adhered through the linkers of the present invention, for example the PM linker. Higher protein coverage density enhances the optical response of the sensor to the analyte. The present method also has a further significant advantage over other approaches. The protein immobilisation method reported in this work site-specifically cross-links the biomolecule with the linker (for example PM) and then, secondly immobilises it on the substrate (for example SWCNT). This has advantages over, for example an approach where DNA is wrapped around the SWCNT prior to linking a protein with suitable functional groups to the ends of the DNA molecule, for example by “click” chemistry. The “click” chemistry reactions are known to have yields less that 70-90% in solutions when the reagents are mobile (Kim, Y., et al. Efficient site-specific labeling of proteins via cysteines. Bioconjugate Chemistry. 19, 786-791 (2008)). The reaction yields could be significantly reduced when the DNAs are adsorbed on the substrate surface. The advantage of the method described in this invention is that the conjugation occurs in the solution and the reaction product can be purified before its site-specific immobilisation onto the substrate.
The effect of GOx concentration on SWCNT suspension was explored. Solutions of GOx were prepared in PBS and protein concentrations were spectroscopically measured. Next, the solutions were mixed with SC-SWCNTs (25 mg L−1) in a ratio 1 to 1, and obtained (i) 0.3, (ii) 0.9, and (iii) 2.8 mg mL−1 final concentrations of GOx. The mixtures were dialysed exchanging the buffer every 4 h. The colorimetric GOx activity assay was performed after 24 and 48 h of dialysis and the results are shown in
The performance of the GOx-PM-SWCNT sensors was evaluated by monitoring the fluorescence intensity peak at 1153±1 nm upon glucose addition (
The sensors according to the present invention can therefore be used as the sensing element in continuous glucose monitoring devices, for example implantable continuous glucose monitoring devices. This is particularly true since the sensor does not contain any toxic reaction mediators which were present in earlier designs of SWCNT-based sensors (Barone, P., et al. Near-infrared optical sensors based on single-walled carbon nanotubes. Nature Materials. 4, 86-92 (2004)). In conclusion, the present invention provides sensors which offer advantages over sensors current known in the art. The present invention provides sensors which allow for the orientation of the biomolecule on the substrate to be optimised. Such optimisation includes improving protein folding by immobilising the protein on the substrate via a linker at a defined site on the protein. Such optimisation includes orienting the biomolecule on the substrate to maximise performance, for example improving charge transfer to the substrate. Such optimisation includes improving sensor stability by providing covalent links to the biomolecule and strong links between the linker and substrate. The present invention also enables the surfactant-exchange-based sensor preparation method, which is scalable and, therefore, attractive for commercial production.
In particular, biosensors, for example optical sensors or electrochemical sensors have been developed using a modified enzyme linked via a linker to a SWCNTs. For example, an optical glucose sensor has been developed using genetically engineered GOx. The cysteine-containing mutants were specifically linked to SWCNTs using a PM linker. Thus, the present invention provides for modified enzymes immobilised in a site-specific way which offers performance advantages. To achieve this, for example, variants with single-cysteine mutations on the surface of the enzyme were developed which were shown to retain enzyme activity but direct site-specific linkage to a linker molecule and thereafter immobilisation to the SWCNT. Successful immobilisation of PM-GOx onto SWCNTs was confirmed in absorbance and NIR fluorescence measurements. The blueshifts of the SWCNT peaks in the NIR fluorescence spectrum of GOx-PM-SWCNTs in comparison to GOx-SWCNTs indicated that GOx-PM has denser coverage of the SWCNT surface than non-specifically adsorbed GOx. The sensor shows a reversible response to a change of glucose, which can be applicable for continuous glucose monitoring. However, it should be understood that other enzymes can also be used to develop sensors for other analytes. For example, cholesterol oxidase or lactate oxidase can be used to form sensors for cholesterol and lactate detection.
No doubt many other effective alternatives will occur to the skilled person. It will be understood that the invention is not limited to the described embodiments and encompasses modifications apparent to those skilled in the art and lying within the spirit and scope of the claims appended hereto.
The invention will now be described in relation to the following clauses:
Using Copper-Free Click Chemistry. Bioconjug. Chem. 27, 1559-1563 (2016).
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Number | Date | Country | Kind |
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LU101273 | Jun 2019 | LU | national |
This application is a Continuation Application, which claims filing priority to U.S. patent application Ser. No. 17/620,343, having a national stage entry date of Dec. 17, 2021, which is the US National Stage Entry of International Patent Application Number PCT/EP2020/066648, having a filing date of Jun. 16, 2020, which claims filing priority to Great Luxembourg Patent Application Ser. No. 101273, having a filing date of Jun. 21, 2019, all of which are incorporated herein by reference in their entirety.
Number | Date | Country | |
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Parent | 17620343 | Dec 2021 | US |
Child | 17858628 | US |