Patent Application
20240280570
The Sequence Listing submitted on Sep. 7, 2023, as a .txt file named “KAUST_2020-172_ST25.txt,” created on Sep. 6, 2023, and having a size of 21,146 bytes, is hereby incorporated by reference pursuant to 37 C.F.R. §§ 1.77(b)(5)(i) and 1.825(c)(2).
This invention relates to organic electrochemical transistors (OECT)-based immunosensor devices and methods useful in detecting an analyte of interest in a sample.
Reliable biomolecular diagnostics are an important tool for early detection of diseases, particularly for preventing the outbreak of infectious diseases such as HIV, Ebola and recently widespread coronavirus (SARS-CoV-2) which has caused one million fatalities worldwide, at the time of this writing. Early stage detection is particularly useful to identify and isolate infected patients without symptoms before spreading the disease. Thus, it is crucial to develop a detection method that can offer rapid, easy-use and accurate results. To date, the practical and commercially available detection methods are mostly based on polymerase chain reaction (PCR) or closely related methods. Although Reverse Transcription PCR (RT-PCR) offers accurate and high-sensitivity detection capability, it requires specialist labor, long assay preparation and expensive equipment and can thus only be performed in specialized labs. For this reason, sample-to-result turn-around times vary from several hours to several days. This delay is severely hampering the response to an unfolding epidemic. Rapid tests based on lateral-flow variants of the Enzyme-linked immunosorbent assay (ELISA) can be performed on the spot and give results in about 15 min. However, the lower signal amplification of this test format limits their sensitivity to approximately 1 million particles per mL which is too low for the detection of many infections (be they bacterial or viral). Moreover, lateral flow ELISA rapid tests cannot provide quantitative information on pathogen load, which is considered an important parameter for the diagnosis of individuals as well as in the management of containment measures.
Hence, label-free, rapid, simple-to-operate and highly sensitive antigen sensors are of great interest for the development of point-of-care technology (POCT) or bedside diagnostics and would have many further applications beyond pathogen detection.
Organic electrochemical transistors (OECTs) have attracted attention as a promising alternative biosensing technology that can surpass other state-of-the-art electrical biosensors approaches such as the better-known Field Effect Transistors (FETs). OECTs possess an organic semi-conducting material in their channel and a transducing gate electrode immersed in an ionic conducting electrolyte (Rivnay et al., 2018). OECTs enable biosensing applications in an aqueous environment with low voltage operation (<1V) and exceptionally high amplification (Lin and Yan, 2012). OECTs detect target analytes by monitoring the capacitive or faradaic changes occurring in the device interfaces. To date, the actual biosensing signal is most commonly provided from enzymatic redox reactions that are fueled by a specific analyte. Analyte binding to an enzyme induces a redox reaction which then causes a potential drop across the device interface which is then amplified into a change of electrical current flowing from transistor source to drain terminals (Bernard et al., 2008; Ohayon et al., 2020). An important advantage of OECT biosensors is that their selectivity can be tuned by incorporating suitable bio-recognition elements without the need for fluorescent-, radio- or other labels (Wustoni et al., 2019; Wustoni et al., 2020). Despite a remarkable sensing performance, the development of immunosensors based on the OECT platform has been more challenging and sparse due to the non-redox nature of the antibody-antigen (Ab-Ag) interaction (Gentili et al., 2018). The lack of channel materials which are more suitable for sensing applications and are compatible with conventional electronic circuits hampers the widespread use of OECTs for sensing. Additionally, the fragility of most antibodies and the lack of control over the conformation and orientation of the immobilized antibodies when used as recognition units results in loss or reduced sensitivity (Trilling et al., 2013). Thus, the development of OECT-based immunosensors with stable molecular recognition units under full orientation control are highly desirable, to create a stable and sensitive biosensor.
It is an object to provide OECT-based immunosensors for use in diagnostic assays.
It is also an object of the present invention to provide methods for making OECT-based immunosensor for use in diagnostic assays.
It is still an object of the present invention to provide methods for detecting analyte in a biological sample, using OECT-based immunosensors.
OECT-based biosensors are provided herein, as well as methods of making and methods of use thereof. The biosensor includes an OECT and a biorecognition layer. The biorecognition layer includes two self-assembled monolayers (SAMs the first of which is formed from organic molecules, chemically modified as disclosed herein and referred to herein as Chem-SAM, and the second of which is formed through a specific biological autocatalytic coupling strategy (herein, Bio-SAM), as disclosed herein. The Bio-SAM includes a biorecognition element preferably, a nanobody (for example, VHH) or related antibody fragment. The biorecognition element includes a binding partner to an analyte of interest, preferably, a pathogen or component thereof in one preferred embodiment, the biorecognition element can bind to the SARS-CoV-2 receptor binding domain (RBD) or Spike protein (S1). In a preferred embodiment, the organic molecules in the SAM include thiols and a synthetic peptide chemically coupled to it.
The organization of the biorecognition element on the OECT surface can be represented by the general formula:
N-L1-AP1-AP2-L2-B- Formula I
Where N is one or more organic molecules capable of self-assembly to form a first SAM, L1 is an optional first linker, AP1 is the first peptide binding partner; AP2 is the second peptide partner; AP1 and AP2 are binding partners, preferably, covalent binding partners; however, they can be members of an affinity pair; L2 is a second linker and B is the biorecognition element. The first SAM formed by N is chemically modified with AP1, resulting in Chem-SAM. Binding or coupling of AP1 and AP2 results in a biologically self-assembled monolayer, herein, Bio-SAM. Thus, the biorecognition layer includes Chem-SAM and Bio-SAM.
In one particular embodiment, AP1 is spyTag and AP2 is spyCatcher.
The biorecognition layer is preferably integrated on the gate electrode of the OECT.
A preferred conducting polymer for the channel is poly(3,4-ethylenedioxythiophene) doped with poly(styrene sulfonate) (PEDOT:PSS) or any other mixed (ionic and electronic) semiconductor. The OECT can operate in depletion or in accumulation mode.
Also disclosed are methods for making OECT devices containing a binding partner for any analyte of interest, for example an antigen from any pathogen. The method includes functionalizing the sensing gate electrode of the OECT device with a biorecognition layer which includes the binding partner for the analyte of interest, as follows: (i) contacting at least a portion of the surface of the electrode with a first solution containing a plurality of organic molecules capable of self-assembling, to produce a SAM-modified surface and (ii) contacting the SAM-modified surface with one or more solutions containing a linker or linker elements and the binding partner for the analyte. Referring to Formula I, the surface of the electrode is contacted with a solution containing organic molecules capable of self-assembling into a SAM for form a first self-assembling mononalayer on the surface of electrode, and contacting this first self-assembling mononalayer with a composition containing AP1 under conditions that result in chemical coupling of AP1 to the first SAM (optionally connected through the first linker L1), thus forming a Chem-SAM; contacting the Chem-SAM with a composition containing AP2-L2-B-under conditions resulting in conjugation of AP1 and AP2 to form a second SAM, which is biologically self-assembled, and referred to herein as Bio-SAM. In one preferred embodiment, the AP1 and AP2 are the spyTag and spyCatcher, respectively. Autocatalytic covalent binding between the spyTag/spyCatcher pair orients the analyte binding partner on the surface of the OECT device. In a particularly preferred embodiment, the method includes contacting the SAM-modified surface with a first solution containing one partner of spyTag/spyCatcher pair followed by contact with a second solution containing the second partner of the spyTag/spyCatcher pair which is in turn linked to the binding partner for the analyte of interest. In one preferred embodiment, the analyte of interest is the SARS-CoV-2 RBD and its binding partner is a specific nanobody.
Methods for identifying an analyte of interest in a sample are disclosed. The method includes contacting the sample with OECT-based biosensor which includes a binding partner for the analyte of interest. Exemplary samples include bodily fluids such as saliva, plasma, serum and blood.
Devices for sensitive and rapid analyte detection using an OECT Sensor are provided. The devices can be used for rapid detection of an infection by a pathogen such as a SARS-CoV-2 by detecting the presence of an antigen (analyte) specific for the pathogen, using a biofunctionalized-OECT Sensor, where the OECT Sensor is functionalized to include a binding partner for the antigen of interest.
The OECT biofunctionalized Sensor is characterized by: high sensitivity (1.8×10−17 M of target molecule, for example SARS-CoV-2-Spike protein, causes 5% change of readout signals) and selectivity (1 nM of other species in the saliva contributes to only 0.5% the sensor readout), delivering accurate results in accordance with gold standard tests (correlated to RNA detection results with the conventional RT-PCR); fast detection time (around 15 minutes after the sample exposure to the sensor surface to the read-out); and low limit of detection (limit of detection (2.8*10−16 M or 1.8×10−20 M of target molecule depending on the channel material, for example SARS-CoV-2-Spike protein, in buffer solution). Additionally, the OECT biofunctionalized Sensor gate electrode is disposable and easy to fabricate, with a path to reliable mass production.
The devices can be used with minute amount of solution (as little as 5 μl) from easily accessible samples including saliva (but also blood from a finger prick); they are accessible and affordable, allowing large-scale application; easy-to-use by minimally trained users or even by the patients themselves; can be operated with an inexpensive, portable, and hand-held readout unit (for example connected to a smartphone); can be designed to detect different targets using the same platform by modular exchange of the biological detection unit.
The device can have multiple channels in an area underneath the gate electrode, meaning that one sensing gate electrode can be used to get multiple readouts simultaneously, improving the sensor accuracy. These channels can be made of different organic materials.
“Affinity interactions” as used herein refers to the combination of non-covalent interactions between a ligand and its binding partner to form a complex.
“Affinity tags” as used herein are peptide sequences appended to proteins so that they can be purified from a crude biological source using an affinity technique.
“Covalent linkage”, refers to a bond or organic moiety that covalently links molecules (e.g. fusion proteins) to a non-cellular surface.
As used herein, the term “polypeptide” refers to a chain of amino acids of any length, regardless of modification (e.g., phosphorylation or glycosylation).
As used herein, a “vector” is a replicon, such as a plasmid, phage, or cosmid, into which another DNA segment may be inserted so as to bring about the replication of the inserted segment. The vectors described herein can be expression vectors.
As used herein, an “expression vector” is a vector that includes one or more expression control sequences
As used herein, an “expression control sequence” is a DNA sequence that controls and regulates the transcription and/or translation of another DNA sequence.
As used herein, “operably linked” means incorporated into a genetic construct so that expression control sequences effectively control expression of a coding sequence of interest.
As used herein, “conservative” amino acid substitutions are substitutions wherein the substituted amino acid has similar structural or chemical properties.
As used herein, “non-conservative” amino acid substitutions are those in which the charge, hydrophobicity, or bulk of the substituted amino acid is significantly altered.
As used herein, the term “host cell” refers to prokaryotic and eukaryotic cells into which a recombinant expression vector can be introduced.
As used herein, “transformed” and “transfected” encompass the introduction of a nucleic acid (e.g., a vector) into a cell by a number of techniques known in the art.
The disclosed devices include an OECT engineered to include a biorecognition layer, including a biorecognition element. The biorecognition element is the component that can specifically interact with its cognate target. The OECT is an electrolyte gated transistor, that is, a three-terminal electronic device which includes a source electrode, a drain electrode, a channel, and a gate electrode. In some preferred embodiments, the biorecognition layer is integrated on the gate electrode of the OECT.
The biorecognition layer is designed to provide a stable complex, preferably, an immunocomplex between a biorecognition element in the biorecognition layer, and its binding partner, which is the analyte/antigen of interest. The biorecognition element is preferably, not a multidomain antibody. The biorecognition layer is preferably integrated on the surface of the gate electrode of the OECT.
The biorecognition layer includes two self-assembled monolayers (SAMs the first of which is formed from organic molecules, chemically modified as disclosed herein and referred to herein as Chem-SAM, and the second of which is formed through a specific biological autocatalytic coupling strategy (herein, Bio-SAM), as disclosed herein. The Bio-SAM includes biorecognition element preferably, a nanobody (
N-L1-AP1-AP2-L2-B- Formula I
Where N is one or more organic molecules capable of self-assembly to form a first SAM, L1 is an optional first linker, AP1 is the first peptide binding partner; AP2 is the second peptide partner; AP1 and AP2 are binding partners, preferably, covalent binding partners; however, they can be members of an affinity pair; L2 is a second linker and B is the biorecognition element. The first SAM formed by N is chemically modified with AP1, resulting in Chem-SAM. Binding of AP1 and AP2 results in a biologically self-assembled monolayer, herein, Bio-SAM. Thus the biorecognition layer includes Chem-SAM and Bio-SAM.
L1 and L2 are preferably peptide linkers sequences which are at least 2 amino acids in length. Preferably the peptide or polypeptide domains are flexible peptides or polypeptides. A “flexible linker” herein refers to a peptide or polypeptide containing two or more amino acid residues joined by peptide bond(s) that provides increased rotational freedom for two polypeptides linked thereby than the two linked polypeptides would have in the absence of the flexible linker. Exemplary flexible peptides/polypeptides include, but are not limited to, the amino acid sequences Gly-Ser, Gly-Ser-Gly-Ser (SEQ ID NO:9), Ala-Ser, Gly-Gly-Gly-Ser (SEQ ID NO:10), (Gly4-Ser)3 (SEQ ID NO:11), and (Gly4-Ser)4 (SEQ ID NO:12), GSGSGSGS (SEQ ID NO:13). Additional flexible peptide/polypeptide sequences are well known in the art. In one embodiment, L1 is SGSG (SEQ ID NO:14).
The nanobody can be a naturally-derived from immunization of an animal or synthetically-derived (i.e., a sybody) or a combination thereof. Sybodies are disclosed for example, in Walter, et al., doi: https://doi.org/10.1101/2020.04.16.045419. In some preferred embodiments, the organic molecules forming the SAM include thiols. In some preferred embodiments, the linker is a biomolecular linker formed by the bioconjugation of two peptides, such as a SpyTag/SpyCatcher bioconjugation (Zakeri, et al., Proc. Natl. Acad. Sci., 109:E690-E697 (2012)).
In a particularly preferred embodiment, the biorecognition layer includes a SAM formed from an alkanedithiol (e.g. 1,6-hexanedithiol) and a SpyTag/SpyCatcher bioconjugation as the linker, which allows for controllable orientation of the nanobody functionalization, which also maximizes the capture density of nanobodies within a small sensor area (0.64 mm2) and enhances the sensitivity of the OECT sensor. For example, at least 30 and up to 45×1012 SpyTag peptides (such as about 39×1012 SpyTag peptides) and at least 8 and up to 10×1012 nanobody-SpyCatcher molecules (such as about 8.6×1012 nanobody-SpyCatcher molecules) are coupled per cm2 on the surface of the gate electrode of the OECT.
i. Chem-SAM
The first-SAM on the OECT gate electrode is typically formed by reacting a plurality of organic molecules on the gate electrode surface of the OECT under conditions resulting in self-assembly, following which it is chemically functionalized to form Chem-SAM, by contacting with a binding partner required for formation of the second SAM, i.e., the Bio-SAM. In some preferred embodiments, the organic molecules in the first SAM include thiols or thiol derivatives. Thiols that are suitable to form the first SAM on the surface of the gate electrode of the OECT may be a monothiol, a dithiol, a trithiol, or a mixture thereof.
Typically, the thiols in the Chem-SAM on gate electrode surface of the OECT have a carbon chain containing up to 20 carbons, up to 18 carbons, up to 16 carbons, up to 15 carbons, up to 12 carbons, up to 10 carbons, up to 8 carbons, up to 6 carbons, at least 2 carbons, at least 3 carbons, in a range from 1 carbon to 20 carbons, from 2 carbons to 20 carbons, from 2 carbons to 18 carbons, from 2 carbons to 15 carbons, from 2 carbons to 12 carbons, from 2 carbons to 10 carbons, from 2 carbons to 8 carbons, or from 2 carbons to 6 carbons.
