Patent Description:
The ability to detect proteins, carbohydrates, nucleic acids, small molecules and other compounds from tissue biopsies or non-invasively (e.g., from blood and urine) is becoming more and more important, particularly those recognized as biomarkers for cancers and other diseases. These biomarkers can be tracked over time in individuals in an attempt to diagnose diseases at early stages, compared in different tissues, individuals or populations, and examined before, during and after treatments. <CIT>, described a novel method to detect compounds (analytes) utilizing antibodies or other protein-binding molecules and nanopore-detectable tags. The use of nanopores, coupled with ionic current readout, provides a single molecule electronic detection solution, offering unique opportunities for multiplexing and quantitation. The latter is more sensitive than current immunological methods, including ELISAs (enzyme linked immunosorbent assays), RIAs (radioimmunoassays) and protein arrays, and less expensive than methods with mass spectrometric (MS) readout (direct application of samples to MS or tandem MS, or carrying out MS after initial <NUM>-D gel separation, ICAT or other procedures). In addition to the use of antibodies to detect and quantify antigenic compounds, the approach can also be adapted to identify ligand-receptor and other protein-protein interactions, as well as a variety of other molecular interactions. Thus, for instance, the system would have the flexibility to monitor both DNA and protein or other biomarkers at the same time.

The focus in <CIT> is, in part, on attaching nanopore-detectable tags to specific analytes (antigens or other molecules) using a variety of approaches. The overall approach was described as follows: (<NUM>) capture antibodies, affibodies or other antibody mimetics, aptamers or ligands specific for a particular analyte (compound) are bound to (or very near) individual membrane-embedded nanopores in a nanopore array; (<NUM>) the tagged compounds are flowed over the nanopore array in an electrolyte solution and bind to the specific antibodies; and (<NUM>) after applying a voltage across the membranes, current recordings are taken, allowing identification of the compound associated with a well containing a specific nanopore. Tags are attached via cleavable linkers in some embodiments. Different tags attached to different compounds will elicit different current blockades, allowing determination of multiple compounds on the same nanopore array at single molecule level. With sufficient numbers of nanopores, quantitative or semi-quantitative results can be obtained. (See <CIT>, which describes the principle of this method).

<CIT> describes apparatuses and methods for analyzing the presence of a target analyte.

Publication "Stochastic Sensing of Proteins with Receptor-Modified Solid-State Nanopores" describes the stochastic sensing of proteins with metallized silicon nitride nanopores, which are chemically modified with nitrilotriacetic acid (NTA) receptors embedded in an otherwise protein-repellant self-assembled monolayer. (Roushan Wei et al.

<CIT> and <CIT> describe systems and methods for sequencing nucleic acids using nucleotide analogues and translocation of tags from incorporated nucleotide analogues through a nanopore.

<CIT> describes a method of determining the presence, absence or characteristics of an analyte.

This application comprises several new embodiments using the single molecule electronic nanopore platform to detect biomarkers, other biological molecules, antigens, antibodies, and a variety of molecular interactions. Several examples involve the use of a tagged second antibody (detection antibody) that can bind to a different site on the same analyte as the initial capture antibody, or to a binding partner of the original molecule attracted by the capture antibody.

The invention provides a method for detecting the presence of a compound of interest in a sample, which comprises:.

thereby detecting the presence of the compound of interest.

The invention encompasses a method of detecting the presence of a compound of interest in a sample, which comprises:.

The invention encompasses a method for determining the presence and/or relative quantities of a plurality of different compounds of interest in a sample, which comprises:.

thereby determining the presence and/or relative quantities of the plurality of different compounds of interest in the sample.

The invention provides a method for determining a molecular interaction of a biological molecule comprising:.

In an embodiment of the invention, step c) occurs prior to step a).

In an embodiment of the invention, step d) occurs prior to step c).

In an embodiment of the invention, step b) occurs prior to step a).

In an embodiment of the invention, step c) occurs before step a). In an embodiment of the invention, step d) occurs before step c). In an embodiment of the invention, step b) occurs before step a).

In an embodiment of the invention, step b) occurs before step a).

In an embodiment of the invention, the tag attached to the capture compounds is cleaved after step d).

In the invention, the capture compound or multiple copies of said capture compound is attached to the nanopore. In an embodiment of the invention, the capture compound is an antibody. In an embodiment of the invention, the capture compound is an antibody mimetic. In an embodiment of the invention, the antibody mimetic is one of an affibody, avibody, affimer, nanoclamp, a pharmaceutical agent, or a small organic molecule.

In an embodiment of the invention, the tagged compound is an antibody. In an embodiment of the invention, the tagged compound is an antibody mimetic. In an embodiment of the invention, the antibody mimetic is one of an affibody, avibody, affimer, nanoclamp, a pharmaceutical agent, or a small organic molecule.

In an embodiment of the invention, the compound or compounds of interest is an antigen. In an embodiment of the invention, the antigen is one of a biomarker, protein, lipid, carbohydrate, DNA, a glycoprotein, a lipoprotein, virus particle, or other composite molecule.

thereby detecting the molecular interaction of a biological molecule.

In an embodiment of the invention, the step b) occurs before step a).

In an embodiment of the invention, the biological molecule or is attached to the nanopore via a flexible linker.

In an embodiment of the invention, the tag is attached to the tagged compound via a cleavable linker, and the tag is cleaved from the tagged compound after step d).

In an embodiment of the invention, the biological molecule is one of a biomarker, protein, lipid, carbohydrate, DNA, a glycoprotein, a lipoprotein, virus particle, or other composite molecule.

In an embodiment of the invention, the putative interacting molecule is one of a biomarker, protein, lipid, carbohydrate, DNA, glycoprotein, a lipoprotein, a virus particle [or other composite molecule.

In an embodiment of the invention, the tagged compound is one of a biomarker, protein, lipid, carbohydrate, DNA, a glycoprotein, a lipoprotein, a virus particle or other composite molecule.

In an embodiment of the methods described herein, the tag or tags comprises a polymeric molecule. In an embodiment of the invention, the polymeric molecule is a polymer comprising one or more of PEG, alkane, peptide, polypeptide, a polynucleotide, or any combination thereof. In an embodiment of the invention, the tag further comprises a modification expanding or reducing the diameter of the tag within the nanopore. In an embodiment of the invention, the tag further comprises a modification that changes the charge of the tag. In an embodiment of the invention, the tag comprises one or more of dSP, C3, Cn, PEG, pyrrolidine, spermine, spermidine, nitro pyrrole, nitro indole, nebulazine, benzimidazole, benzene, <NUM>-deazapurine, <NUM>-substituted pysrimidine, fluorescein-dT, fluorescein, rhodamine, ROX, cyanine dye, or any combination thereof.

In an embodiment of the methods described herein, the nanopore is a solid state nanopore, wherein step b) occurs before step a) or wherein step b) is omitted. In an embodiment of the methods described herein, the nanopore is a solid state nanopore, in which case the capture compound is attached to the nanopore in the first step. In an embodiment of the invention, the electrically resistive barrier comprises graphene, molybdenum disulfide, or silicon nitride.

In an embodiment of the methods described herein, the nanopore comprises a biological nanopore. In an embodiment of the invention, the nanopore is α-hemolysin. In an embodiment of the invention, the nanopore is α-hemolysin, MspA, or OmpG, or FraC, or Aerolysin, or other transmembrane pore complex of beta-barrel class, or transmembrane pore complex of other class. In an embodiment of the invention, the electrically resistive barrier is a lipid bilayer.

In an embodiment of the invention, the nanopore is a hybrid protein-solid state nanopore.

In an embodiment of the invention, the nanopore comprises an integrated electronic sensor.

As used herein, and unless stated otherwise, each of the following terms shall have the definition set forth below.

"Antibody" shall include, without limitation, (a) an immunoglobulin molecule comprising two heavy chains and two light chains and which recognizes an antigen; (b) a polyclonal or monoclonal immunoglobulin molecule; and (c) a monovalent or divalent fragment thereof. Immunoglobulin molecules may derive from any of the commonly known classes, including but not limited to IgA, secretory IgA, IgG, IgE and IgM. IgG subclasses are well known to those in the art and include, but are not limited to, human IgG1, IgG2, IgG3 and IgG4. Antibodies can be both naturally occurring and non-naturally occurring. Furthermore, antibodies include chimeric antibodies, wholly synthetic antibodies, single chain antibodies, and fragments thereof. Antibodies may be human or nonhuman. Antibody fragments include, without limitation, Fab fragments, Fv fragments and other antigen-binding fragments.

"Nanopore" includes, for example, a structure comprising (a) a first and a second compartment separated by a physical barrier, which barrier has at least one pore with a diameter, for example, of from about <NUM> to <NUM>, and (b) a means for applying an electric field across the barrier so that a charged molecule such as DNA, nucleotide, nucleotide analogue, or tag, can pass from the first compartment through the pore to the second compartment. The nanopore ideally further comprises a means for measuring the electronic signature of a molecule passing through its barrier. The nanopore barrier may be synthetic or naturally occurring in part. Barriers can include, for example, lipid bilayers having therein α-hemolysin, oligomeric protein channels such as porins, and synthetic peptides and the like. Barriers can also include inorganic plates having one or more holes of a suitable size. Herein "nanopore", "nanopore barrier" and the "pore" in the nanopore barrier are sometimes used equivalently. It is understood that the electric field of a nanopore may be adjustable. It is also understood that a charged molecule such as DNA, nucleotide, nucleotide analogue, or tag, does not need to pass from the first compartment through the pore to the second compartment in order to produce an electronic signature. Such electronic signature may be produced by localization of the molecule within the pore.

Nanopore devices are known in the art and nanopores and methods employing them are disclosed in <CIT>; <CIT>; <CIT>; <CIT>; <CIT>; <CIT>; <CIT>; <CIT>; <CIT>; <CIT>; <CIT>; and <CIT>, <CIT>, and <CIT>.

"Blockade signature" of a molecule passing through a pore via application of an electronic field (e.g., applied voltage) shall include, for example, the duration of the molecular tag's passage through the pore together with the observed amplitude of current during that passage. Blockade signature for a molecule is envisioned and can be, for example, a plot of current (e.g. pA) versus time for the molecule to pass through the pore via application of an electric field. Alternatively, blockade signature is also determinable for a molecule which does not pass through a pore. Blockade signature of such a molecule is also envisioned and can be, for example, a plot of current (e.g. pA) versus time for the molecule to enter into or pass adjacent to the pore. Herein "blockade signature", "blockade signal", and "electronic signature" are sometimes used equivalently. Herein, "voltage" and "electronic field" are sometimes used equivalently.