Exemplary thiols that can form the first SAM on the surface of the gate electrode of the OECT include, but are not limited to, alkane monothiols (e.g. methanethiol, ethanethiol, 2-propanethiol, butanethiol, pentanethiol, ter-butyl mercaptan, 1-hexanethiol, 1-octanethiol, 1-nonanethiol, 1-decanethiol, 1-undecanethiol, 1 dodecanethiol, 1-tridecanethiol, 1-tetradecanethiol, 1-pentadecanethiol, 1-hexadecanethiol, 1-octadecanethiol, 1-nonadecanethiol, and 1-icosanethiol, etc.), alkane dithiols (e.g. 1,2-ethanedithiol, 1,4-butanedithiol, 1,3-butanedithiol, 1,5-pentanethiol, 1,6-hexanedithiol (HDT), 1,7-octanedithiol, 1,8-nonanedithiol, 1,3-propanedithiol (PDT), etc.), 3-mercaptopropionic acid (MPA), thiophenol, dimercaptosuccinic acid, glutathione, cysteine, 2-mercaptoethanol, lipoic acid, and 1,4-benzenedimethanethiol. Additional exemplary thiols that can form a SAM on the surface of the gate electrode of the OECT are disclosed in Love, et al., Chem. Rev., 105:1103-1169 (2005).
The first SAM on the gate electrode surface of the OECT may be formed from a single type of thiol or a mixture of different types of thiols. For example, the first SAM on the surface of the gate electrode of the OECT is formed from a dithiol (e.g. HDT or PDT), a mixture of different types of dithiols (e.g. a mixture of HDT and PDT), or a mixture of a dithiol and a monothiol (e.g. a mixture of PDT and MPA).
In some preferred embodiments, the first SAM on the gate electrode surface of the OECT is formed from a dithiol (e.g. HDT) or a mixture of different types of dithiols. A first SAM formed from a dithiol (i.e. HS—R—SH) on the gate electrode surface can contain two types of sulfur species: a thiolate-type sulfur (i.e. the sulfur bound to a surface atom, such as Au—SR) and a tail thiol sulfur (i.e. free thiol, R—SH). The partially bound dithiol molecules are in a standing up configuration (formed as a result of the method of making the first SAM, exemplified in the examples below) with an upright molecular structure, where the dithiol molecules are bound to the gate electrode surface via the thiolate linkage from one of the thiol groups, and the other thiol group is free (i.e. unbounded) interfacing air or solution. When all thiol groups of the dithiol molecules are converted to thiolates linked to the gate electrode surface, the dithiol molecules are in a laying down configuration. In some preferred embodiments, the first SAM on the gate electrode surface of the OECT is formed from a dithiol, where the dithiol molecules are in the standing up configuration upon formation of the first SAM. The standing up configuration of the dithiol molecules in the first SAM allows for uniform orientation of the linker and the biorecognition elements such that the biorecognition events can be more precise and compact, which also maximizes the capture capability of the biorecognition elements within a small sensor area (such as a gate surface area of 0.64 mm2) and enhances the sensitivity of the OECT sensor.
In a particularly preferred embodiment, the first SAM on the gate electrode surface of the OECT is formed from HDT where the HDT molecules are in a standing up configuration upon formation of the SAM.
Referring to Formula I:
N-L1-AP1-AP2-L2-B- Formula I
Chem-SAM is formed by N-L1-AP1, Where N is one or organic molecules capable of self-assembly and is self-assembled on the surface of the OECT gate electrode, L1 is an optional first linker, AP1 is the first peptide binding partner; AP2 is the second peptide partner; AP1 and AP2 are binding partners, preferably, covalent binding partners; however, they can be members of an affinity pair; L2 is a second linker and B is the biorecognition element.
The first SAM is preferably directly conjugated to AP1, preferably provided by a suitable conjugation reaction such functionalization with maleimide.
ii. Bio-SAM
The biorecognition layer integrated on the gate electrode of the OECT includes a second SAM, which is a biologically self-assembled monolayer formed as a result of covalent binding of two binding partners or affinity interactions of an affinity pair, thereby forming a Bio-SAM, which includes the biorecognition element, which can be a non-antibody protein or an antibody, and is preferably a non-antibody protein. In one preferred embodiment, the biorecognition element is a fusion protein as described herein.
Referring to Formula I:
N-L1-AP1-AP2-L2-B- Formula I
Bio-SAM is formed by interaction of the first peptide binding partner AP1 with the second peptide partner, AP2, resulting in the formation of a second SAM, the Bio-SAM, which includes the biorecognition element B, exposed for interaction with its binding partner in a sample with which it is contacted.
AP1 or AP2 in a particularly preferred embodiment include the spyTag/spyCatcher pair, with AP1 is preferably, spyTag in some preferred embodiments, for example, AHIVMVDAYKPTK (SEQ ID NO:6), i.e., spyTag, and in preferred embodiments the spyTag consists of SEQ ID NO:6; VPTIVMVDAYKRYK (SEQ ID NO:7) i.e., spytag002 (Keeble, et al., Angew. Chem. Int. Ed. Engl. 2017, 56, 16521-16525) or RG VPH IVMVDAYK RYK (SEQ ID NO:8). i.e., spyTag 0003 (Keeble, et al: Proc Natl Acad Sci USA. 2019 Dec. 26; 116(52): 26523-26533).
A preferred SpyTag/SpyCatcher bioconjugation system is disclosed in Zakeri, et al., Proc. Natl. Acad. Sci., 109:E690-E697 (2012). It is based on a modified domain from a Streptococcus pyogenes surface protein (SpyCatcher), which recognizes a cognate 13-amino-acid peptide (SpyTag). Upon recognition, the two form a covalent isopeptide bond between the side chains of a lysine in SpyCatcher and an aspartate in SpyTag. The SpyTag/SpyCatcher bioconjugation is a robust method for conjugating recombinant proteins where the peptide SpyTag can spontaneously react with the protein SpyCatcher in a facile manner and with high specificity (Zakeri, et al., Proc. Natl. Acad. Sci., 109:E690-E697 (2012); Keeble, et al., Angew. Chem. Int. Ed. Engl. 2017, 56, 16521-16525. The peptide SpyTag (13 amino acids) spontaneously reacts with the protein SpyCatcher (12.3 kDa) to form an intermolecular isopeptide bond between the pair. In some preferred embodiments, the SpyTag peptide is functionalized with a maleimide functional group and the SpyCatcher is linked to the biorecognition elements (e.g. nanobodies), such that upon bioconjugation between the SpyTag and the SpyCatcher, the biorecognition elements are integrated on the gate electrode surface in a uniform orientation. In optional embodiments, the SpyTag may include a linker.
Other binding partners can be used as AP1/AP2, for example, snoopTag peptide, (Veggiani, et al., PNAS 2016 113 (5) 1202-1207) MoonTag/MoonCatcher (homologue of SpyCatcher); the snapTag labelling system; the Sortase reaction which is connecting two shorter peptides; Coating the surface with Streptavidin and then coupling a site-specifically biotinylated nanobody can also be employed. SnoopTag, is a peptide which binds covalently to SnoopCatcher protein (KLGDIEFIKVNK) (SEWQ ID NO: 18). A second generation, SnoopTagJr, has been developed to bind to either SnoopCatcher or DogTag (mediated by SnoopLigase) (KIGSIEFIKVNK) (SEQ ID NO:19). DogTag is, a peptide which covalently binds to SnoopTagJr, mediated by SnoopLigase (DIPATYEFTDGKHYITNEPIPPK) (SEQ ID NO:20); SdyTag is, a peptide which binds covalently to SdyCatcher protein (DPIVMIDNDKPIT) (SEQ ID NO:21) SdyTag/SdyCatcher has a kinetic-dependent cross-reactivity with SpyTag/SpyCatcher. These systems are known in the art (reviewed Hatlem, et al., Int J Mol Sci. 2019 May; 20(9): 2129)). NAP- and CLIP-tag protein labeling systems enable the specific, covalent attachment of virtually any molecule to a protein of interest. There are two steps to using this system: cloning and expression of the protein of interest as a SNAP-Tag® fusion, and labeling of the fusion with the SNAP-tag substrate of choice. The SNAP-tag is a small protein based on human 06-alkylguanine-DNA-alkyltransferase (hAGT), a DNA repair protein.
SNAP-tag substrates are dyes, fluorophores, biotin, or beads conjugated to guanine or chloropyrimidine leaving groups via a benzyl linker. In the labeling reaction, the substituted benzyl group of the substrate is covalently attached to the SNAP-tag. CLIP-Tag™ is a modified version of SNAP-tag, engineered to react with benzylcytosine rather than benzylguanine derivatives. When used in conjunction with SNAP-tag, CLIP-tag enables the orthogonal and complementary labeling of two proteins simultaneously in the same cells.
a. Non-Antibody Protein Biorecognition Element
Preferred biorecognition elements for incorporation into the disclosed devices are not whole antibodies, but more compact recognition domains such as a nanobody or a sybody. As used herein, non-antibody protein refers to a protein that is not a whole antibody which is a multidomain protein. By contrast, a nanobody, also known as a single domain antibody, is an antibody fragment consisting of a single monomeric variable antibody domain. Like a whole antibody, it is able to bind selectively to a specific antigen. With a molecular weight of only 12-15 kDa, single-domain antibodies are much smaller than common antibodies (150-160 kDa) which are composed of two heavy protein chains and two light chains, and are also smaller than Fab fragments (˜50 kDa, one light chain and half a heavy chain) or single-chain variable fragments (scFv, ˜25 kDa fusion of two variable domains, one from a light and one from a heavy chain).
Camelids naturally produce one class of antibodies composed only of heavy chains in which the target recognition module is composed of a single variable domain (VHH or Nb). (De Meyer, et al., 2014; Kubala, et al., 2010). The nanobody offers unique properties, simpler structural conformation and high stability in a range of different conditions (De Meyer, et al., 2014).
In one preferred embodiment, the devices include a nanobody, which binds to an antigen from the SAR-CoV-2, such as the spike protein. Specific nanobodies against SARS-CoV-2 Spike protein (S protein) or, more specifically, against the Receptor Binding Domain (RBD) within the S1 subunit of the protein are available (Wrapp, et al., Science 2020, 367 (6483), 1260-1263). Sybodies are disclosed for example, in Walter, et al., doi: https://doi.org/10.1101/2020.04.16.045419. Examples include the SARS 1/2 nanobody (VHH72), shown below:
Suitable biorecognition elements can also include other antibody fragments and variants and fusion proteins thereof (e.g., and synthetic proteins containing at least the antigen binding variable domain of an antibody). For example, an antigen binding fragment of an antibody can be used as the biorecognition element. In some embodiments, the antigen binding fragment binds to a SARS-CoV and/or MERS-CoV antigen, such as the spike protein or nucleocapsid. In some embodiments, the antigen binding fragment binds to a SARS-CoV-2 antigen, such as the S1 (e.g., the receptor-binding domain (RBD)) or S2 domains of the spike protein. Exemplary antibody fragments and variants and fusion proteins thereof include, without limitation, Fab, Fab′, F(ab′)2, Fv, Fc, scFv, di-scFv, tri-scFv, scFv-Fc, Fab-Fc, scFv-zipper, scFab, and crossFab.
b. Other Proteins
In some embodiments, the devices can include an antibody, as the biorecognition element for example. In some embodiments, the antibody binds to a SARS-CoV and/or MERS-CoV antigen, such as the spike protein or nucleocapsid. In some embodiments, the antibody binds to a SARS-CoV-2 antigen, such as the S1 (e.g., the receptor-binding domain (RBD)) or S2 domains of the spike protein.
Antibodies that can be used include whole immunoglobulin (i.e., an intact antibody, such as IgA, IgD, IgE, IgG, and IgM, and including subclasses or isotypes, e.g., IgG1, IgG2, IgG3, IgG4, IgA1 and IgA2). Suitable antibodies encompass, but are not limited to, monoclonal antibodies, polyclonal antibodies, chimeric antibodies, bispecific antibodies, multispecific antibodies, heteroconjugate antibodies, mutants thereof, humanized antibodies, human antibodies, and any other modified configuration of the immunoglobulin molecule that includes an antigen recognition site of the required specificity,
In some embodiments, the antibody can be a humanized antibody. Methods for humanizing non-human antibodies are well known in the art. Generally, a humanized antibody has one or more amino acid residues introduced into it from a source that is non-human. These non-human amino acid residues are often referred to as “import” residues, which are typically taken from an “import” variable domain. Antibody humanization techniques generally involve the use of recombinant DNA technology to manipulate the DNA sequence encoding one or more polypeptide chains of an antibody molecule.
Native antibodies, and some other antigen binding proteins including some non-antibody antibody fragments and fusion proteins, can be heterotetrameric glycoproteins having two identical light chains and two identical heavy chains. Other antigen binding proteins including some non-antibody antibody fragments and fusions proteins may have few or more domains. Each heavy chain has at one end a variable domain (“VH”) followed by a number of constant domains (“CH”). Each light chain has a variable domain at one end (“VL”) and a constant domain (“CL”) at its other end. The variable domains differ in sequence among antibodies and are used in the binding and specificity of each particular antibody for its particular antigen. However, the variability is not usually evenly distributed through the variable domains of antibodies. It is typically concentrated in three segments called complementarity determining regions (CDRs) or hypervariable regions both in the light chain and the heavy chain variable domains. The more highly conserved portions of the variable domains are called the framework (FR). The variable domains of native heavy and light chains each contain four FR regions, largely adopting a beta-sheet configuration, connected by three CDRs, which form loops connecting, and in some cases forming part of, the beta-sheet structure. The CDRs in each chain are held together in close proximity by the FR regions and, with the CDRs from the other chain, contribute to the formation of the antigen binding site of antibodies. Therefore, the antibodies typically contain at least the CDRs necessary to recognize and/or bind a target antigen (e.g., a SARS-CoV-2 antigen). Non-antibody antigen binding proteins such as antibody fragments and fusion proteins may also include at least the CDRs necessary to recognize and/or bind a target antigen (e.g., a SARS-CoV-2 antigen).
In some embodiments, the antibodies or non-antibody antigen binding proteins such as antibody fragments and fusion proteins may include one of each of a heavy chain CDR1, CDR2, and CDR3 in combination with one of each of a light chain CDR1, CDR2, and CDR3.
Anti-SARS-CoV-2 antibodies (e.g., used for detection and/or neutralization) are known in the art and are suitable for use herein. For example, suitable antibodies include commercially available antibodies such as MAB105801, MAB105802, MAB108271, LMAB10869, MAB105406, MAB105806, MAB 105807, and MAB105808 from R&D Systems; and MA1-7403, MA5-35943, MA5-36271, MA5-35945, MA1-41093, and MA1-41173 from ThermoFisher Scientific.
Anti-SARS-CoV-2 antibodies are also described in U.S. Pat. Nos. 10,975,139 and 11,021,532 which are both hereby incorporated by reference in their entirety. Any antibody or antibody fragment disclosed in U.S. Pat. Nos. 10,975,139 and 11,021,532 can be used.
In some embodiments, a suitable antibody or non-antibody antigen binding protein such as an antibody fragment or fusion protein includes a VH having an amino acid sequence of SEQ ID NO:22 or a sequence that is at least 80%, 85%, 90%, 95%, 98%, 99%, or 100% identical to SEQ ID NO:22, and a VL having an amino acid sequence of SEQ ID NO:23 or a sequence that is at least 80%, 85%, 90%, 95%, 98%, 99%, or 100% identical to SEQ ID NO:23.
CDR1-3 are the bolded and italicized sequences, respectively, from left to right).
DIVMTQSPDSLAVSLGERATINCKSSQSVFSSSNNKNYLAWYQ QKPGQPPKLLIYWASTRESGVPDRFSGSGSGTDFTLTISSLQAEDVAV YYCQQYYSTPLTFGGZTKVEIKR (SEQ ID NO:23; CDR1-3 are the bolded and italicized sequences, respectively, from left to right).
In some embodiments, a suitable antibody or non-antibody antigen binding protein such as an antibody fragment or fusion protein includes one or more of the CDRs of SEQ ID NO:22 or SEQ ID NO:23. For example, a suitable antibody can include CDR1, CDR2, and/or CDR3 of SEQ ID NO:22, CDR1, CDR2, and/or CDR3 of SEQ ID NO:23, or any combination thereof.