A specific event diagram is constructed which is the plot of translocation time versus blockade current. This specific event diagram (also referred to as an blockade signature) is used to distinguish molecules by single-channel recording techniques based on characteristic parameters such as translocation current, translocation duration, and their corresponding dispersions in the diagram.

As used herein, a "tag" or a "tag moiety" is any chemical group or molecule that is capable of producing a unique blockade signature detectable with a nanopore. In some cases, a tag comprises one or more of ethylene glycol, an amino acid, a carbohydrate, a peptide, a dye, a fluorescent compound, a chemiluminiscent compound, a mononucleotide, a dinucleotide, a trinucleotide, a tetranucleotide, a pentanucleotide, a hexanucleotide, a polynucleotide, a nucleotide monophosphate, a nucleotide diphosphate, a nucleotide polyphosphate, an aliphatic acid, an aromatic acid, an unsubstituted alcohol or thiol, an alcohol or a thiol substituted with one or more halogens, a cyano group, a nitro group, an alkyl group, an alkenyl group, an alkynyl group, an azido group, or a combination thereof.

As used herein, unless otherwise specified, a tag moiety which is different or distinguishable from the tag moiety of a referenced molecule means that the tag moiety has a different chemical structure from the chemical structure of the other/referenced tag moiety. That a tag moiety is different or distinguishable from the tag moiety of a referenced molecule could also mean that the tag moiety has a different blockade signature from the blockade signature of the other/referenced tag moiety.

As used herein, a tag which "localizes" within a pore is a tag located inside or adjacent to the pore. A tag which localizes within a pore does not necessarily pass through or translocate the pore.

As used herein, "proteinaceous" compound means any biopolymer formed from amino acids, such as peptides, proteins, antibodies, antigens, or a fragment or portion thereof. Such compound may be naturally occuring or non-naturally occuring.

As used herein, "alkyl" includes both branched and straight-chain saturated aliphatic hydrocarbon groups having the specified number of carbon atoms and may be unsubstituted or substituted. Thus, C1-Cn as in "C1-Cn alkyl" includes groups having <NUM>, <NUM>,. , n-<NUM> or n carbons in a linear or branched arrangement. For example, a "C1-C5 alkyl" includes groups having <NUM>, <NUM>, <NUM>, <NUM>, or <NUM> carbons in a linear or branched arrangement, and specifically includes methyl, ethyl, n-propyl, isopropyl, n-butyl, t-butyl, and pentyl.

As used herein, "alkenyl" refers to a non-aromatic hydrocarbon group, straight or branched, containing at least <NUM> carbon to carbon double bond, and up to the maximum possible number of non-aromatic carbon-carbon double bonds may be present, and may be unsubstituted or substituted. For example, "C2-C5 alkenyl" means an alkenyl group having <NUM>, <NUM>, <NUM>, or <NUM>, carbon atoms, and up to <NUM>, <NUM>, <NUM>, or <NUM>, carbon-carbon double bonds respectively. Alkenyl groups include ethenyl, propenyl, and butenyl.

The term "alkynyl" refers to a hydrocarbon group straight or branched, containing at least <NUM> carbon to carbon triple bond, and up to the maximum possible number of non-aromatic carbon-carbon triple bonds may be present, and may be unsubstituted or substituted. Thus, "C2-C5 alkynyl" means an alkynyl group having <NUM> or <NUM> carbon atoms and <NUM> carbon-carbon triple bond, or having <NUM> or <NUM> carbon atoms and up to <NUM> carbon-carbon triple bonds. Alkynyl groups include ethynyl, propynyl and butynyl.

The term "substituted" refers to a functional group as described above such as an alkyl, or a hydrocarbyl, in which at least one bond to a hydrogen atom contained therein is replaced by a bond to non-hydrogen or non-carbon atom, provided that normal valencies are maintained and that the substitution(s) result(s) in a stable compound. Substituted groups also include groups in which one or more bonds to a carbon(s) or hydrogen(s) atom are replaced by one or more bonds, including double or triple bonds, to a heteroatom. Non-limiting examples of substituents include the functional groups described above, and for example, N, e.g. so as to form -CN.

It is understood that substituents and substitution patterns on the compounds of the instant invention can be selected by one of ordinary skill in the art to provide compounds that are chemically stable and that can be readily synthesized by techniques known in the art, as well as those methods set forth below, from readily available starting materials. If a substituent is itself substituted with more than one group, it is understood that these multiple groups may be on the same carbon or on different carbons, so long as a stable structure results.

In choosing the compounds of the present invention, one of ordinary skill in the art will recognize that the various substituents, i.e. R<NUM>, R<NUM>, etc. are to be chosen in conformity with well-known principles of chemical structure connectivity.

In the compound structures depicted herein, hydrogen atoms, except on ribose and deoxyribose sugars, are generally not shown. However, it is understood that sufficient hydrogen atoms exist on the represented carbon atoms to satisfy the octet rule.

Where a range of values is provided, unless the context clearly dictates otherwise, it is understood that each intervening integer of the value, and each tenth of each intervening integer of the value, unless the context clearly dictates otherwise, between the upper and lower limit of that range, and any other stated or intervening value in that stated range, is encompassed within the invention. The upper and lower limits of these smaller ranges may independently be included in the smaller ranges, and are also encompassed within the invention, subject to any specifically excluded limit in the stated range. Where the stated range includes one or both of the limits, ranges excluding (i) either or (ii) both of those included limits are also included in the invention.