In some embodiments, the biorecognition elements are expressed as fusion proteins that contain a first polypeptide domain, a linker domain and a purification tag. Biorecognition elements such as nanobodies, sybodies, antibody fragments, antibodies, etc. can readily be expressed in various formats by fusion to other proteins, peptides or effector domains, thereby tailoring their utility. Taking advantage of this feature, the disclosed biorecognition element are expressed as fusion proteins, which include a linker and preferably, a protein purification tag; and can be represented by the following general formula II:
AP1/AP2-L2-B—C—PT Formula II,
Where AP1/AP2 and L2 are as defined above for formula I, and PT is a purification tag (an amino acid sequence that allows the polypeptides to be captured onto an affinity matrix) and C is an optional cleavage site, for example, the 3C cleavage site. In one embodiment, the biorecognition element B is oriented first in the fusion protein sequence (i.e., N-terminal). However, the biorecognition element B can be at the C-terminal end of the fusion protein. For example, a tag such as c-myc, hemagglutinin, polyhistidine, or Flag™ (Kodak) can be used to aid polypeptide purification. Such tags can be inserted anywhere within the polypeptide, including at either the carboxyl or amino terminus. The polyhistidine affinity tag, also known as the His-tag or His6, usually consists of six consecutive histidine residues, but can vary in length from two to ten histidine residues; glutathione S-transferase (GST); Maltose binding protein (MBP), calmodulin binding peptide (CBP); the intein-chitin binding domain (intein-CBD), the streptavidin tag, etc.
One preferred fusion protein is MTGQVQLQESGGGLVQAGGSLRLSCAASGRTFSEYAMGWFRQAPG KEREFVATISWSGGSTYYTDSVKGRFTISRDNAKNTVYLQMNSLKPD DTAVYYCAAAGLGTVVSEWDYDYDYWGQGTQVTVSSGSGSGSGS GSVDTLSGLSSEQGQSGDMTIEEDSATHIKFSKRDEDGKELAGATME LRDSSGKTISTWISDGQVKDFYLYPGKYTFVETAAPDGYEVATAITFT VNEQGQVTVNGKATKGDAHISGLEVLFQGPTGHHHHHHHH (SEQ ID NO:15) where the bolded and italicized residues constitute a linker (8 amino acids long), between the SAR1/2-nanobody and SpyCatcher-3C cleavage site-His8. His8 is shown in bold font and the HRV (Human rhinovirus) 3C protease cleavage site is within the underlined sequence. HRV 3C Protease is a recombinant 3C protease derived from human Rhinovirus type 14 expressed in E. coli. The enzyme has the same activity as the native protein and cleaves a specific amino acid sequence (LEVLFQ↓GP) (SEQ ID NO:16).
iii. Blocking Agents
Optionally, the biorecognition layer includes a blocking agent. Exemplary blocking agents include, but are not limited to, bovine serum albumin (BSA), ethanolamine (ETA) and Casein. In some preferred embodiments, the blocking agent included in the biorecognition layer is BSA. While not being bound by theory, the blocking agent provided to capture potentially contaminating proteins in samples included analyte, which are contacted with the biorecognition layer for binding of the analyte to its binding partner (i.e., biorecognition element) present in the biorecognition layer.
The disclosed device includes a biorecognition layer described above and its integration with a high gain, ion-to-electron transducing device, the OECT. The device may include one OECT channel or more than one OECT channel in the form of an array. The OECT or each OECT in an array of OECT (i.e. two or more OECTs) in the device is a three-terminal transistor which includes a source electrode, a drain electrode, a channel, and a gate electrode. The channel electronically connects the source electrode and drain electrode. The gate electrode that is integrated/functionalized with a biorecognition layer.
The source electrode and the drain electrode are placed apart and connected electronically by a corresponding channel. In some embodiments, the source electrode, the drain electrode, and the channel can be patterned on a supporting substrate, such as a glass substrate, a silicon substrate, or a plastic substrate, such as a polyimide substrate or a textile. The gate electrode is placed separately from the source electrode, the drain electrode, and the channel separated by an electrolyte. The channel is in direct contact with an electrolyte solution, into which the gate electrode is also immersed. Optionally, the OECT includes a reservoir to contain the electrolyte solution. The reservoir (i.e. PDMS well) is placed on top of the channel to contain the electrolyte solution such that the channel and the gate electrode are in contact with the electrolyte solution. The source and drain contacts are also in contact with the electrolyte but they are insulated with an insulator such as parylene or SU-8. The source electrode, drain electrode, and channel are patterned on a glass substrate.
When the device contains an array of OECTs, each OECT may contain a source electrode, a drain electrode, and a corresponding channel, and all the OECTs in the array use a common gate electrode. For example, if the OECT array includes a plurality of OECTs, for example 2, 3, 4, 5 or 6 OECTs, where each OECT contains a source electrode, a drain electrode, and a corresponding channel. However all the OECTs in the array use a common gate electrode that is integrated with a biorecognition layer. The source electrode, drain electrode, and corresponding channel of each of the OECTs are patterned on a supporting substrate′. Optionally, when the device contains an array of OECTs, each OECT may contain a source electrode, a drain electrode, a corresponding channel, and a gate electrode, such that each gate electrode can be engineered with the same or different biorecognition element for detecting one or more than one analyte simultaneously. The device may be incorporated into a microfluidics configuration.
The channel is typically made of an ion-permeable organic electronic material, through which holes or electrons flow from the source electrode to the drain electrode. The OECT relies on ions that are injected from the electrolyte solution into the ion-permeable organic electronic material, thereby changing its doping state and thus its conductivity. The operation of OECT is controlled by voltages applied to the gate electrode (gate voltage, VG) and to the drain electrode (drain voltage, VD), which are referenced with respect to the source electrode. The drain voltage induces a current (drain current, ID), which is proportional to the quantity of mobile holes or electrons in the channel, and thus probes the doping state of the organic electronic material. The gate voltage controls the injection of ions into the channel and thus the doping state of the organic electronic material, resulting in a change in ID. The change in ID may be expressed as a normalized response (also referred herein as “NR”) which can be calculated based on equation 1:
where I0 is the drain current obtained after incubation of the OECT with a blank solution (i.e. a solution in the absence of the target analytes) under the same measurement conditions as the biological sample.
The doping changes in OECT occur over the entire volume of the channel because of the injection barrier-free penetration of electrolyte ions into the bulk of the organic channel, causing a large modulation of the carrier density therein. The device translates small ionic fluxes in the electrolyte into a large electrical readout from the channel. Therefore, the transducing event is coupled with amplification, and endows the OECT with high gain at low voltages (<1V).
i. Source and Drain Electrodes
The source and drain electrodes are made from materials capable of conducting an electric current. The electrode materials can be organic or inorganic in nature, as long as it is able to conduct electrons and inject electronic charges into the channel material. The electrodes can be a polymeric electrode, a metallic electrode, a carbon-based material, a metal oxide, or a modified electrode. In some embodiments, the source and drain electrodes are made from an electrochemically inert material such as gold, platinum, or a conductive form of carbon. In some embodiments, the source and drain electrodes are gold electrodes. They are insulated using an insulator such as parylene. In some embodiments, SU-8 (epoxy based photoresist used to pattern electronics with photolithography (also used as an insulator)) is used.
In some embodiments, the electrodes are made from a metallic conductor. Suitable metallic conductors include but are not limited to gold, chromium, platinum, iron, nickel, copper, silver, stainless steel, mercury, tungsten and other metals suitable for electrode construction. The metallic conductor can be a metal alloy which is made of a combination of metals disclosed above, such as gold/chromium. In addition, conductive substrates which are metallic conductors can be constructed of nanomaterials made of gold, cobalt, diamond, and other suitable metals.
In other embodiments, the electrodes are made from carbon-based materials. Exemplary carbon-based materials are conducting polymers (in the form of films or fibers) carbon cloth, carbon paper, carbon screen printed electrodes, carbon paper, carbon black, carbon powder, carbon fiber, singe-walled carbon nanotubes, double-walled carbon nanotubes, multi-walled carbon nanotubes, carbon nanotube arrays, diamond-coated conductors, glassy carbon and mesoporous carbon. In addition, other exemplary carbon-based materials are graphene, graphite, uncompressed graphite worms, delaminated purified flake graphite, high performance graphite and carbon powders, highly ordered pyrolytic graphite, pyrolytic graphite, and polycrystalline graphite.
The electrodes can be doped semiconductors. Suitable semiconductors are prepared from silicon and germanium, which can be doped (i.e., the intentional introduction of impurities into an intrinsic semiconductor for the purpose of modulating its electrical and structural properties) with other elements. The semiconductors can be doped with phosphorus, boron, gallium, arsenic, indium or antimony, or a combination thereof.
Other electrode materials can be metal oxides, metal sulfides, main group compounds, and modified materials. Exemplary materials of this type are nanoporous titanium oxide, tin oxide coated glass, glass, cerium oxide particles, molybdenum sulfide, boron nitride nanotubes, aerogels modified with a conductive material such as gold, solgels modified with conductive material such as carbon, ruthenium carbon aerogels, and mesoporous silicas modified with a conductive material such as gold.
The source and drain electrodes can be any shape appropriate such as cuboid, cubic, circular, and cylindrical. In some preferred embodiments, the electrodes are cuboid gold electrodes. In some embodiments, each of the source and drain electrodes has a first dimension (i.e. width), a second dimension (i.e. length), and a third dimension (i.e. thickness). For example, each of the source and drain electrodes has a width in a range from 100 μm to 1 mm (e.g. 0.8 mm), a length in a range from 100 μm to 1 mm (e.g. 0.8 mm), and a thickness of about 100 nm.
ii. Channel
Generally, the channel is configured to establish the electrochemical connection between a pair of source and drain electrodes such that holes or electrons flow from the source electrode to the drain electrode.
The channel is typically made of an ion-permeable organic electronic material, such as a conducting polymer disclosed in, for example, Rivnay, et al., Nature Reviews, 3:17086 (2018) and Sun, et al., J. Mater. Chem. C, 6:11778-11784 (2018). An exemplary conducting polymer for the channel is poly(3,4-ethylenedioxythiophene) doped with poly(styrene sulfonate) (PEDOT:PSS). The conducting PEDOT is p-type doped (oxidized), which leads to mobile holes that can hop from one chain to another, resulting in a hole current once a drain voltage is applied. These holes are compensated by the sulfonate anions of PSS. Channels made of PEDOT:PSS can work as depletion mode OECTs. For example, in the absence of a gate voltage, a hole current flows in the channel. Once a positive gate voltage is applied, cations from the electrolyte are injected into the channel and the anions are compensated, resulting in a decrease in the number of holes in the channel. This results in a decrease in the drain current. Alternatively, the channel can be made of materials that work in accumulation mode OECT, such as a semiconductor based on a polythiophene with a sulfonate group attached to the backbone with a hexyl chain (PTHS) (Inal, et al., Adv. Mater., 26:7450-7455 (2014)), an ethylene glycol unit attached to bithiophenes (Moser, et al., Adv. Mater., 32:2002748 (2020)) or a g7-NDI-Br and NDI-T2 copolymer (P-90) (Giovannitti, et al., Chem. Mater., 30:2945-2953 (2018)). In accumulation mode p-type OECT, application of a negative gate voltage causes injection of anions into the channel and a corresponding accumulation of holes, leading to an increase in the drain current ID. One can also use n-type semiconductors and build accumulation mode n-type OECTs. In accumulation mode n-type OECT, application of a positive gate voltage causes injection of cations into the channel and a corresponding accumulation of electrons, leading to an increase in the drain current ID.
Other suitable conducting polymers for the channel include, but are not limited to, conductor based on PEDOT with a pendant sulfonate group (PEDOT-S), PEDOT doped with tosylate (PEDOT:TOS), PEDOTOH:ClO4, PEDOT-co-PEDOTOH:ClO4 (Schmode, et al., Chem. Mater., 31(14):5286-5295 (2019)), poly(2-(3,3′-bis(2-(2-(2-methoxyethoxy) ethoxy)ethoxy)-[2,2′ bithiophen]-5 yl)thieno[3,2 b] thiophene), p(g2T TT), poly((ethoxy)ethyl 2-(2-(2 methoxyethoxy) ethoxy)acetate)-naphthalene 1,4,5,8 tetracarboxylic-diimide-co 3,3′ bis(2-(2-(2 methoxyethoxy)ethoxy) ethoxy)-(bithiophene)) p(gNDI g2T), P3HT (poly(3-hexylthiophene-2,5-diyl)), BBL (polybenzimidazo-benzoisoquioline), PTHS-TMA+-co-P3HT (poly[(6-thiophen-3-yl)hexane-1-sulfonate-co-3-(hexylthiophene)]), poly(N,N′-bis(7-glycol)-naphthalene-1,4,5,8-bis(dicarboximide)-co-2,2′-bithiophene-co-N,N′-bis(2-octyldodecyl)-naphthalene-1,4,5,8-bis(dicarboximide), naphthalene-1,4,5,8-tetracarboxylic-diimide-bithiophene (NDI-T2) based polymer with 90% glycol chain percentage (P-90), and glycolated Diketopyrrolopyrroles (DPPs) or glycolated thiophenes, bithiophenes such as p(g0T2-g6T2) (Moser, et al., Advanced Materials, 32:2002748 (2020)).
Examples of suitable polymers for the channel in a depletion mode OECT are PEDOT polymers or copolymers thereof, such as polymers based on PEDOT with a pendant sulfonate group (PEDOT-S), PEDOT doped with tosylate (PEDOT:TOS), PEDOTOH:ClO4, PEDOT-co-PEDOTOH:ClO4, and PEDOT:PSS.
Examples of suitable polymers for the channel in an accumulation mode OECT are poly(2-(3,3′-bis(2-(2-(2-methoxyethoxy) ethoxy)ethoxy)-[2,2′ bithiophen]-5 yl)thieno[3,2 b] thiophene), p(g2T TT), poly((ethoxy)ethyl 2-(2-(2 methoxyethoxy) ethoxy)acetate)-naphthalene 1,4,5,8 tetracarboxylic-diimide-co 3,3′ bis(2-(2-(2 methoxyethoxy)ethoxy) ethoxy)-(bithiophene)) p(gNDI g2T), P3HT (poly(3-hexylthiophene-2,5-diyl)), BBL (polybenzimidazo-benzoisoquioline), PTHS-TMA+-co-P3HT (poly[(6-thiophen-3-yl)hexane-1-sulfonate-co-3-(hexylthiophene)]), poly(N,N′-bis(7-glycol)-naphthalene-1,4,5,8-bis(dicarboximide)-co-2,2′-bithiophene-co-N,N′-bis(2-octyldodecyl)-naphthalene-1,4,5,8-bis(dicarboximide), naphthalene-1,4,5,8-tetracarboxylic-diimide-bithiophene (NDI-T2) based polymer with 90% glycol chain percentage (P-90), and glycolated Diketopyrrolopyrroles (DPPs) or glycolated thiophenes, bithiophenes such as p(g0T2-g6T2).
Typically, the channel has a first dimension (i.e. width) and a second dimension (i.e. length). The length is the distance between the source and drain electrodes. Width is the remaining dimension of that rectangle The length and width of the channel can be a value between about 5 μM and about 5 mm, for example, between 5 μm and 1000 μm, between 5 μm and 100 μm, between 5 μm and 100 μm, or between 10 μm and 100 μm, for example, about 10 μm or about 100 μm. The width of the channel can be between 10 μm and 1000 μm, between 20 μm and 500 μm, or between 20 μm and 200 μm, for example, about 100 μm.
The first dimension and the second dimension can be the same or different. In some embodiments, the width of the channel is the same as the length of channel. For example, the channel has a width of about 100 μm and a length of about 100 μm. In some embodiments, the width of the channel is smaller than the length of the channel. In some preferred embodiments, the width of the channel is larger than the length of the channel. For example, the channel has a width of about 100 μm and a length of about 10 μm. In some embodiments, the OECT having a small channel (e.g. a width of about 100 μm and a length of about 10 μm) is more sensitive (i.e. higher NR) than the same OECT but having a larger channel (e.g. a width of about 100 μm and a length of about 100 μm) under the same measurement conditions (e.g. VG, VD, incubation time, temperature, and pressure).
Typically, the channel remains unmodified, i.e., it is not chemically modified to anchor binding partners. The analyte recognition takes place at the functionalized gate electrode, which is not in physical contact with the channel. This configuration allows prolonged shelf life of the device compared with OECT containing channels modified with binding partners. For example, the OECT disclosed herein can preserve its drain current (i.e. change of drain current is less than about 5% compared with a fresh sensor) after storing at ambient conditions (i.e. about 25° C. at 1 atm) for at least 6 months in air or for at least 1 year in nitrogen or vacuumed environment For example, the OECT disclosed herein can preserve its NR determined with a standard solution containing the same amount of the same analyte (i.e. change of NR is less than about 5% compared with a fresh sensor) after storing at ambient conditions (i.e. about 25° C. at 1 atm) for 6 months in air or 1 year in nitrogen or vacuumed environment.
The channel materials can be spin casted, drop casted or inkjet or screen printed from solutions.
iii. Gate Electrode
The gate electrode is configured to control the injection of ions into the channel, typically placed in the measurement solution with the source electrode, the drain electrode and the channel, but not in physical contact with these components.
The gate electrode can be any shape appropriate such as cuboid, cubic, circular, and cylindrical. In some embodiments, the gate electrode is a circular electrode having a diameter in a range from 0.5 mm to 10 mm, from 1 mm to 10 mm, from 0.5 mm to 5 mm, or from 1 mm to 5 mm, such as 2.8 mm. In some preferred embodiments, the gate electrode is a square electrode having a length in a range from 0.1 mm to 10 mm, from 0.1 mm to 8 mm, from 0.1 mm to 5 mm, from 0.5 mm to 10 mm, or from 0.5 mm to 5 mm, such as about 0.8 mm or about 4.8 mm. In some preferred embodiments, the gate electrode is a square electrode having a length of about 0.8 mm.
In some embodiments, the OECT contains a gate electrode having any shape and size as described above and a channel having any shape and size as described above. In some preferred embodiments, the OECT contains a square electrode having any length as described above and a rectangular channel having any size (i.e. width and length) as described above. In a particularly preferred embodiment, the OECT contains a square gate electrode having a length of about 0.8 mm and a rectangular channel having a width of about 100 μm and a length of about 10 μm.
Generally, the gate electrode can be made from a substrate coated with any conducting materials descried above for the source and the drain electrodes (e.g., Pt or Au) or a conducting polymer, such as poly(fluorine)s, polyphenylenes, polypyrenes, polyazulenes, polynaphthalenes, poly(pyrrole)s, polycarbozoles, polyindoles, polyzaepines, polyanilines, poly(thiophene)s, poly(3,4-ethylenedioxythiophene), poly(p-phenylene sulfide), poly(acetylene)s, or poly(p-phenylene vinylene). In some embodiments, the gate electrode contains two or more conducting materials. For example, the gate electrode contains two conducting materials, where the first conducting material can be a material disclosed above for the source and the drain electrodes and a second conducting material can be a conducting polymer. In some preferred embodiments, the gate electrode contains two conducting materials, where the first conducting material is a metallic conductor of a first type and the second conducting material is a metallic conductor of a second type. The two conducting materials may be coated simultaneously or subsequently on the substrate. A preferred gate electrode is formed from a Kapton (polyimide) substrate sputter coated with Cr and Au.
Typically, the gate electrode is engineered to include a biorecognition layer. For example, the gate electrode is modified sequentially with a SAM, a linker, and a biorecognition element, such as nanobody, to form the biorecognition layer on the gate electrode.
iv. Electrolyte Solution
The electrolyte solution is in electrically contact with the channel and the gate electrode, and the source electrode and the drain electrode (the last two are insulated with an insulator). The electrolyte solution is a solution that contains ions or molecules that have lost or gained electrons, and is electrically conductive and mostly aqueous. Electrolyte solutions include, but are not limited to, water, buffers such as phosphate buffered solution, phosphate buffered saline, salt water, MES buffer, Bis-Tris buffer, ADA, ACES, PIPES, MOPSO, Bis-Tris propane, BES, MOPS, TES, HEPES, DIPSO, MOBS, TAPSO, Trizma, HEPPSO, POPSO, TEA, EPPS, Tricine, Gly-gly, Bicine, HEPBS, TAPS, AMPD, TABS, AMPSO, CHES, CAPSO, AMP, CAPS, CABS. The electrolyte solution can have a pH between about 4 and about 8.5, between about 4.5 and about 8.5, between about 5 and about 8.5, between about 5.5 and about 8.5, between about 6 and about 8, or between about 6.5 and about 7.5, preferably about 7.4.
v. Reservoir
The device may include a reservoir to contain the electrolyte solution. The reservoir may be incorporated in the OECT by any suitable methods. For example, the reservoir is glued on top of the channel. The reservoir can also be a microfluidic channel.
The reservoir is typically defined by a side wall and a bottom surface, and contains an opening configured to allow the electrolyte solution to enter the reservoir. The reservoir may have any suitable shapes, such as a cylindrical well, a cubic shape, or a cuboid shape. The bottom surface is formed from at least a portion of the channel and optionally, at least a portion of the side wall is formed from the source electrode and the drain electrode respectively. For example, the reservoir is a cylindrical well and has a bottom surface formed from at least a portion of the channel. The side wall is perpendicular to the surface of the channel and at least a portion of the side wall is in contact with the source electrode and drain electrode. The cylindrical reservoir contains an opening to allow the electrolyte solution to enter the reservoir. An exemplary OECT containing a cylindrical reservoir to contain the electrolyte solution is shown in
For example, the reservoir is a cuboid defined by a bottom surface and four side walls. The bottom surface is formed by at least a portion of the channel and each of the first and second side walls are parallel to each other and vertically placed on top of each of the source electrode and drain electrode. The third and fourth side walls are parallel to each other and perpendicular to the first and second side walls, such that the reservoir contains an opening to allow the electrolyte solution to enter the reservoir.
For example, the reservoir is a cuboid and has a bottom surface formed by the channel, a first side wall formed from a portion of the source electrode, a second side wall formed from a portion of the drain electrode, and a third side wall and a fourth side wall that are parallel to each other and perpendicular to the first side wall and second side wall, such that the reservoir contains an opening to allow the electrolyte solution to enter the reservoir. When an electrolyte solution is in the reservoir, the channel, at least a portion of the source electrode and the drain electrode, and the gate electrode are in contact with the electrolyte solution.
The reservoir can be made from any suitable inert material, such as plastic, glass, or a polymeric material, such as polydimethylsiloxane (PDMS).
The disclosed biosensors integrate OECT technology engineered to include a biorecognition layer by functionalizing the sensing electrode (i.e. gate electrode), sequentially, via a SAM, a binding partners, preferably, covalent binding partners or an affinity pair (e.g. the SpyTag/SpyCatcher conjugation system), and a biorecognition element. Optionally, the biorecognition layer is also exposed to a blocking agent, which can be introduced simultaneously with the biorecognition element or subsequently to the biorecognition element.
Methods of making an OECT or an array of two or more OECTs are known. An exemplary method of making an OECT array is described in the Examples. The biorecognition elements, such as nanobody units, can be immobilized with uniform orientations using the methods described herein; this allows the biorecognition layer to be more precise and compact.
Generally, methods of integrating a biorecognition layer on an electrode, such as a gate electrode of an OECT, include: (i) contacting at least a portion of the surface of the electrode with a first solution containing a plurality of organic molecules under conditions that result in self-assembly of the organic molecules, to produce a SAM-modified OECT surface, (ii) contacting the SAM-modified surface with a second solution containing a first peptide to produce a first peptide-SAM-modified surface, referred herein as Chem-SAM, and (iii) contacting the Chem-SAM-modified surface with a third solution containing a second peptide (which is a binding partner to the first peptide), a biorecognition element for the analyte of interest and optionally, a blocking agent, where the first peptide conjugates with the second peptide to form a second monolayer, referred to herein as Bio-SAM. The OECT electrode modified by Chem-SAM and BioSAM results in a modified OECT gate electrode surface, with the recognition element exposed for interaction with an analyte (to which it binds) from a sample. (See
Referring to Formula I, (i) the surface of the electrode is contacted with a solution containing organic molecules (N) capable of self-assembling into a SAM, to form a first SAM; (ii) the first SAM is contacted with a composition including AP1 (with/or without L1) under conditions that result in chemical coupling of the AP1 to the first SAM, thus forming a Chem-SAM on the OECT electrode surface, and (iii) contacting the Chem-SAM with a composition including AP2-L2-B-under conditions resulting in conjugation of AP1 and AP2 to form a biologically self-assembled monolayer, herein Bio-SAM. (
A. Modification with Chem-SAMs
Generally, a plurality of organic molecules are dissolved in a solvent to form a first incubation solution. A portion of or the entire surface of the electrode to be modified, such as the gate electrode of an OECT, is immersed in the first composition containing the plurality of organic molecules. The electrode surface is incubated with the first composition, optionally in the dark, for a time period sufficient to form a SAM on the surface of the electrode. Typically, the incubation time period sufficient to form the SAM on the surface of the electrode is in a range from 10 minutes to 36 hours, from 10 minutes to 24 hours, from 10 minutes to 12 hours, from 10 minutes to 10 hours, from 10 minutes to 5 hours, from 10 minutes to 2 hours, or from 10 minutes to 1 hour, such as about 1 hour.
Suitable solvents that can be used to dissolve the plurality of organic molecules used to form the first SAM on the surface of the OECT electrode, are known. Exemplary solvents for the incubation solution for SAM formation include, but are not limited to, methanol, ethanol, Dimethyl sulfoxide (DMSO), toluene, hexane, water, and a buffer as described above, and a combination thereof.
Suitable organic molecules that can form a SAM on an electrode are known, for example, thiol molecules, phosphine molecules, or silicon oxide derivatives. In some preferred embodiments, the organic molecules forming the SAM on the electrode surface of the OECT, such as the gate electrode surface, are thiol molecules. Any thiols as described above or a mixture thereof can be used to form the SAM layer on the electrode surface of the OECT. The SAM may be formed from a single type of thiol or a mixture of two or more types of thiols. For example, the SAM may be formed from HDT or PDT, or a mixture of PDT and MPA.
Typically, the total concentration of the organic molecules in the incubation solution is in a range from 0.1 mM to 50 mM, from 0.1 mM and 40 mM, from 0.1 mM and 30 mM, from 0.1 mM and 25 mM, from 0.1 mM and 20 mM, from 0.1 mM and 15 mM, from 0.1 mM and 12 mM, from 0.1 mM and 10 mM, from 0.1 mM and 5 mM, or from 0.5 mM and 5 mM. The term “total concentration of organic molecules” refers to the total mol of the organic molecules relative to the total volume of the solvent. For example, when the incubation solution contains a single type of thiol molecules, such as HDT, the concentration of the HDT molecules in the incubation solution is in a range from 0.1 mM to 50 mM, from 0.1 mM and 40 mM, from 0.1 mM and 30 mM, from 0.1 mM and 25 mM, from 0.1 mM and 20 mM, from 0.1 mM and 15 mM, or from 0.1 mM and 12 mM, from 0.1 mM and 10 mM, from 0.1 mM and 5 mM, or from 0.5 mM and 5 mM, such as about 1 mM. For example, when the incubation solution contains two types of thiol molecules, such as PDT and MPA, the total concentration of the PDT molecules and MPA molecules in the incubation solution is in a range from 0.1 mM to 50 mM, from 0.1 mM and 40 mM, from 0.1 mM and 30 mM, from 0.1 mM and 25 mM, from 0.1 mM and 20 mM, from 0.1 mM and 15 mM, or from 0.1 mM and 12 mM, such as about 12 mM.
When the incubation solution contains two or more types of organic molecules, the concentration of each type of the organic molecules can be in a suitable range to provide a total concentration of the two or more types of organic molecules in a range from 0.1 mM to 50 mM, from 0.1 mM and 40 mM, from 0.1 mM and 30 mM, from 0.1 mM and 25 mM, from 0.1 mM and 20 mM, from 0.1 mM and 15 mM, or from 0.1 mM and 12 mM, such as about 12 mM. For example, the incubation solution contains a mixture of PDT and MPA, where the concentration of PDT is in a range from 0.05 mM to 49.9 mM, from 0.1 mM and 30 mM, from 0.1 mM and 25 mM, from 0.1 mM and 20 mM, from 0.1 mM and 15 mM, or from 0.1 mM and 12 mM, such as about 10 mM, and the concentration of MPA is in a range from 0.05 mM to 49.9 mM, from 0.1 mM and 30 mM, from 0.1 mM and 25 mM, from 0.1 mM and 20 mM, from 0.1 mM and 15 mM, or from 0.1 mM and 12 mM, such as about 2 mM, such that the total concentration of PDT and MPA is in a range from 0.1 mM to 50 mM, such as about 12 mM.
Optionally, following incubation, the SAM-modified electrode surface is rinsed with a first rinsing composition and optionally dried with a gas stream, such as Nitrogen gas. Exemplary rinsing compositions include, but are not limited to methanol, ethanol, and water, and a combination thereof.
B. Modification with a First Peptide
Generally, a first peptide (of a binding pair) is dissolved in a buffer as described above, such as PBS to form a second incubation composition. The first peptide can be a modified peptide, which includes a short linker and/or a chemical modification such as modified with a maleimide functional group(s). The SAM-modified electrode surface is immersed in the second incubation composition containing the first peptide for a time period sufficient to couple the first peptide to the SAM (i.e., the first SAM) on the surface of the electrode such that a first peptide-SAM modified surface is produced. Typically, the incubation time period sufficient to couple the first peptide to the SAM on the surface of the electrode is in a range from 10 minutes to 24 hours, from 10 minutes to 20 hours, from 10 minutes to 15 hours, from 10 minutes to 12 hours, from 10 minutes to 10 hours, from 10 minutes to 5 hours, from 10 minutes to 2 hours, from 10 minutes to 1.5 hours, or from 10 minutes to 1 hour, such as about 1 hour.
The first peptide can couple to the first SAM and conjugate with a second peptide as described below. An exemplary first peptide is SpyTag peptide, unmodified, or preferably, which is modified with a short linker (SEQ ID NO:1) (disclosed in Zakeri, et al., Proc. Natl. Acad. Sci., 109:E690-E697 (2012)), preferably modified with a maleimide functional group); this allows the SpyTag peptide to conjugate with the free thiol group(s) in the SAM via thiol-maleimide “click” chemistry reaction.
Typically, the concentration of the first peptide in the second incubation solution is in a range from 0.01 mg/mL to 20 mg/mL, from 0.01 mg/mL to 15 mg/mL, from 0.01 mg/mL to 10 mg/mL, from 0.05 mg/mL to 20 mg/mL, from 0.05 mg/mL to 15 mg/mL, from 0.05 mg/mL to 10 mg/mL, from 0.01 mg/mL to 5 mg/mL, from 0.01 mg/mL to 1 mg/mL, from 0.05 mg/mL to 5 mg/mL, or from 0.05 mg/mL to 1 mg/mL, such as about 0.1 mg/mL.
Optionally, following incubation, the first peptide-SAM-modified electrode surface is rinsed with a second rinsing composition, such as a buffer as described above.
Fusion proteins of Formula II can be obtained by, for example, by chemical synthesis, and more preferably, by recombinant production in a host cell. To recombinantly produce a fusion proteins of Formula II, a nucleic acid containing a nucleotide sequence encoding the polypeptide can be used to transform, transduce, or transfect a bacterial or eukaryotic host cell (e.g., an insect, yeast, or mammalian cell). In general, nucleic acid constructs include a regulatory sequence operably linked to a nucleotide sequence encoding a fusion proteins of Formula II. Regulatory sequences (also referred to herein as expression control sequences) typically do not encode a gene product, but instead affect the expression of the nucleic acid sequences to which they are operably linked. The nucleotide sequences encoding the fusion protein are usually inserted into a recombinant vector which may be any vector, which may conveniently be subjected to recombinant DNA procedures, and the choice of vector will often depend on the host cell into which it is to be introduced. Thus, the vector may be an autonomously replicating vector, i.e. a vector, which exists as an extrachromosomal entity, the replication of which is independent of chromosomal replication, e.g. a plasmid. Alternatively, the vector may be one which, when introduced into a host cell, is integrated into the host cell genome and replicated together with the chromosome(s) into which it has been integrated. The vector is preferably an expression vector in which the DNA sequence encoding the fusion protein is operably linked to additional segments required for transcription of the DNA. In general, the expression vector is derived from plasmid or viral DNA, or may contain elements of both. The term, “operably linked” indicates that the segments are arranged so that they function in concert for their intended purposes, e.g. transcription initiates in a promoter and proceeds through the DNA sequence coding for the fusion protein. Expression vectors for use in expressing the fusion protein will comprise a promoter capable of directing the transcription of a cloned gene or cDNA. The promoter may be any DNA sequence, which shows transcriptional activity in the host cell of choice and may be derived from genes encoding proteins either homologous or heterologous to the host cell. Expression vectors for use in expressing the fusion protein will comprise a promoter capable of directing the transcription of a cloned gene or cDNA. The promoter may be any DNA sequence, which shows transcriptional activity in the host cell of choice and may be derived from genes encoding proteins either homologous or heterologous to the host cell. Examples of suitable promoters for directing the transcription of the DNA in mammalian cells are the SV40 promoter (Subramani et al., Mol. Cell. Biol. 1 (1981), 854-864), the MT-1 (metallothionein gene) promoter (Palmiter et al., Science 222 (1983), 809-814), the CMV promoter (Boshart et al., Cell 41:521-530, 1985) or the adenovirus 2 major late promoter (Kaufman and Sharp, Mol. Cell. Biol, 2:1304-1319, 1982).