The use of the terms first and second antibody (<NUM>st and <NUM>nd antibody; antibody <NUM> and <NUM>; capture antibody and detection antibody), are not equivalent to primary and secondary antibody, which do not generally apply to methods disclosed herein, except for example <NUM>. Secondary antibodies are antibodies raised to the primary antibody, which is in turn raised to the antigen of interest. In the subject application, first and second antibodies are both raised to the same antigenic protein or other molecule, or to two interacting molecules.

Target, target molecule, antigen, antigenic molecule, and biomarker are used interchangeably in this document. The exception is examples <NUM> and <NUM>, where the target is the antibody or an antigen-antibody complex, not just the antigen. It should be understood that some antigens of interest may not be established as biomarkers, and some biomarkers may not be antigenic, but may have binding partners that can be used in this approach. Analyte is an additional term that is sometimes used to refer to the target molecule.

Herein, the term composite molecule is taken to include any molecular compound, such as a lipoprotein or glycoprotein, or complex including but not limited to a protein complex and a complete virion.

Some embodiments of the invention disclosed herein include tagging of a second antibody (detection antibody) that can bind to a different epitope on the same analyte as the initial antibody.

All combinations of the various elements described herein are within the scope of the invention, in as far as they fall within the scope of the claims.

All sub-combinations of the various elements described herein, in as far as they fall within the scope of the claims, are also within the scope of the invention. This invention will be better understood by reference to the Experimental Details which follow, but those skilled in the art will readily appreciate that the specific experiments detailed are only illustrative of the invention as described more fully in the claims which follow thereafter.

As a general case, outlined in <FIG>, and described more fully in Example <NUM>, the procedure would be as follows: (<NUM>) capture antibodies, affibodies or other antibody mimetics, aptamers or ligands specific for a particular analyte (compound) would be bound to (or - in an instance not part of the invention - very near) individual membrane-embedded nanopores in a nanopore array; (<NUM>) the sample containing the analytes to be identified will be flowed over the nanopore array and bind to the specific capture antibodies or antibody mimetics; (<NUM>) the tagged second antibodies (or affibodies or other antibody mimetics, aptamers or ligands specific for a particular analyte (compound)) would be flowed over the nanopore array in an electrolyte solution and bind to a different site on the analyte, in a version of an antibody sandwich technique; and (<NUM>) after applying a voltage across the membranes, current recordings would be taken, allowing identification of the compound associated with a well containing a specific nanopore. The concept can be further expanded to a format where the reaction steps (<NUM>-<NUM>) related to binding the biomarker are performed in solution phase, and then the enriched nanopore-antibody-biomarker-tagged antibody complexes are applied to a nanopore array and assessed at the single-molecule level.

Different tags attached to second antibodies for different analytes would elicit different current blockades, allowing determination of multiple targets on the same nanopore array. With sufficient numbers of nanopores, quantitative or semi-quantitative results can be obtained (<FIG>).

<CIT>, described the covalent attachment of a specific tag to a specific analyte (compound of interest). This tagging is carried out prior to flowing the analytes over the chip. In a novel approach disclosed herein, tagged second antibodies (detection antibodies) are used, in combination with capture antibodies to the same target, resulting in a flexible approach for single molecule detection by nanopore allowing various multiplex and quantitation strategies. As long as multiple (or even the same) antibodies are available for a protein biomarker that bind to it at different epitopes, no special sample preparation is required. Unlike protein arrays, where binding of antibodies to a surface may reduce their ability to bind antigen, attachment of the first antibody to a nanopore via a flexible linker should preserve its ability to bind to its antigen. Moreover, the resulting complex should be readily accessible to the tagged second antibody. The invention disclosed herein retains all the advantages of a nanopore-based approach, including: (<NUM>) single-molecule electronic readout, resulting in rapid speed and high accuracy; (<NUM>) high throughput due to parallelization of reads on many nanopores; (<NUM>) multiplexing based on the ability to easily discriminate multiple tags and to take advantage of multiple flow cells; (<NUM>) ability to quantify protein biomarker levels due to the digital nature of the output (essentially counting electronic readings on a multiplicity of nanopores); and (<NUM>) small instrument size and cost. Compared with immunodetection methods based on fluorescent tags, the method can provide a substantially higher sensitivity and dynamic range.

Variations on the above general approach may include the attachment of multiple capture antibodies or small antibody mimetics (e.g., affibodies, Avibodies(TM), affimers, nanoclamps), generally via flexible linkers, to the nanopore, and use of multiple copies of the tag on the detection antibody.

Example <NUM>: Attaching the capture antibody to the nanopore. The attachment of the capture antibody (<NUM>st antibody or antibody <NUM>) to the nanopore is identical in the original and new methods. A person skilled in the art will know several methods to derivatize the antibody, taking advantage of key amino acid residues such as lysines or cysteines. These linkages can involve homo- or heterobifunctional reagents, or two-linker systems such as that available from TriLink® Biotechnologies (Chromalink® reagents) or those involving a Diels-Alder reaction (see below). Other possibilities include the generation of fusion proteins incorporating SpyCatcher/SpyTag interaction partners (Zakeri et al. In one embodiment the Fc portion of the immunoglobulin (Ig) is bound to the nanopore, leaving the Fab'<NUM> portion free to react with the antigen. The presence of NHS esters or isothyiocyanate groups on the end of a linker molecule will allow its attachment to the N terminal amino group or primary amino groups on lysines of the antibody. Though lysines are present in both the Fc and Fab portions, this straightforward method generates a large percentage of acceptable attachments. A second possibility is attachment to cysteine residues in the hinge region of the Ig molecule. The presence of maleimide or iodoacetamide on a linker would allow its attachment to the SH group on cysteines, which would require reduction of the disulfide bonds connecting two cysteines. This will affect the binding of the two large subunits of the Ig to each other. While this may somewhat reduce the overall avidity of binding, it is one of the simplest and more site directed alternatives. Another attractive possibility is to conjugate amine- or hydrazide-modified linkers to the periodate-oxidized carbohydrate groups occurring on the Fc constant domains, following by reduction of the resulting Schiff bases with borohydrides. Other possibilities for conjugation include click chemistry (e.g., alkyne-azide) reactions and biotin-streptavidin interactions. A Diels-Alder heterobifunctional conjugation strategy for attaching DNA polymerase to α-hemolysin (αHL) nanopores has been previously reported (<CIT>), and the attachment of antibodies to these nanopores would follow the same approach (<FIG>). Implementing the conjugation strategies described above takes advantage of alpha-hemolysin mutant proteins we have already generated, in which single cysteines have been introduced at specific positions on one or more of the seven pore subunits, rendering them specifically reactive with maleimide and other sulfhydryl-reactive moieties. Finally, directed attachment strategies based on incorporating orthogonal amino acid analogs into the protein can be performed. Regardless of the specific method used, the goal is to attach a single or just a few copies of a specific antibody to each nanopore in a nanopore array. (See <FIG> top left for capture antibody structures and conjugation sites. ) An alternative strategy is herein disclosed in which beads containing clusters of identical capture antibodies are used to increase the likelihood of target capture (e.g., <FIG>).

A variety of protein and solid-state nanopores can be used. While we have used the α-hemolysin nanopore including a wide variety of mutant forms in sequencing by synthesis studies (<CIT>, <CIT>, <CIT>, <CIT>, <CIT>, <CIT>, Kumar (<NUM>), Fuller (<NUM>), and Stranges (<NUM>)), other protein nanopores such as MspA Derrington et al <NUM>), OmpG (Sanganna Gari et al <NUM>), FraC (Huang et al <NUM>), aerolysin (Wang et al <NUM>), anthrax protective antigen (Jiang et al <NUM>), other beta-barrel transmembrane pores (Heuck et al <NUM>) and various commercial bespoke nanopores, their mutants and derivatives can be used.

For these, most of the attachment and conjugation chemistries described above can be utilized. Other options include solid-state nanopores based on graphene (Merchant and Drndic <NUM>), MoS<NUM>(Graf et al <NUM>), Si<NUM>N<NUM> (Rollings et al <NUM>) and other materials (Shi et al <NUM>), hybrid protein-solid state nanopores (Hall et al <NUM>), and nanopores with integrated electronic sensors (Rosenstein et al <NUM>). In these cases, a wide variety of derivatization and coupling strategies, many identical to those above, and all well known in the art, can be used. Multiple copies of the antibody can be attached to the nanopore.

Finally, the <NUM>st antibody or the nanopore associated with it can be specifically tagged with a nanopore-detectable tag, so that their identity can be later recognized on the nanopore array in complex multiplexing formats even in the absence of the bound biomarkers. Among many methodological benefits, this implementation provides for directly measuring the absence of a specific biomarker in the complex analyte mixtures. Binding can be assessed by use of gel shift assays. This approach is described in more detail in Example <NUM> below, where it is described for multiplex detection of target molecules.

Example <NUM>: Attaching the tag to the second antibody (detection antibody). The second antibody will be attached to a nanopore-detectable tag. Poly(ethylene)glycol (PEG)-based tags (<CIT> and Kumar (<NUM>)), with a voltage gradient across the membrane from positive (cis side) to negative (trans side) have been reported. More recently, tags with negatively charged polynucleotide backbones requiring a reverse voltage polarity (negative on cis side and positive on trans side) have been reported (<CIT>, Fuller (<NUM>), and Stranges (<NUM>)). The oligonucleotides will be modified with a terminal amine for attachment to NHS ester-containing linkers (see <FIG> and <FIG> for two different methods for attachment of such a linker to the detection antibody), though a variety of other modifications of the tag for linker attachment are also well known. The attachment positions on the second antibody will be identical to those described in the previous paragraph for attaching linkers to the first antibody. Notwithstanding the specific method used, the goal will be to attach a single tag (or a few copies of the tag to increase likelihood of signal detection) to each detection antibody. (See <FIG> top right for detection antibody structures and conjugation sites.

Again, as mentioned above in Example <NUM>, the <NUM>st antibody or the nanopore associated with it can be specifically tagged with a nanopore-detectable tag, so that their identity can be later recognized on the nanopore array in complex multiplexing formats even in the absence of the bound biomarkers. Among many methodological benefits, this implementation provides for measuring directly the absence of a specific biomarker in the complex analyte mixtures. Binding of the tag to the <NUM>nd antibody can be assessed by gel shift assays and/or with the use of fluorescent labels included in the tag, preferably at the opposite end from the amino modification.

Example <NUM>: Alternatives to antibodies. While antibodies are the most commonly used and probably best-understood molecules for binding to a wide range of targets (antigens), recently a variety of antibody mimetics including affibodies (Lofblom et al <NUM>), Avibodies™ (avipep Pty Ltd) , affimers (Tiede et al <NUM>), nanoclamps (Suderman et al <NUM>) and a variety of other small organic molecules have been produced, many of which have been developed as pharmaceutical agents. In addition, fusion proteins consisting of antibody fragments can be used in place of whole antibodies.