Useful prokaryotic and eukaryotic systems for expressing and producing polypeptides are well known in the art include, for example, Escherichia coli strains such as BL-21, and cultured mammalian cells such as CHO cells.
In eukaryotic host cells, a number of viral-based expression systems can be utilized to express fusion proteins of Formula II. Viral based expression systems are well known in the art and include, but are not limited to, baculoviral, SV40, retroviral, or vaccinia based viral vectors.
The expressed tagged or fusion proteins produced by the cells may be recovered from the culture medium by conventional procedures including separating the host cells from the medium by centrifugation or filtration, releasing the fusion protein by mechanical cell disruption, such as ultrasonication or pressure, precipitating the proteinaqueous components of the supernatant or filtrate by means of a salt, e.g. ammonium sulphate. After sonication a suitable concentration of NaCl can be added to further decrease the ability of host cell contaminants to bind to the cation exchange matrix. After cation-exchange chromatography the fusion protein may be eluted in a salt gradient and eluate fractions containing the fusion protein are collected. In some preferred forms, fusion protein is captured from lysate through its His tag. So IMAC (immobilized metal affinity chromatography) was used and then, after concentration of protein-containing fractions, they are subjected to size exclusion chromatography (SEC) for final purification. In particularly preferred embodiments for nanobody purification, the nanobody is purified from the periplamic space, where the host cell is bacteria, for example, E. coli. This would include (1) centrifugation, (2) osmotic shock to release the protein from the cell wall compartment, (3) IMAC (Immobilized Metal Ion Affinity Chromatography), (4) SEC (Size Exclusion Chromatography).
D. Modification with Biorecognition Elements
Generally, a second peptide-biorecognition element conjugate and a blocking agent are dissolved in a binding buffer solution, such as HEPES, to form a third incubation solution. Preferably, the blocking agent contained in the third incubation solution is BSA.
Typically, the concentration of the blocking agent in the third incubation solution is in a range from 0.01% w/v to 10% w/v, from 0.01% w/v to 5% w/v, from 0.01% w/v to 1% w/v, from 0.05% w/v to 10% w/v, from 0.05% w/v to 5% w/v, or from 0.05% w/v to 1% w/v, such as about 0.1% w/v.
The first peptide-SAM-modified electrode surface is immersed in the third incubation solution containing the second peptide-biorecognition element conjugate and the blocking agent. Generally, the second peptide of the peptide-biorecognition element conjugate is capable of conjugating with the first peptide to form a biomolecular linker and thus attached the biorecognition element on the electrode surface. An exemplary second peptide is SpyCatcher peptide as disclosed in Zakeri, et al., Proc. Natl. Acad. Sci., 109:E690-E697 (2012). For example, a SpyTag/SpyCatcher linker is formed to control the oriented immobilization of the biorecognition elements (e.g., nanobodies) on the electrode surface. For example, after linker formation, the biorecognition element (e.g., nanobody) is functionalized on the gate electrode surface of the OECT, in a configuration vertical to electrode surface and is vertical relative to the channel surface, allowing for binding with an analyte in a sample, when the sample contacts the biorecognition element-functionalized electrode. The biorecognition elements can vary depending on the analytes of interest. For example, the biorecognition element is a nanobody such as an anti-GFP nanobody or an anti-SARS-1-RBD nanobody or an anti-MERS RBD nanobody (See TABLE 2).
The conjugation between SpyTag and SpyCatcher is a robust method for conjugating the recombinant proteins where the peptide SpyTag can spontaneously react with the protein SpyCatcher in a facile manner and with high specificity (Zakeri, et al., Proc. Natl. Acad. Sci., 109:E690-E697 (2012); Keeble et al., 2017). Maleimide functional groups can be constructed in the SpyTag peptide and nanobodies as fusion to the SpyCatcher proteins, and expressed as fusion protein in any suitable protein expression system, preferably with a tag such as a His tag, to aid in its purification.
The first peptide-SAM-modified electrode surface is incubated with the third incubation solution for a time period sufficient to form the linker (i.e. first peptide/second peptide conjugate), such that a biorecognition element-linker-SAM modified electrode surface is produced (biorecognition layer integrated on the electrode surface.
Typically, the incubation time period sufficient to form the second peptide/first peptide conjugate on the surface of the electrode is in a range from 5 minutes to 24 hours, from 10 minutes to 20 hours, from 10 minutes to 15 hours, from 10 minutes to 12 hours, from 10 minutes to 10 hours, from 10 minutes to 5 hours, from 10 minutes to 2 hours, from 10 minutes to 1.5 hours, or from 10 minutes to 1 hour, such as about 1 hour.
Typically, the concentration of the second peptide-recognition element conjugate in the third incubation solution is in a range from 1 μM to 100 μM, from 1 μM to 100 μM, from 1 μM to 90 μM, from 1 μM to 80 μM, from 10 μM to 100 μM, from 10 μM to 90 μM, from 10 μM to 80 μM, from 5 μM to 100 μM, from 5 μM to 90 μM, from 5 μM to 80 μM, from 20 UM to 100 M, from 20 μM to 90 μM, or from 20 μM to 80 μM, such as about 50 μM.
Optionally, following incubation, the biorecognition layer-integrated electrode surface is rinsed with a third rinsing solvent, such as a buffer as described above.
An exemplary method of preparing a biorecognition layer-integrated electrode surface is described in the Examples.
A preferred method uses p-type depletion (PEDOT:PSS) and accumulation (such as p(g0T2-g6T2)) mode materials in the OECT channel while the gate electrode is gold. The gate electrode (preferably gold) surface is functionalized with a biorecognition layer, i.e., the nanobody. The gate electrode surface is electrochemically cleaned and then exposed to 1,6-hexanedithiol (HDT) to form a thiol-self assembled monolayer (SAM). Particularly preferred is a modified peptide (SpyTag) with a terminal of maleimide functional group, conjugated with the thiol SAM layer via thiol-maleimide “click” chemistry reaction. After that, the specific nanobody, which is the recognition element-spycatcher conjugate is diffused into the SpyTag proteins to form the biofunctional layer.
The disclosed methods above can be used to make OECT devices containing a nanobody whose binding partner is any analyte of interest, for example an antigen from any pathogen. The disclosed device is used to measure the presence, the absence, or the concentration of any analyte in a sample, where the analyte is a binding partner to the biorecognition element functionalized onto the device. The biorecognition element functionalized-OECT Sensor features: improved sensitivity high sensitivity over prior art devices (aM or zM compared to fM) and selectivity, delivering accurate results in accordance with gold standard tests (where possible and applicable, correlated to DNA or RNA detection results with the conventional PCR method); fast detection time (less than 15 minutes after the sample exposure to the sensor surface to the read-out); and high limit of detection (lower limit of detection (LOD) exemplified below for SARS-CoV-2 S1 in saliva is 1.2×10−21M).
The OECT sensor relies on the channel made from ion-permeable organic electronic material, through which holes or electrons flow from the source electrode to the drain electrode. When ions are injected from the electrolyte solution into the channel, its doping state is changed and thus its conductivity is changed. The operation of OECT is controlled by voltages applied to the gate electrode (gate voltage, VG) and to the drain electrode (drain voltage, VD), which are referenced with respect to the source electrode. The drain voltage induces a current (drain current, ID), which is proportional to the quantity of mobile holes or electrons in the channel, and thus probes the doping state of the organic electronic material. The gate voltage controls the injection of ions into the channel and thus the doping state of the organic electronic material, resulting in a change in ID. The change in ID may be expressed as a normalized response (also referred herein as “NR”) which can be calculated based on equation 1:
where I0 is the drain current obtained after incubation of the OECT with a blank solution (i.e. a solution in the absence of the target analytes) under the same measurement conditions as the biological sample.
As the nanobody selectively captures its target, in this case GFP protein or SAR-CoV-2 protein or MERS-CoV protein, this binding event changes the capacitance of the gate electrode and induces the potential across the gate/electrolyte interface, suppressing the gating of the OECT. Therefore, the OECT signal varies depending on the concentration of GFP down to femtomolar and attomolar range. This strategy of utilizing nanobody units will open up a new avenue for the design of electronic biosensors and can be further expanded into different sensing platforms and various target proteins.
Generally, a method of using the disclosed device for testing the presence, the absence, and/or concentration of analytes in a biological sample includes: (i) adding an electrolyte solution into the reservoir; (ii) incubating the gate electrode (functionalized with a biorecognition layer as described above) with a blank solution, for example a buffer like PBS, universal transport medium (UTM), or virus transport medium (VTM); (iii) placing the gate electrode on top of the channel covered by the electrolyte, (iv) applying a VG and a VD; (v) measuring a first ID; (vi) incubating the gate electrode with the biological sample for a time period sufficient to allow binding between the analyte and the biorecognition element; (vii) rinsing the gate electrode with a rinsing buffer; and (viii) measuring a second ID, where a difference between the second ID and the first ID is indicative of the absence, the presence, or the concentration of the analyte in the biological sample. The second ID may be larger, the same or substantially the same as, or smaller than the first ID. Optionally, steps (v)-(vii) are repeated one or more times.
The electrolyte solution added into the reservoir can be any electrolyte solution described above, for example, a PBS at pH about 7.4. The blank solution may be a buffer solution that does not contain the analyte of interest and is used to establish a baseline drain current, i.e. I0. Typically, a drop of the blank solution is applied onto the gate electrode and incubated for about 10 minutes. Generally, the time period for incubating the gate electrode with the blank solution is the same as the incubation time period sufficient to allow binding between the analyte and the biorecognition element. Optionally, the gate electrode is rinsed with a rinsing buffer following incubation with the blank solution for about 10-15 second. The rinsing buffer may be any electrolyte solution as described above, such as PBS.
Typically, the VG and VD are applied simultaneously to the gate electrode and the drain electrode, respectively. In some embodiments, the VG is applied to the gate electrode by sweeping from a first gate voltage to a second gate voltage at a gate voltage step and the VD is applied to the drain electrode by sweeping from a first drain voltage to a second drain voltage at a drain voltage step. For example, the VG is applied to the gate electrode by sweeping from −1 V to 1 V, from −0.8 V to 0.8 V, or from −0.6 V to 0.6 V, at a gate voltage step of 0.05 V, 0.1 V, 0.2 V, or 0.5 V and the VD is applied to the drain electrode by sweeping from 0 V to 1 V, from 0.5 V to −1 V, from 0 V to −1 V, from 0 V to −0.8 V, or from 0 V to −0.6 V, at a drain voltage step of 0.05 V, 0.1 V, 0.2 V, or 0.5 V. In some preferred embodiments, the VG is applied to the gate electrode by sweeping from −0.6 V to 0.6 V at a gate voltage step of 0.1 V and the VD is applied to the drain electrode by sweeping from 0 V to −0.6 V at a drain voltage step of 0.1 V. When both VG and VD are applied by sweeping, a range of IDs can be collected.
In some embodiments, a fixed VG is applied to the gate electrode and a fixed VD is applied to the drain electrode. The fixed VG and fixed VD may be the same or different. For example, a fixed VG in the range from −1 V to 1V, from −0.6 V to 0.6 V, or from −0.1 V to 0.1 V, such as −0.6V, −0.1 V, or 0.6 V is applied to the gate electrode, and a fixed VD in the range from −1 V to 1V, from −0.6 V to 0.6 V, 0 V to −0.6 V, or from −0.1 V to 0.1 V, such as −0.6 V, −0.1 V, or 0.6 V, is applied to the drain electrode. In some embodiments, a VG of −0.1 V is applied to the gate electrode and a VD of −0.1 V is applied to the drain electrode. In some embodiments, a VG of 0.1 V is applied to the gate electrode and a VD of 0.1 V is applied to the drain electrode. In some embodiments, a VG of −0.1 V is applied to the gate electrode and a VD of 0.1 V is applied to the drain electrode. In some embodiments, a VG of 0.1 V is applied to the gate electrode and a VD of −0.1 V is applied to the drain electrode. In some embodiments, a VG of −0.6 V is applied to the gate electrode and a VD of −0.6 V is applied to the drain electrode. In some embodiments, a VG of 0.6 V is applied to the gate electrode and a VD of 0.6 V is applied to the drain electrode. In some embodiments, a VG of 0.6 V is applied to the gate electrode and a VD of −0.6 V is applied to the drain electrode. In some embodiments, a VG of −0.6 V is applied to the gate electrode and a VD of 0.6 V is applied to the drain electrode. When a fixed VG and a fixed VD are applied, a single ID can be collected.
The biological sample is typically in a liquid form and applied onto the gate electrode as a drop and incubates for a period of time sufficient to allow binding between the analytes and the biorecognition element (e.g. nanobody) immobilized on the gate electrode of the OECT. Typically, the volume of the biological sample sufficient for incubation is small. For example, the volume of the biological sample sufficient for incubation is less than 20 μL, less than 10 μL, or preferably, ≤5 μL, and more preferably, about 5 μL.
The biological samples can be a bodily fluid, such as whole blood, plasma, serum, saliva, nasal swab, mucus, sputum (processed or unprocessed), bronchial alveolar lavage (BAL), bronchial wash (BW), cerebrospinal fluid (CSF), and urine.
In some embodiments, the biological sample is not a bodily fluid, but is a liquid obtained from a solid specimen, such as tissue (e.g., biopsy material), feces, rectal swab, nasopharyngeal swab, and throat swab. When the biological sample is not a bodily fluid, the above-described exemplary method can be modified to include an initial step of processing the specimen t to obtain a sample in liquid form, which is then subjected to steps (i)-(v) described above for a method of using the disclosed device for testing the presence, the absence, and/or concentration of analytes in a biological sample. Processing methods to transform a specimen (which is not a fluid) into a liquid form are known. For example, when the specimen is a nasopharyngeal swab, it is processed by placing the proximal portion of the swab in a buffer to produce the biological sample in a liquid form (Lopez, et al., Pediatr. Res., 86(5):651-654 (2019)). Optionally, when specimen processing is needed, the method also includes a desalting step prior to specimen processing, where the buffer is run through a desalting column to remove any redox reagents, such as dithiothreitol (DTT), to reduce interference signals caused by non-specific interactions of the redox reagents with the gate electrode surface. Optionally, the desalting step is performed following specimen processing and prior to step (v), where the obtained biological sample in a liquid form is run through a desalting column to remove any redox reagents introduced during the specimen processing step.
In some embodiments, the above-described exemplary method includes a step of adding a protease inhibitor into the biological sample prior to other steps, such as prior to any one of steps (i)-(v), particularly prior to step (vi). The protease inhibitor can prevent or reduce the damage to the sensor's protein-based recognition layer caused by protease activity in the biological or environmental sample.
In some embodiments, the above-described exemplary method includes a step of diluting the biological sample using a sensor binding buffer, prior to other steps, such as prior to any one of steps (i)-(vi), particularly prior to step (vi). The dilution factor for the biological sample following the dilution step can be from 0.1:1 to 1:10, from 0.5:1 to 1:10, from 0.5:1 to 1:5, from 1:1 to 1:10, or from 1:1 to 1:5, such as about 1:1 or about 1:3 in the sensor binding buffer.
For example, the above-described exemplary method includes a step of diluting a biological sample collected on a nasal swab using a sensor binding buffer. Generally, the sensor binding buffer contains one or more buffering agents, one or more salts, one or more detergents, and one or more protease inhibitors. Optionally, the sensor binding buffer also contains one or more antimicrobial agents and/or one or more blocking agents as described above. The sensor binding buffer is at the physiological pH, i.e. about pH 7.4.
The buffering agents in the sensor binding buffer can stabilize pH of the buffer and can be tolerated by proteins. Examples of buffering agents that are suitable for use in the sensor binding buffer include, but are not limited to, Tris, HEPES, sodium hydrogen phosphate, sodium dihydrogen phosphate, potassium hydrogen phosphate, potassium dihydrogen phosphate, sodium borate, potassium borate, citric acid, TAPS, Bicine, Tricine, TAPSO, TES, MOPS, PIPES, cacodylate, and MES, and a combination thereof. The total concentration of the one or more buffering agents in the sensor binding buffer can be in a range from about 5 mM to about 100 mM, from about 10 mM to about 100 mM, from about 5 mM to about 50 mM, from about 10 mM to about 50 mM, or from about 20 mM to about 50 mM, such as about 20 mM or about 50 mM.
The salts in the sensor binding buffer can maintain the solubility and structural integrity of proteins. These can be salts that are near the middle of the Hofmeister series and thus not promoting “salting out” (precipitation of proteins) but also not promoting denaturing of proteins. Examples of salts that are suitable for use in the sensor binding buffer include, but are not limited to, potassium fluoride, potassium bromide, potassium hydrogen phosphate, potassium acetate, potassium citrate, lithium fluoride, lithium bromide, lithium hydrogen phosphate, lithium acetate, and lithium citrate, and a combination thereof. The total concentration of the one or more salts in the sensor binding buffer can be in a range from about 50 mM to about 1 M, from about 100 mM to about 1 M, from about 150 mM to about 1 M, from about 100 mM to about 500 mM, or from about 150 mM to about 500 mM, such as about 150 mM, about 250 mM, or about 500 mM.
The detergents in the sensor binding buffer are typically non-ionic and non-denaturing detergents, such as detergents with polyoxyethylene head groups that contain alkylpolyethylene ethers with the general formula CnH2n+1(OCH2CH2)xOH or a phenyl ring between the alkyl chain and the ether group (not denaturing detergents such as SDS and ethyl trimethyl ammonium bromide). Examples of detergents that are suitable for use in the sensor binding buffer include, but are not limited to, Tween, Triton-X100, Nonidet P40, IGEPAL CA-630, Brij-35, Brij-58, and Triton X-114, and a combination thereof. The total concentration of the one or more detergents (by volume) in the sensor binding buffer can be in a range from about 0.01% to about 10%, from about 0.01% to about 5%, from about 0.05% to about 5%, from about 0.05% to about 2%, from about 0.05% to about 1%, or from about 0.1% to about 1%, such as about 0.05% or 1%. The total concentration of the one or more detergents (by weight) in the sensor binding buffer can be in a range from about 0.01% to about 10%, from about 0.01% to about 5%, from about 0.05% to about 5%, from about 0.05% to about 2%, from about 0.05% to about 1%, or from about 0.1% to about 1%, such as about 0.05% or 1%
The protease inhibitors in the sensor binding buffer can be inhibitors capable of inhibiting protease activity in a biological sample, such as in saliva. Examples of protease inhibitors that are suitable for use in the sensor binding buffer are commercially available, such as complete protease inhibitor cocktail from Sigma Aldrich and SigmaFast protease inhibitor tablets. The concentration of the protease inhibitors in the sensor binding buffer can follow the by the manufacture recommendations, or can be 2×, 3×, 4×, 5×, or 10× the concentration recommended by the manufacture, such as 4× the concentration recommended by the manufacture.
The sensor binding buffer optionally contains one or more antimicrobial agents and/or one or more blocking agents. The blocking agents that are suitable for use in the sensor binding buffer can be any of the blocking agents described above, such as BSA. The total concentration of the one or more blocking agents (by volume) in the sensor binding buffer can be in a range from about 0.01% to about 5%, from about 0.05% to about 5%, from about 0.05% to about 2%, from about 0.05% to about 1%, from about 0.1% to about 1%, or from about 0.1% to about 0.5%, such as about 0.1% or 0.5%. The total concentration of the one or more detergents (by weight) in the sensor binding buffer can be in a range from about 0.01% to about 5%, from about 0.05% to about 5%, from about 0.05% to about 2%, from about 0.05% to about 1%, from about 0.1% to about 1%, or from about 0.1% to about 0.5%, such as about 0.1% or 0.5%.
The antimicrobial agents in the sensor binding buffer can extend the shelf-life of the buffer solution by preventing microbial growth, such as sodium azide. The total concentration of the one or more antimicrobial agents (by volume) in the sensor binding buffer can be in a range from about 0.002% to about 0.2%, from about 0.005% to about 0.2%, from about 0.01% to about 0.2%, from about 0.01% to about 0.1%, or from about 0.01% to about 0.05%, such as about 0.02%. The total concentration of the one or more detergents (by weight) in the sensor binding buffer can be in a range from about 0.002% to about 0.2%, from about 0.005% to about 0.2%, from about 0.01% to about 0.2%, from about 0.01% to about 0.1%, or from about 0.01% to about 0.05%, such as about 0.02%.
In some embodiments, the sensor binding buffer is a non-lysis buffer containing a detergent that can keep the virus of interest intact. Such non-lysis buffers can contain one or more the above-described buffering agents, one or more the above-described salts, Tween, one or more the above-described protease inhibitors, and optionally one or more the above-described antimicrobial agents. Each of the components in the non-lysis buffers can have any of the concentration ranges described above for the respective component. For example, the non-lysis buffer contains HEPES at a concentration in a range from about 10 mM to about 50 mM, an above-described salt at a concentration in a range from about 100 mM to about 300 mM, Tween at a concentration in a range from about 0.01% to about 1% (by volume or weight), a protease inhibitor cocktail or tablet, and an above-described antimicrobial agent at a concentration in a range from about 0.01% to about 0.05% (by volume or weight). An exemplary non-lysis buffer contains 100 mM HEPES (pH 7.4), 150 mM NaCl, 0.05% vol/vol Tween-20, 0.02% wt/vol NaN3 and 4× complete, which can be used to dilute the biological sample to achieve any of the dilution factors described above, such as a 1:1 dilution in the buffer, prior to any one of steps (i)-(vi), particularly prior to step (vi).
In some embodiments, the sensor binding buffer is a lysis buffer that can dissolve the virus membrane in the biological sample, thereby inactivate the virus and dissolve the target protein from the virus membrane for detection. Such lysis buffers can contain one or more the above-described buffering agents, one or more the above-described salts, one or more detergent that can dissolve virus membrane and thus deactivate the virus, one or more the above-described protease inhibitors, one or more the above-described blocking agent, and optionally one or more the above-described antimicrobial agents. Examples of detergent that are suitable for use in the lysis buffers include, but are not limited to, Triton-X100, Nonidet P40, IGEPAL CA-630, Brij-35, Brij-58, and Triton X-114, and a combination thereof. Each of the components in the lysis buffers can have any of the concentration ranges as described above for the respective component. For example, the lysis buffer contains Tris or HEPES or phosphate salts at a concentration in a range from about 10 mM to about 100 mM, an above-described salt at a concentration in a range from about 200 mM to about 1 M, a virus-inactivating detergent as described above, such as Nonidet P40 or TritonX-100, at a concentration in a range from about 0.5% to about 2% (by volume or weight), an above-described protease inhibitor cocktail or tablet, an above-described blocking agent, such as BSA, at a concentration in a range from about 0.05% to 1% (by volume or weight), and optionally an above-described antimicrobial agent at a concentration in a range from about 0.01% to about 0.05% (by volume or weight). Optionally, the lysis buffer further includes an RNA digestive enzyme, such as an RNAse A enzyme, at a concentration in a range from about 1 mg/L to about 50 mg/L, from about 1 mg/L to about 20 mg/L, from about 2 mg/L to about 25 mg/L, from about 2 mg/L to about 20 mg/L, or from about 1 mg/L to about 10 mg/L, such as about 5 mg/L of the lysis buffer. Other examples of RNA digestive enzymes that are suitable for use in the lysis buffer include, but are not limited to, RNase H, RNase III, RNase L, RNase P, RNase PhyM, RNase T1, RNase T2, RNase U2, RNase V, RNase E, and RNase G, and a combination thereof. Specific examples of lysis buffer suitable for use in the disclosed method are as follows:
Lysis buffer A: 50 mM Tris pH 7.4, 250 mM NaCl, 1% Nonidet P40 (NP40), 0.02% NaN3, 0.5% BSA, and 4× protease inhibitor complete with EDTA;
Lysis buffer B: 20 mM HEPES pH 7.4, 500 mM NaCl, 1% TritonX-100, 0.02% NaN3, 0.1% BSA, and 4× protease inhibitor complete with EDTA; and
Lysis buffer B′: 20 mM HEPES pH 7.4, 500 mM NaCl, 1% TritonX-100, 0.02% NaN3, 0.1% BSA, 4× protease inhibitor complete with EDTA, and RNAse A enzyme added to a final concentration of 5 mg/L.
For example, the above-described exemplary method includes a step of diluting a biological sample, such as saliva, using a lysis buffer, such as Lysis buffer A, B, or B′ described above, to achieve any of the dilution factors described above, such as a 1:3 dilution in the lysis buffer, prior to any one of steps (i)-(vi), particularly prior to step (vi).
In some embodiments, methods using a lysis buffer, such as Lysis buffer A, B, or B′, particularly Lysis buffer B or B′, can reduce the noise level for measurements and thereby increase the sensitivity of the sensor, compared to methods using a sensor binding buffer that leaves the virus intact upon dilution, such as a buffer containing 100 mM HEPES (pH 7.4), 150 mM NaCl, 0.05% vol/vol Tween-20, 0.02% wt/vol NaN3 and 4× cOmplete.
The biological sample is incubated with the gate electrode for a time period sufficient to allow binding between the analytes in the biological sample and the biorecognition element (e.g. nanobody) modified on the gate electrode surface. Typically, the incubation time period is up to 60 minutes, up to 50 minutes, up to 40 minutes, up to 30 minutes, up to 20 minutes, or up to 10 minutes. For example, the biological sample is incubated with the gate electrode for about 10 minutes to allow binding between the analytes in the biological sample and the nanobody modified on the gate electrode surface. The incubation may be performed statically, under shaking, or with up and down pipetting, and in some embodiments, for about 3-5 minutes. In some preferred embodiments, the incubation is performed with pipetting to facilitate binding between the analytes in the biological sample and the biorecognition element (e.g. nanobody) modified on the gate electrode surface and thereby reduce the time needed for the incubation. When pipetting is performed during incubation, the biological sample is mixed up and down with a pipette for a time period in a range from 5 seconds to 1 minute, from 5 seconds to 50 seconds, from 5 seconds to 40 seconds, from 10 seconds to 1 minute, from 10 seconds to 50 seconds, from 10 seconds to 40 seconds, or from 20 seconds to 1 minute, such as about 30 seconds and the pipetting is repeated for at least one time or at least two times. For example, during a 10-minute incubation, the biological sample is mixed up and down with pipetting for about 30 seconds and the pipetting is performed for a total of 3 times (i.e. 3×30-second pipetting or a 30-second pipetting every 3 minutes during the 10-minute incubation period).
Following this incubation step (v), the gate electrode is rinsed with a rinsing buffer to remove any unbounded analytes, for example, it can be rinsed for up to 1 min, 30 secs, 15 secs etc., and in some embodiments, it is rinsed by dipping in (for about 15 secs) and out of the rinsing buffer, and repeating this, twice. The rinsed gate electrode is then brought back in contact with the electrolyte solution prior to step (vii) measuring a second ID. The rinsing buffer may be any electrolyte solution as described above, such as PBS.
Optionally, the above-described method includes a step of exposing the gate electrode surface to a glycine solution at a pH less than 5, less than 4, or less than 3, such as about 2, following step (vii). The acidic glycine solution can disrupt the binding between the analyte and the recognition element (e.g. the analyte/nanobody binding) and thus regenerate the OECT sensor for further sample measurements. For example, following the regeneration step, the ID generated from the OECT is comparable to the I0 (i.e. the difference between the ID obtained after regeneration and I0 is less than about 10%).
The exemplified methods can be used to make OECT devices containing a nanobody whose binding partner is any analyte of interest, for example an antigen from SAR-CoV-2, such as the spike protein. Specific nanobodies against SARS-CoV-2 Spike protein (S protein) or, more specifically, against the Receptor Binding Domain (RBD) within the S protein are available. Nanobodies are ultra-compact, robust single-chain antibody fragments engineered from camelid antibodies. Two nanobodies that were originally targeting SARS-1 RBD have very recently been shown to also recognize SARS-CoV-2 RBD with high affinity9. There are other nanobodies, engineered from a human antibody framework, that were specifically developed for SARS-CoV-2 Wu, et al., Fully human single-domain antibodies against SARS-CoV-2. bioRxiv 2020. The human ACE2 receptor protein, to which the virus binds with high affinity, can be used an alternative recognition module. The subject can be symptomatic or asymptomatic. In some embodiments, the subject has been exposed to the virus, however, the subject may have no known exposure to the virus.
Particular preferred embodiments of the device, methods of making and methods of using are exemplified below.
Sodium chloride, Tween-20, glycerol, HEPES, bovine serum albumin (BSA), (3-glycidyloxypropyl) trimethoxysilane (GOPS), sodium dodecylbenzenesulfonate (DBSA), ethylene glycol (EG), 1,6-hexanedithiol (HDT), 1,3-propanedithiol (PDT), 3-mercaptopropionic acid (MPA), human serum, and PBS (pH 7.4) were purchased from Sigma-Aldrich and used as received. Poly(3,4-ethylenedithiophene) doped with poly(styrene sulfonate), PEDOT:PSS, (PH1000) was received from Heraeus. All aqueous solutions were prepared with ultrapure water (Millipore Milli-Q). p(g0T2-g6T2) was synthesized according to a procedure reported previously35.
Protein purification materials: Agar, LB broth, 2× YT Broth, Kanamycin, Glucose, Isopropyl β-D-1-thiogalactopyranoside (IPTG), BugBuster (Novagen), complete Protease Inhibitor mix (Sigma), Benzonase (Novagen), Egg-Lysozyme (Fluka), Tris(2 carboxyethyl)phosphine (TCEP), Tris(hydroxymethyl)aminomethane hydrochloride (Tris-HCl), Imidazole, Glycerol, Dithiothreitol (DTT), Ethylenediaminetetraacetic acid (EDTA), D-Desthiobiotin, 10K Amicon ultra spin concentrators (Milipore).
Purification columns and SPR materials were purchased from GE Healthcare: HisTrap-HP 5 ml, StrepTrap-HP 5 ml, Superdex75 16/600, Biacore NTA SPR sensor chips (BR100034). Maleimide-SpyTag peptide (Genscript, peptide synthesis).
Viral target proteins were purchased from Sino Biological: SARS-CoV RBD (40150-V08B2), SARS-CoV-2 RBD (40592-V08H), SARS-CoV-2 S1 (40591-V08B1), MERS-CoV S1 (40069-V08H). Universal Transport Medium (UTM) Kit was purchased from Noble Biosciences, Inc.
OECTs were microfabricated on glass substrates based on established protocols using standard photolithography and Parylene-C peel-off techniques38,39. The process starts with the first layer of photoresist (AZ5214) spin coated and exposed to UV light using contact aligner to create Au electrodes and interconnection pads. The photoresist patterns were generated with AZ 726 MIF developer, followed with metal sputtering of 10 nm of Cr and 100 nm of Au and a standard lift-off process using hot DMSO. Next, the second layer of photoresist AZ9260 was coated on the substrates and developed using AZ developer. A parylene-C layer was deposited to insulate the gold interconnects. The OECT channel was patterned by reactive ion etching (RIE) and using a second layer of a Parylene C which was peeled-off to yield a length of 10 μm in and width of 100 μm. The aqueous dispersion of poly(3,4-ethylenedioxythiophene) doped with poly(styrene sulfonate) (PEDOT:PSS) containing EG (5 vol %), DBSA (0.25 vol %), and GOPS (1 wt %) was sonicated for 30 min and then spin coated (3000 rpm, 45 s) on the substrates leading to a film thickness of about 160 nm. The PEDOT:PSS OECTs were annealed at 140° C. for 1 h to activate GOPS and avoid dissolution of the polymer film in aqueous medium. P(g0T2-g6T2) films were spin coated (800 rpm, 45 s) from a chloroform solution (5 g/L) on the substrates to yield a film thickness of about 70 nm in the channel. All devices were rinsed with DI water before use.