Example <NUM>: Types of target antigens (analytes). While the most typical antigens will be protein molecules, and many proteins have indeed been identified as biomarkers, antigens can include a variety of other small molecules or macromolecules, including lipids, carbohydrates, DNA, or composite molecules such as glycoproteins or lipoproteins, or larger complexes such as viral particles, again largely focusing on biomarkers for cancers and other diseases, including but not limited to infectious processes. In addition to pathology, other physiological and pre-disease states can be identified and monitored with appropriate biomarkers, including pregnancy, aging, drug responses, etc. Samples of particular interest will be blood, urine and other fluids for non-invasive diagnostics, but will also include tissue biopsies or appropriately preserved archival autopsy material.

Example <NUM>: Protein-protein and other molecular interactions. In addition to antigen-antibody (or antibody mimetic) interactions, the method can also be used to identify other molecular interactions. Key molecular interactions in biology include those between proteins, protein-DNA and protein-RNA interactions, binding of small molecules and cofactors to macromolecules such as drug-enzyme and drug-receptor interactions, and many others (Vidal et al <NUM>). Classic biochemical and genetic methods for recognizing these interactions have many shortcomings. For instance, for protein-protein interactions, gel shift assays can examine the protein interactions for a given bait protein. The method is limited to one bait protein at a time. Similarly, the yeast two-hybrid and related methods can identify the targets of a particular protein used as bait. While in principle protein chips using multiple bait proteins can be designed, maintaining these surface-bound proteins in a form that can recognize their natural partner proteins is difficult, and unlike with antibody-based protein chips, for which many Ab's already exist, these would have to be developed specifically for each bait protein. Here the bait protein (or other interacting molecule) would be attached to the nanopore via a flexible linker in such a way that it preserves its structure and binding properties.

Thus, herein is disclosed an approach for identifying protein-protein interactions, in which the capture antibody (antibody <NUM>) is specific for the bait protein, and the tagged detection antibody (antibody <NUM>) is specific for the bait's potential target proteins. In this protocol, as illustrated in <FIG>, the following series of steps are performed: (<NUM>) antibody <NUM> is conjugated to the nanopore, which is already or subsequently inserted into the membrane; (<NUM>) the sample containing putative interacting proteins is added to the chip to bind the bait protein and any associated proteins (a cross-linking step may be performed to maintain these protein-protein interactions either before or after adding to the chip); (<NUM>) tagged antibody <NUM> (attached via a cleavable linker if antibody <NUM> was not attached directly to the pore (e.g. to the surface or membrane); attached via a non-cleavable linker if antibody <NUM> was attached directly to nanopore) specific for a putative target protein is added to the chip in an electrolyte solution; (<NUM>) cleavage of the tag is performed if required; and (<NUM>) a voltage is applied across the membrane and ion current recorded; identification of the expected signal (ionic current blockade) for the tag is indicative of binding of the target to the bait.

As mentioned above, the concept can be further expanded to a format where the reaction steps (<NUM>-<NUM>) related to binding the bait and target with the nanopore complex and the appropriate antibodies are performed in solution phase, and then the enriched nanopore-antibody-bait-target-tagged antibody complexes are applied to a nanopore array and assessed at the single-molecule level. Formation of the complexes can be assessed by gel shift assays or with the use of fluorescent labels, prior to applying to the array.

Though single capture antibody molecules are shown in <FIG>, one can bind multiple capture antibodies or small antibody mimetics to the nanopore to increase the chance of capture, and thus sensitivity.

Example <NUM>: Nature of the tags. The tags are typically polymeric molecules that penetrate the channel of the nanopore to reduce the ionic current to a defined extent when a given voltage is applied across the membrane into which the nanopore is inserted. A wide variety of polymers have been developed for this purpose (<CIT>, <CIT>, <CIT>, and <CIT>). Examples comprise polymers containing PEG, alkane, peptide/polypeptide, and polynucleotide backbones, or a combination of these. These polymers may, in turn, be modified in a variety of ways to expand or reduce their diameters in key positions of the channel, to have more negative or more positive overall or focal charge, to be more or less polar, or to have affinitive properties for the nanopore. Many examples of such tags have been presented (<CIT>, <CIT>, and <CIT>). <FIG> shows the separation of ionic current readings that can be obtained with different tags entering the pore. <FIG> and <FIG> show examples of tags, many of which have been synthesized and reported elsewhere (Kumar (<NUM>), Fuller (<NUM>), and Stranges (<NUM>)).

Example <NUM>: Basic Protocol for Nanopore Based Protein Sensing Using Antibodies <NUM> and <NUM>, Each to a Different Portion of the Protein. In the exemplary approach, presented in <FIG>: (<NUM>) the antibody <NUM> (capture antibody)-labeled nanopore will be inserted into membranes on the chip, ideally one nanopore per sensor on the array; (<NUM>) Next, the chip will be incubated with antigens present in a sample; (<NUM>) Then, typically, the chip will be incubated with tagged antibody <NUM> (detection antibody) in an electrolyte solution; (<NUM>) Finally, a voltage will be applied across the membranes and the resulting ionic current measured: sustained current blockade indicative of tag entry into the nanopore channel will indicate binding of antigen to the complex. Washes are carried out between incubations, as necessary to remove unbound molecules from the previous incubations, which may inhibit or compete with subsequent steps. The electrolyte solutions can be adjusted over a wide range with regard to particular ions and their concentration depending on the desired conditions for distinguishing ionic current levels. While single nanopore setups (e.g., Axopatch, EBS) can be used to perform test experiments, nanopore arrays have been developed (Fuller et al <NUM>) and are desirable for further optimization of the system and essential for multiplexing and digital quantitation.