For the fabrication of the gate electrode, 175 μm-thick Kapton (polyimide) substrates were used. The Kapton was first cut with a CO2 laser (Universal Laser Systems-PLS6.75) into a circular geometry that defined the sensor active area (the final diameter used in sensors is 0.8 μm); then the substrates were sonicated, first in isopropyl alcohol and then in deionized (DI) water for 30 min each. 10 μm of chromium or titanium was sputtered and 100 μm of Au on these cleaned substrates. Before the functionalization, the electrodes were electrochemically cleaned in 10 mM sulfuric acid (H2SO4) using cyclic voltammetry (CV). 10 CV cycles with a potential between −0.2 V to 1.2 V were applied at scan rate 100 mV s−1.
The chemical SAM solution was prepared in absolute ethanol containing 1 mM of HDT, as described by others40. The Au electrodes were immersed in this solution for one hour30. Electrodes were rinsed with absolute ethanol and dried under a N2 stream. Electrodes were then incubated for one hour with the synthetic Maleimide-modified SpyTag peptide (0.1 mg/mL) in PBS, and washed in PBS. Electrodes were then incubated for one hour with Nanobody-SpyCatcher fusion protein (anti-GFP, anti-SARS-CoV-1, or anti-MERS-CoV) diluted to 50 μM in sensor binding buffer (100 mM HEPES pH 7.4, 150 mM NaCl, 0.05% v/v Tween-20, 0.02% w/v NaN3, 0.1% w/v BSA) and then rinsed with PBS. Nanobody-functionalized gate electrodes were stored for up to one week at 4° C. in the sensor binding buffer until use.
XPS analysis was performed using a KRATOS Axis SUPRA instrument equipped with a monochromatic Al Kα X-ray source (1468.6 eV). The source was operated at 75 W under UHV condition (˜10−9 mbar). The spectra were recorded in a hybrid mode using electrostatic and magnetic lenses and an aperture slot of 300 by 700 μm. The survey and high-resolution spectra were acquired at fixed analyzer pass energies of 80 eV and 20 eV, respectively. The samples were mounted in a floating mode to avoid differential charging. The spectra were then acquired under charge neutralization conditions. The spectra was calibrated to reference of C 1s at 284.8 eV and deconvoluted it using Gaussian and Lorentzian methods. The Tougaard method was used for the background subtraction.
Quartz Crystal Microbalance with Dissipation Monitoring (QCM-D)
QCM-D measurements were conducted using a Q-sense analyzer (QE401, Biolin Scientific). The piezoelectrically active gold sensor (0.7854 cm2) was firstly modified with HDT SAM under the same reaction conditions and then mounted into the QCM-D setup. First, the QCM-D signals, including the change in frequency (Δf) and dissipation (ΔD) were stabilized in PBS. Second, the peptide solution (0.1 mg/mL SpyTag peptide in PBS) was injected into the chamber with a flow rate of 100 μL/min controlled by a peristaltic pump. After ensuring that the sensor was fully covered with the solution, the pump was stopped for an hour and rinsed the sensor surface with PBS injected to the system for 15 min. The same procedure was employed to treat the surface with SpyCatcher-linked nanobody solution (50 μM in the binding buffer). To quantify the mass accumulating on the sensor (Δm) during the functionalization steps, the Sauerbrey equation41 was used:
where n is the overtone number selected for the calculations and −17.7 is a constant calculated based on the resonant frequency, active area, density and shear modulus of the quartz crystal sensor. The mass of the binding molecules on the sensor surface was then estimated using their molecular weight. The (Sauerbrey) thickness (nm), ds, was calculated as:
where Δm is the change in mass (ng), A is the area (cm2) and r is the estimated density of the layer (g cm−3; assumed to be the same as water, which is taken as 1 g cm−3).
The electrochemical characteristics of the gold electrode were investigated before and after the formation of Chem-SAM and Bio-SAM using electrochemical impedance spectroscopy (EIS) and cyclic voltammetry (CV) performed in a three-electrode setup using a potentiostat (Autolab PGstat128N, MetroOhm). A platinum wire was used and an Ag/AgCl electrode as the counter electrode and reference electrodes, respectively, while the gold electrode was connected as the working electrode. All measurements were carried out in 5 mL of 10 mM PBS (pH 7.4) containing 10 mM of [Fe(CN)6]3−/4−. For CV measurements, the potential window was between −0.2 V and 0.5 V and the scan rate was 100 mV s−1. Electrochemical impedance spectra were recorded at a DC voltage of 0 V versus open circuit potential (Voc) and an AC modulation of 10 mV over a frequency range of 0.1-100000 Hz. For the analysis of GFP nanobody-functionalized electrodes, the electrodes were incubated with GFP solutions for 10 min and washed in 10 mM PBS before the measurements. The data was analyzed using Nova software.
Nanobody-SpyCatcher fusion proteins were designed based on available structures (nanobody: PDB 4PFE42; SpyCatcher: PDB 4MLI43) with the nanobody placed at the N-terminal end of the fusion protein in order to orient the common VHH target-binding interface towards the bulk solution, away from the sensing surface. Protein sequences were reverse-translated and codon-optimized for expression in E. coli with an in-house Python script based on DNAChisel44. Plasmids for protein expression were gene synthesized by Twist Bioscience (U.S.A.) or BioBasic (Canada) in a customized expression vector pJE411c with kanamycin resistance and modified with an RBS insulator (BCD2) cassette45 for improved translation initiation. Plasmids were transformed into E. coli BL21 (DE3) and starter cultures were inoculated overnight from a single colony. 1 L production cultures in 2× YT medium with 50 mg/L kanamycin and 1% glucose were inoculated 1:100, grown at 37° C. and 250 rpm to OD600 0.8, induced with 0.5 mM IPTG and incubated shaking for 18 h at 25° C. Cells were harvested by centrifugation for 10 min at 6,000 g at 4° C., washed once with cold PBS, resuspended in lysis buffer [25 mM Tris-HCl (pH 7.4), 500 mM NaCl, 10 mM Imidazole, 10% glycerol, SigmaFAST protease inhibitor, 25 U/ml Benzonase HC (Milipore), 2 mM DTT], and homogenized with a cell disruptor (Constant Systems, UK). Earlier purifications of mCherry, GFPnanobody and msfGFP used different lysis methods (chemical lysis with BugBuster (Novagen) for mCherry, sonication for the other two). Lysates were cleared by centrifugation at 87,000 g for 45 min, the supernatant filtered through Miracloth tissue (Milipore) and subjected to affinity chromatography on an Äkta FPLC (GE Healthcare) using either StrepTrap HP or HisTrap HP columns (GE Healthcare), depending on the purification tag. The Strep-tag binding buffer was 100 mM Tris-HCl (pH 8), 150 mM NaCl, 1 mM EDTA, 5% glycerol, 0.5 mM TCEP and elution was performed with 2.5 mM Desthiobiotin in binding buffer. The His-tag binding buffer was 25 mM Tris-HCl pH 7.4, 500 mM NaCl, 10 mM Imidazole, 10% Glycerol, 2 mM DTT and elution was performed with a four-step imidazole gradient up to 0.5M. Fractions were pooled and concentrated using 10K Amicon ultra (Milipore) followed by gel filtration on a Superdex75 16/600 column (GE Healthcare) into 20 mM HEPES pH 7.5, 300 mM NaCl, 10% Glycerol, 50 μM EDTA. After spin-concentration, aliquots were snap-frozen in liquid nitrogen and stored at −80° C. Protein purity and quality was monitored by SDS-PAGE as well as SEC-MALS on a Dawn Heleos II & OptiLab T-rEx (Wyatt, U.S.A.). Protein concentrations were determined on a Nanodrop spectrophotometer by absorbance at 280 nm using sequence-specific extinction coefficients47.
SARS-CoV-1/2 and MERS target proteins, expressed and purified from HEK293 or insect cell culture, were received lyophilized from Sino Biological (China) and dissolved to a standard concentration of 0.25 mg/ml as per manufacturer instructions, then aliquoted, snap-frozen in liquid nitrogen and stored at −80° C. N-terminally Maleimide-labelled SpyTag peptide was synthesized by GenScript Biotech (Singapore), received lyophilized, dissolved in PBS and stored at −20° C.
Target and non-target proteins were thawed on ice and centrifuged at 15.000 rpm at 4° C. for 30 to 45 min in order to remove any potential aggregates (although no aggregation was observed). Sino Biologicals proteins were then used as-is for the preparation of a dilution series starting at 320 or 640 nM. Equivalent dilutions of the Sino Biologicals storage buffer by itself did not give any sensor response. Weak background sensor signals were recorded from dilutions of DTT. In-house proteins were therefore stored or exchanged into DTT-free buffer before use. The higher-concentrated proteins from in-house production were first diluted to intermediate concentrations that could still be validated and corrected spectrophotometrically. Protein dilutions were prepared in standard sensor binding buffer (100 mM HEPES pH 7.4, 150 mM NaCl, 0.05% v/v Tween-20, 0.02% w/v NaN3, 0.1% w/v BSA) which was modified for saliva measurements to include complete protease inhibitor cocktail with EDTA (Sigma) at 4 times the manufacturer-recommended concentration (giving a two-fold concentration in the final 1:1 mixture with saliva). BSA was not included in this saliva buffer. For measurements in the regular binding buffer, 4-fold dilution series were prepared in 96-well microplates over 23 steps starting from 320 nM. For measurements in serum, saliva and UTM, target protein dilution series were prepared in the appropriate buffer (standard or saliva binding buffer) starting from 640 nM so that final concentrations were identical after 1:1 mixture with serum, saliva or UTM.
Surface plasmon resonance measurements were performed on a Biacore T200 instrument using Nickel-NTA sensor chips (GE Healthcare) and a modified running buffer (20 mM HEPES pH 7.4, 150 mM NaCl, 0.05% Tween-20, 0.02% w/v NaN3, 50 μM EDTA, prepared at room temperature and filtered) mirroring the sensor binding buffer. All analyte proteins were desalted into the running buffer (HiPrep 26/10 column, GE Healthcare) before the preparation of dilution series in the same running buffer. The GFP nanobody: GFP interaction was measured with the His10-tagged nanobody immobilized (ligand) and msfGFP in solution. For the remaining measurements, since all viral target proteins arrived with a non-cleavable His-tag, target proteins were immobilized instead of the nanobody. All ligand proteins gave stable immobilization responses with minimal signal loss over time. His tags were removed from nanobody-spyCatcher proteins by overnight cleavage with excess 3C protease (produced in-house), followed by gel filtration on a Superdex200 Increase 10/300 GL column. All ligand proteins were immobilized to equal loading levels of around 100 RU at 10 μl/min flow rates. Binding and unbinding experiments were run at a flow rate of 80 μl/min. Two replicates were prepared of each dilution series and measured in the course of the same experiment. Between each measurement cycle, the sensor surface was regenerated with 0.35 M EDTA in running buffer and re-charged with 0.5 mM NiSO4 in water. Biacore results were analyzed with the manufacturer analysis software version 2.1 following standard procedures (double-subtraction of reference channel and buffer injection signal) applying a 1:1 binding model and simultaneous curve-fitting. SARS-CoV-2 RBD results were instead fit a heterologous ligand binding model.
The GFP nanobody functionalized gold electrodes before and after its incubation with a GFP solution together with the negative controls (the biofunctional electrode before and after incubation with mCherry) were imaged using fluorescence microscopy. Imaging was performed on a DMI8 inverted fluorescence microscope (Leica Microsystems) coupled with a pE-4000 fluorescence illumination system (CoolLED), and the images were processed using ImageJ software. Electrodes were placed between two cover slips in the presence of PBS in order to keep the flexible material in plane and in focus. The presence or absence of BSA was studied by adding fluorescently labeled BSA (albumin-fluorescein isothiocyanate conjugated bovine protein) to the nanobody-SpyCatcher solution during functionalization of the sensing surface. The capture of GFP was examined by imaging already functionalized gold electrodes before and after incubation with GFP or control solutions. Pictures were recorded on a fluorescent inverted microscope DMI8 (Leica Microsystem) coupled with pE-4000 fluorescence illumination system (CoolLED).
A Keithley source meter was used to apply drain (VD) and gate voltages (VG) and obtain gate and channel currents (IG and ID) in ambient conditions. A PDMS well was glued on top of the channels and filled with 75 μL of 10 mM PBS. The steady-state transistor characteristics were obtained by measuring ID vs. VD at various VG, for PEDOT:PSS applied between −0.6 V to 0.6 V with 0.1 V step (2.5 V/s) and for p(g0T2-g6T2) from 0.2 V to −0.6 V with 0.05 V step (1.25 V/s). VD was swept from 0 V to −0.6 V. A channel was first chosen and obtained its transfer curve (ID vs. VG) in PBS using the nanobody-functionalized gate electrode incubated for 10 min in the buffer solution (buffer, saliva, UTM or serum, in the absence of target proteins). The currents obtained were used as the baseline signal (ID).
The same gate electrode was then incubated with 5 μL of the solution (buffer, saliva, UTM or serum) that contains the protein target for 10 min (pipetting 30 s every 3 min). The electrode was washed thoroughly with PBS to remove any unbound proteins. To obtain calibration curves, various concentrations of the target protein were prepared and collected device data starting from the most diluted one. The normalized response (NR) of the sensor was calculated according to the following equation:
where ID is the current response of the sensor to an analyte solution that the gate was exposed to.
According to IUPAC, the LOD was calculated as the concentration leading to a response that equals to the average of the noise level plus three times the noise standard deviation14,46. The level-of-noise
was taken from the relative current variation in negative control sensors.
where
is the average response of the blank sample, δ is the relative standard deviation, a and b are the intercept and slope of the calibration curve, respectively.
The clinical samples (saliva samples and nasopharyngeal swabs) used in this study (
Additional lysis buffers were prepared having the following components. Lysis buffer B: 20 mM HEPES pH 7.4; 500 mM NaCl; 1% TritonX-100; 0.02% NaN3; 0.1% BSA; 4× protease inhibitor complete with EDTA. Lysis buffer B′ was prepared with the same components as Lysis buffer B, however, RNAse A enzyme added to final concentration of 5 mg/L.
Sensor protein modules are described in Tables 1 and 2
SGSG
AHIVMVDAYKPTK (SEQ ID NO: 1)
There are hardly any reports of label-free OECT immunosensors18. Presumably, the large size of regular antibodies and lack of control over their immobilization density or orientation has impeded progress in this area19.
Therefore, the present studies devised an alternative functionalization strategy that relies on the self-assembling binding partners, exemplified herein by SpyTag/SpyCatcher system20, to covalently capture chemically unmodified recombinant proteins in a defined orientation at very high physical density on the sensing electrode. The protein design disclosed herein maximizes the molecular flexibility of these nanobodies in order to create an extended recognition layer that can capture and kinetically trap antigens at ultra-low concentrations on a disposable gate electrode. The sensor performance was further enhanced by optimizing the transistor geometry and the biochemical blocking and incubation strategies. Last but not least, a novel organic semiconductor was used which improved signal strength and stability and reduced the power requirements as compared to the classic OECT channel material, poly(3,4-ethylenedioxythiophene) doped with poly(styrene sulfonate) (PEDOT:PSS). The development of this platform (
Nanobodies (and modified versions thereof) can be efficiently expressed in Escherichia coli. A recombinant protein was designed where the well-characterized anti-GFP nanobody26 is fused, through a flexible peptide linker, to a SpyCatcher domain. The SpyCatcher domain is specifically recognized by a short SpyTag peptide, triggering the autocatalytic formation of a covalent isopeptide bond of very high stability between both of them. Originally engineered from a bacterial adhesion protein20, the SpyTag/SpyCatcher protein conjugation system has been used for several applications27, but not yet for FET nor OECT biosensors. The only related application of a nanobody-SpyTag fusion was a passive, impedance-based sensor for the detection of microalgae28 which relied on the chemical immobilization of separate SpyCatcher proteins as a capture reagent.