The same antibody may be used as both the capture and detection antibody, so long as they can bind to different positions on the antigen (e.g., polyclonal antibodies that recognize multiple epitopes on the antigen).

This basic approach can be performed in a format where the reaction steps related to binding the biomarkers with the nanopore-conjugated antibody <NUM> and tagged antibody <NUM> are performed in solution phase, e.g. in an approprate microfluidic device, and then the enriched nanopore-antibody-biomarker-tagged antibody complexes are applied to a nanopore array and assessed at the single-molecule level.

In some applications it may be advantageous to perform the microfluidic reactions of nanopore antibody-antigen binding and washing steps on magnetic beads (for example, as described in Ng et al. (<NUM>)) but then cleave off the nanopore complexes from the beads and detect them on the chip. The enriched nanopore-antibody-biomarker-tagged antibody complexes are applied to a nanopore array and assessed at the single-molecule level as described in the previous examples. In this case the nanopore complex will be tethered to the paramagnetic particles via a cleavable linker, such as those presented in <FIG>.

In the approach illustrated in <FIG>, a single capture antibody (antibody <NUM>) is shown attached to the nanopore. If desired, multiple capture antibodies, or small antibody mimetics (e.g., affibodies, avibodies, affimers, etc.) can be attached to the nanopore, increasing the likelihood of target capture, which will be advantageous if the target is present in low abundance, and higher sensitivity is required.

In an exemplary embodiment of Example <NUM>, the capture antibody and detection antibody can be directed against breast cancer biomarkers comprising MUC-<NUM>, carcinoembryonic antigen, CA-<NUM> and estrogen receptors such as HER2 (Gam <NUM>; Mueller et al <NUM>).

An alternative approach (<FIG>) that can be used to further enhance sensitivity of the method would be the use of capture antibody-studded nanometer-scale magnetic beads attached to the nanopore via biotin-streptavidin, digoxigenin-anti digoxigenin, or any of the alternative conjugation methods described earlier. In this case, the beads would be used to capture antigenic biomarker targets from the serum or other sample. The beads would also possess chemical substitutions on the surface for binding to nanopores (a wide variety of chemical interaction partners, including but not limited to those mentioned above, are available for conjugation). The nanopore-bound complex would be inserted into lipid membranes on a nanopore array chip, one nanopore per sensor (electrode) position. Next the chip would be incubated with tagged detection antibodies, specific for the biomarker of interest. This would result in identification of the bound biomarker following application of a voltage across the membranes with capture of the nanopore distinguishable tag in the channel of the nanopore and the resulting tag-specific ionic current blockade. The advantage of the use of magnetic beads would be the enhanced sensitivity, since there is both an increased chance of binding the biomarker due to the presence of many capture antibodies on the bead, and an increased chance of binding the detection antibody increasing the likelihood of tag capture by the nanopore.

Attachment of Capture Antibody to Bead and Bead to Nanopore. In a preferred embodiment, amino group derivatized magnetic beads will be incubated with both maleimide NHS ester and biotin NHS ester at an appropriate ratio such that the beads will be derivatized with both maleimide and biotin at a <NUM>:<NUM> or higher ratio. A subsequent conjugation reaction with antibody will yield capture antibody-bound beads vis a thiol-ene reaction, with a small amount of biotin coexisting on the bead. The biotin will be used as a binding compound (binding compound <NUM>) to attach the capture antibody decorated beads to a streptavidin (binding compound <NUM>)-bearing nanopore through a biotin streptavidin interaction. The resulting nanopore with capture antibody-studded bead is then inserted into the lipid membrane and the procedure described in the previous paragraph is followed to detect the compound of interest at high sensitivity.

Example <NUM>: Detection of Antibodies in Serum or Tissues. In infectious disease studies, rapid detection of circulating antibodies to the virus, bacterium or other agent is often highly desirable for early diagnosis, as growing and identifying the infectious agents can often take several days, and in some cases may not be possible. An example of the use of a novel ELISA approach for such a purpose has been described recently (Ng et al. Similarly, the single-molecule nanopore system described herein can easily be adapted for that purpose and will be especially useful when assaying for several potential infectious agents in a patient. In the simplest scenario, the antigen of interest (e.g., a coat protein on the virus, an immunogenic component of a bacterial cell), can be attached to the nanopore by any of the methods outlined above (<FIG>) including the use of biotin-streptavidin (<FIG>)or digoxigenin-anti digoxigenin antibody (<FIG>) interactions. Thus the antigen itself will serve as the capture reagent (<FIG>, <FIG> and <FIG>). In combination with a flexible linker, this method of attachment will further increase binding affinities, reduce molecular crowding, and increase access for subsequent binding steps. Next, the serum with putative antibodies will be added to the chip. Practically all serum proteins including any serum Ig's would be tagged, in which case, the bound antibody will have a tag that can be immediately detected in the nanopore. To select for the serum Ig's of interest, thus reducing complexity, in an alternative strategy, one can use a nanopore tagged secondary antibody to the captured antibody, either directed against the Fc portion and raised in a different species (e.g., a goat-anti human antibody (secondary antibody)) (<FIG>), or in cases where the antibody of interest has been well characterized, an anti-idiotypic antibody, which adds further specificity and allows multiplexing for different serum antibodies on the same nanopore array chip. Having a collection of tagged secondary anti-Fc or anti-idiotypic antibodies avoids the serum tagging step and reduces costs. As an alternative to the secondary antibody, protein A or G could be used to bind to the primary antibody. Interacting molecules between the serum antibodies and the secondary antibody such as biotin-streptavidin (<FIG>) or digoxigenin-anti-digoxigenin antibody (<FIG>) can be used. In combination with a flexible linker, this method of attachment will further increase binding affinities, reduce molecular crowding, and increase access for subsequent binding steps.