The disclosed design instead wanted to avoid any steps where any protein (neither nanobody nor SpyCatcher domain) is chemically modified or immobilized in a way that could partially impair its function. Instead, the design opted for the immobilization of chemically modified SpyTag, obtained through regular commercial peptide synthesis, on a 1,6-hexanedithiol (HDT) self-assembling monolayer (SAM), thus forming a combined Chem-SAM on top of the gold gate electrode. The anti-GFP nanobody26-SpyCatcher fusion protein was genetically encoded, gene synthesized and produced in E. coli. The purified protein was then incubated under physiological conditions with the Chem-SAM, thus completing the sensing surface with a self-assembled Bio-SAM. This strategy leads to a defined biofunctionalization layer in a controllable molecular configuration and orientation, which can be modelled at atomic resolution (
All three immobilization steps (HDT, SpyTag, and nanobody-SpyCatcher) were monitored through X-ray photoelectron spectroscopy (XPS), quartz crystal microbalance with dissipation (QCM-D), cyclic voltammetry (CV), and electrochemical impedance spectroscopy (EIS). Upon functionalization with the HDT layer, the gold electrode displayed characteristic thiol-gold (S—Au) and free thiol (—SH) peaks in its high-resolution S 2p XPS spectrum, indicating the upright orientation of HDT linked to gold through only one of the two-SH moieties (with the other terminal is vertical to, and pointing away from the surface) (
The peaks at 161.4 and 162.6 eV stem from the sulfur chemisorbed on the gold surface through a thiolate bond (Au—S)1,2. The resolution of these peaks indicates the high-quality HDT formed on the surface. The signal at 162.8 and 164 eV, on the other hand, corresponds to the free thiol group (terminal R—SH), suggesting two types of sulfur species present in the monolayer; thiolate-type sulfur (Au—SR) and tail thiol sulfur (R—SH). These results suggest that the HIDT molecules are in a standing-up configuration with an upright molecular structure. They are bound to gold via the thiolate link using one of their thiol groups, while the other thiol group is free and located at the SAM-air interface. If the HDT molecules were present exclusively in a lying-down configuration, we would be only detecting thiolate components, as all S atoms would be thiolate linked to the gold surface. As we introduced the SpyTag peptide and nanobody-SpyCatcher on this surface, a new peak appeared at ca. 163.2 eV, originating from the Sulphur in methionine.
In the high-resolution of C Is, the C—C peak of the HDT-functionalized gold was detected, attributed to the six-carbon chain of the HDT molecule. The C—O, C—N and C—OOR peaks originate from the amino acids in SpyTag peptide and the nanobody-SpyCatcher. The N 1s spectra show that nitrogen groups appear on the gold surface upon the introduction of the Bio-SAM proteins. Formation of all layers was further corroborated by electrochemical impedance spectroscopy (EIS) and cyclic voltammetry measurements, which showed a decrease in the electrochemical capacitance of the gold electrode and an increase in its charge transfer resistance with the addition of (insulating) Chem-SAM and Bio-SAM (
The gold electrode exhibits the well-known reversible peaks for the [Fe(CN)6]3−/4− redox couple with a peak potential separation of approximately 180 mV (
To assess the packing density of biomolecules on the surface, the immobilization of (i) the maleimide-modified SpyTag peptide and, (ii) the nanobody-SpyCatcher fusion protein on the Chem-SAM was monitored by QCM-D. The mass gained from the two conjugates was quantified to be 114 and 406 ng cm−2, respectively (
Based on molecular weights of 1.76 kDa and 28.4 kDa for the SpyTag peptide and nanobody-SpyCatcher protein, respectively, 39×1012 SpyTag peptides and 8.6×1012 nanobody-SpyCatcher molecules were coupled per cm2. This density translates to mean inter-particle distance of only 3.4 nm between the SpyCatcher domains at the base of the Bio-SAM. Given the size of this domain (about 4×2.5 nm), it is thus approaching the maximum coupling density that is physically feasible. The formation of this exceptionally high-density biorecognition layer is further facilitated by the compact nanobody, which has similar dimensions to the SpyCatcher domain but is given additional freedom to pack and reposition itself through the flexible inter-domain linker (
Operating as a very sensitive balance, QCM-D can quantitatively monitor the real-time changes in the mass of the Au electrode upon each biofunctionalization step, i.e., the SpyTag coupling followed by the nanobody-SpyCatcher capture.7 When mass (e.g. peptide, nanobody, BSA) is accumulated on the gold sensor, a decrease in its oscillation frequency is observed. As shown in
Detection of GFP with the anti-GFP nanobody-conjugated gate electrode was used as a model to ascertain multiple parameters of the sensor design. The biofunctionalized gate electrode was incubated with increasing GFP concentrations and then stacked vertically on top of the channel separated by PBS (phosphate-buffered saline, pH 7.4, ionic strength 0.162 M) to complete the OECT biosensor (
The optimized poly(3,4-ethylenedioxythiophene) doped with poly(styrene sulfonate) (PEDOT:PSS) OECTs were operated in PBS under ambient conditions by varying the gate voltage (VG) between-0.6 V and 0.6 V while the drain voltage (VD) was swept from 0 to −0.6 V. The sensing signal was assessed by monitoring the drain current (ID) as a function of the VG at a fixed VD=−0.6 V. The reference (blank) response of the sensor was acquired by exposing the nanobody-functionalized gate electrode to the binding buffer without GFP (PBS) (
The trend in ID and gm can be clearly attributed to the specific binding of GFP to the nanobody-functionalized gate electrode. Fluorescence images confirmed the specific capture of GFP, but not mCherry (data not shown). As GFP is bound to the nanobody functionalized Au electrode, the film, which is originally nonfluorescent at the chosen wavelength emits green fluorescence. As the electrode is incubated in the mCherry solution, only a few spots on the edge of the sensor show red fluorescence. This signal is caused by the mCherry which can be non-specifically absorbed, mostly on the rough or damaged edges of the surface resulting from the laser cutting process (data not shown). The GFP-nanobody interaction increases the impedance at the gate/electrolyte interface (
The capacitance of the gate electrode is affected by the molecular binding events, i.e., upon generation of a non-conducting/dielectric layer. Our impedance data suggest that binding events cause the gate capacitance to decrease (Cg→Cg, off). In the OECT, we consider two double layer capacitancesformed at the channel and gate electrode interfaces, connected in series 13. The applied gate voltage isdistributed at these two interfaces, depending on the magnitude of the capacitance at each surface. The fractional voltage drop at the gate electrode is described by the following set of equations:
where, UCh is the voltage drop at the channel surface, j is the complex number, ω is the angular frequency, CCh is the channel capacitance, Cg is the gate capacitance and Rsol, is the solution resistance. For the DC regime, the equation 4.1 can be simplified to:
The corresponding fractional voltage drop at the gate electrode can be expressed as:
As proteins bind to the gate electrode, Cg decreases. A lower C! leads to a larger proportion of the applied gate voltage to drop at the gate/electrolyte interface. The binding between the nanobody and the protein at the gate electrode therefore results in a less efficient transistor operation, where all the gate voltage should ideally drop at the channel/electrolyte interface.
Hence, a reduction in the current and its modulation was measured as GFP-binding weakens the electrical driving force acting on the cations. The decrease in ID is not due to a degradation of the channel over consecutive I-V cycles (
To quantify the sensor response and to minimize device-to-device variations, the normalized response (NR) of the OECT was calculated by normalizing the target protein-induced change in ID at a single VD and VG, to its value previously measured after exposure to blank solution. The normalized response (NR) vs. GFP calibration curve revealed that the nanobody-functionalized OECT detects GFP with a lowest limit of detection (LOD) of 23 fM (
Sensing with Accumulation Mode OECTs
OECTs can be constructed for either depletion- or accumulation-mode operation. The channel often used is PEDOT:PSS, which is intrinsically doped and thus operates in depletion mode, that is, ID decreases with an increase of VG.
Application of a positive gate voltage VG injects cations into the channel, which compensate for the depleted holes and switch the transistor off. For continuous and long-term use, the depletion-mode operation may negatively affect material stability and power consumption as it implies high operating currents and relatively high VG to run the device. Recent studies expanded the available OECT channel materials through the chemical design of undoped, conjugated backbones which were functionalized with hydrophilic side chains that facilitate ion injection and transport in the film16,34. OECTs made using these materials operate in accumulation mode, that is, the channel is initially OFF and generates a current only upon application of a small gate voltage15. This operation mode allows for low power electronics applications, improves device stability, and is more compatible with integrated circuit designs that conventionally involve accumulation mode transistors. Nevertheless, accumulation mode OECTs for biochemical sensing have not yet been reported. PEDOT:PSS was therefore replaced with a novel conjugated polymer, p(g0T2-g6T2)35.
p(g0T2-g6T2) is a mixed (ionic and electronic) conductor. A negative VG pushes anions into the film that compensate for the holes injected from the metal contacts, turning the device ON (
The maximum gm (15 mS) occurs at a VG of ca. −0.3 V (
From a biochemical point of view, the observation of binding at such low concentrations was initially surprising. The 14 aM detection limit lies 30 million-fold below the consensus equilibrium dissociation constant (KD˜0.5 nM) reported for the interaction between nanobody and GFP37. Previous sutues using electrolyte gated organic FET recognizing IgG attributed single-molecule detection to a combination of: (1) the 1000-fold amplification of input to output signal provided by the transistor; and (2) the perturbation of a tight hydrogen-bonding network in their chem-SAM, which was suggested to propagate as a defect over larger areas of the electrode. In contrast, the sensor disclosed herein does not have a hydrogen-bonding network in or near the chem-SAM. However, the OECTs developed in this work have higher gains (the gm is on the order of mS rather than μS of typical electrolyte-gated organic FETs), permitting the amplification of input signals by a factor of one million. Indeed, without the amplification endowed by the OECT circuitry, gate capacitance changes cannot be resolved at such low concentrations (
At (local) equilibrium, analyte binding can be described by the simple mass action law:
KD is the dissociation constant and [A], [R], [AR] denote the respective concentrations. Replacing [A]=[A0]−[RA], the fraction of bound analyte at a certain free receptor concentration is obtained:
As long as the local free receptor concentration [R]>>K−, we can therefore assume ˜100% binding of analyte molecules entering the capture area on top of the sensor surface. The inverse question can also be asked: At which free analyte concentration [A] will the very first receptor capture a single analyte molecule: Starting point is the Langmuir adsorption model
Y is now the fraction of the receptor bound to analyte. Instead of as concentration, AR is expressed as a number or density on the surface. For one out of 55 billion receptors bound Y=1/R0 and it follows:
Assuming KD=0.5×10−9 M (for the GFP nanobody) and 5.5×1010 binding sites, we obtain the analyte concentration limit of 9×10−20 mol/L or 9 zM. For the binding of SARS-CoV-2 spike protein the dissociation constant is higher (weaker affinity) KD=2.3×10−8 M leading to a limit of analyte concentration of 418 zM or 0.4 aM. Note that this is only an upper (less favorable) boundary for detection limits for an infinite incubation time. In reality, the larger binding volume cannot reach equilibrium in reasonable time scales and unbinding is very unlikely. Binding is kinetically driven by the molecular on-rate near the surface and is dominated by diffusion under mass transport limitation in the larger measurement volume. Equation 5.5 does however more readily apply to unspecific binders (i.e., contaminants) which have much weaker affinity (higher KDs with very fast koff rates). Binding of contaminants can therefore be eliminated through washing steps that ensure their sufficient dilution into a larger washing volume.
Once bound, the interaction's low koff rate37 (˜1.5×104 s−1 corresponding to 80 min half-life) will trap the target molecule throughout all washing steps. In fact, our surface plasmon resonance (SPR) measurements indicate an even lower, essentially unmeasurable, off rate for this complex with our own protein and buffer conditions (
VHH72-SpyCatcher fusion construct expressed well in E. coli and could be purified to a high yield (54 mg 1-1 culture) as a monomeric protein. Although SARS-CoV-2 was the initial diagnostic target, constructs for the detection of MERS-CoV based on the previously reported nanobodies VHH83, VHH04 (Raj, et al., Sci. Adv. 4, eaas9667 (2018)) and VHH55 (Wrapp, et al. Cell 181, 1004-1015.e15 (2020)) were also designed and expressed. The VHH04-SpyCatcher fusion yielded high-quality monomeric protein and was advanced to OECT experiments. Both VHH72 and VHH04 bind to the RBD of the homotrimeric (SARS or MERS, respectively) coronavirus spike protein.
SARS-CoV nanobody functionalized OECTs showed an excellent response to SARS-CoV-2 receptor binding domain (RBD) and SARS-CoV-2 S1, regardless of the channel material used (
Having confirmed that the SARS-CoV-1 nanobody-functionalized OECTs are sensitive and specific to SARS-2 proteins in the buffer, the focus shifted to the requirements of point-of-care applications. Considering the ease of collection, the minimum patient discomfort during sample collection and the presence of the virus therein, human saliva samples were chosen as the preferred specimen medium. Human saliva samples were collected and mixed with predetermined amounts of target and non-target proteins to characterize the sensing ability of SARS-CoV-1 nanobody-functionalized OECTs comprising p(g0T2-g6T2) channels. The NR increased with the concentration of SARS-CoV-2 proteins in saliva and showed only a negligible change when the same gate electrode was exposed to GFP at the same concentration range (
The gate electrode was then exposed to saliva solutions that contained random concentrations of SARS-CoV-2 S1 to evaluate the performance of the sensor in an environment closer to actual screening conditions. The NR values varied according to the protein content in saliva and corresponded to the values obtained in dose curves (
Our findings thus demonstrate the sensitivity and selectivity of nanobody-OECTs in complex biological media and at physiologically and clinically relevant protein concentrations. A comparison of our OECT sensor performance with other similar thin-film transistor-based devices developed for immunosensing indicates the superiority of this sensor technology (for example, in terms of dynamic range, power consumption, miniaturization and compatibility with unprocessed human samples; Table 4).
OECTs also compare favorably to optical methods for single-molecule detection, such as flow-based immuonassays, and plasmonic nanosensors: Targets are not limited by size, and the lack of labeling allows for very short sample preparation and device operation times.
Finally, the sensors were validated using human patient nasopharyngeal swabs and saliva. The swabs were stored in a universal transport medium (UTM) whereas saliva was collected and kept without an additional buffer. The calibration curves obtained for SARS-CoV-2 S1 protein in UTM using anti-SARS-CoV-1 and anti-GFP gates confirm that sensor operation is maintained in this medium (LOD for SARS-CoV-2 S1 in UTM was 1.9×10−14 M) (
The control measurements were performed using multiple anti-GFP gate electrodes and the results were verified independently by RT-PCR on the same samples. In a second validation, saliva was collected from six healthy volunteers and seven volunteers who had recently been confirmed as COVID-19 positive. Each sample was diluted fourfold in a modified, virus-inactivating lysis buffer (lysis buffer A) and subjected to three independent measurements. Positive samples were additionally measured with one GFP nanobody gate electrode each. Quantitative PCR with reverse transcription (RT-qPCR) on each sample (calibrated against N-gene complementary DNA) confirmed the six negatives and revealed a wide range of viral loads from 2,700 to 1.8×1012 copies per ml for the others (
In direct comparison of lysis buffers used with saliva samples, buffer B′ performed better than buffer A in experiments performed on two fresh saliva samples from two SARS-CoV-2 positive patients. This buffer is a lysis buffer as well but uses a different detergent. It also has increased salt concentration. Moreover, RNAse A enzyme was added to reduce viscosity that may arise from viral RNA in the sample. The results are shown in
A modular nanobody was developed and optimized-OECT architecture that allows the detection of very low antigen concentrations in 10 min with a sample volume of ≤5 μL and close to single-molecule sensitivity. Autocatalytic immobilization with the SpyTag/SpyCatcher coupling strategy is here shown to be a robust method for conjugating recombinant proteins on biosensor surfaces with very high packing density, full control over molecular orientation and no need for chemical activation or modification of the protein. This work is the first demonstration of a nanobody-functionalized OECT sensor for fast detection of target antigens. Rapid detection of various analytes at close to single-molecule concentrations in buffer, serum and saliva were achieved, respectively. The OECT sensors are thus capable of detecting protein antigens with high sensitivity and selectivity but negligible non-specific binding in complex biological media. The platform is highly modular and can be adapted for the detection of any target analyte for which a specific nanobody is available.
This application is a National Phase application under 35 U.S.C. 371 of PCT/IB2021/055981, filed Jul. 2, 2021, which claims the benefit of and priority to U.S. Provisional Application No. 63/047,547 filed Jul. 2, 2020 and U.S. Provisional Application No. 63/106,218 filed Oct. 27, 2020, which are hereby incorporated herein by reference in their entirety.
| Filing Document | Filing Date | Country | Kind |
|---|---|---|---|
| PCT/IB2021/055981 | 7/2/2021 | WO |
| Number | Date | Country | |
|---|---|---|---|
| 63047547 | Jul 2020 | US | |
| 63106218 | Oct 2020 | US |