To increase sensitivity for viral or other antibody capture, viral particles (Ricks et al <NUM>) or fragments can be attached to the nanopore using amine-NHS or a wide variety of other reactivities, as mentioned above. Because there are many copies of the viral coat proteins on the viral particles or even viral particle fragments, this provides many sites for binding of serum antibodies. In one approach, the viral antibodies can be pre-tagged (non-specifically) (<FIG>) and in a second approach the serum antibodies can be left untagged whereas tags will be present on secondary antibodies raised to the Fc portion of these primary antibodies (<FIG>).

As described in Example <NUM>, this method can be adapted for quantitation of one type or multiple types of viral antibodies, by prior labeling of the viral particles or viral proteins bound to the nanopores with a cleavable tag specific for the antigen. After detection of signals due to capture of this tag to identify which viral antigen is present on a given nanopore overlying a particular sensor of a nanopore array, the tags are cleaved as in <FIG>. Then the nanopore array chip is incubated with the serum to capture the non-specifically tagged viral antibodies (<FIG>) or untagged viral antibodies followed by non-specifically tagged secondary antibodies (<FIG>) and the non-specific tag signals detected. Thus, the initial tag defines the viral antibody that can be detected at that position on the array and the second tag indicates whether that antibody is indeed present.

As an example of a specific implementation of the approach, killed Rubella (German measles) or Rubeola (measles) virus particle coated nanopores or nanopores derivatized with Rubella or Rubeola antigens will be used in a microfluidic station to capture the related tagged antibodies in a blood sample. The sample will be diluted in PBS supplemented with <NUM>% BSA and <NUM>% Tetronic 90R4 exposed to nanopore coated with the viral particles or antigens and washed four times with PBS/Tetronic 90R4 in the microfluidic device. After washing, the antibodies can be detected as shown in <FIG>. For multiplexing, the derivatized nanopores will also bear a cleavable nanopore tag specific to the Rubella or Rubeola virus. After cleaving and detecting the tag to determine which antigen is present at each position in the nanopore array (the tag may be directly attached to the nanopore or to the antigens on the nanopore), the chip will be incubated with either serum antibodies labeled with a non-specific tag as in <FIG> in PBS/BSA/Tetronic 90R4, or unlabeled serum antibodies followed by a secondary antibody conjugated with a non-specific tag (as in <FIG>), both in PBS/BSA/Tetronic 90R4, to reveal the presence/absence and titer of the viral antibodies in the serum sample. Attachment of the virus particles to the nanopore is accomplished using standard approaches described above or through site specific mutagenesis of amino acids (Chatterjiee et al <NUM>).

This method also can incorporate viral protein studded magnetic beads (<FIG>) (Ng et al. In this case the beads with the viral protein clusters would be mixed with the blood or other sample as a method of capturing multiple copies of the antibody for the given viral protein. The magnetic bead would also have chemical substitutions on its surface for binding to the nanopore. The resulting complex is inserted into the membrane on the nanopore array, one nanopore per sensor position. Finally, the array will be incubated with secondary antibodies targeted to the initial antibodies and labeled with a nanopore detectable tag specific for the target of interest. Application of a voltage across the membrane will allow capture of the tag and determination of the presence of the viral (or other) antibody of interest based on the resulting current blockade signal. The advantage of this approach is that even antibodies present in the serum in very low concentrations would have a high likelihood of being detected given the large number of antigenic (viral) proteins on the magnetic bead. Thanks to the use of this sandwich approach, multiple tagged secondary antibodies will be bound, also increasing the likelihood that the tags will enter the nanopore channel to produce the desired signature. Clearly, with the use of different beads bearing proteins from different viruses, the same chip can be used to detect different viral targets at high sensitivity on the same chip. Further, with a mixture of viral-specific tags on the beads or antigens, and non-specific tags on a secondary antibody, quantitative or semi-quantitative multiplexing can be accomplished. The preparation of the capture antibody attached beads and their attachment to the nanopore is described in Example <NUM>.

A further variation of the above approach for detection of antigen-antibody complexes, commonly found in serum during the course of autoimmune and other diseases, that is closer to the more general approach described herein involves the use of both a capture antibody attached to the nanopore and a detection antibody (<FIG>). This capture antibody would pull out potential antigen-antibody complexes from the serum. Subsequently a tagged anti-Fc or anti-idiotypic antibody raised to the antibody in the antigen-antibody complex will be flowed over the chip, and a tag-dependent ionic current blockade event will reveal the presence of the antigen-antibody complex in the serum. This variation can optionally include the use of antibody-coated capture beads to further increase sensitivity. Also, instead of using an antibody attached to the nanopore as the capture reagent to pull antigen-antibody complexes from the serum, one could use the antigen as the capture agent. In this case, after binding the antibody-antigen complex, a tagged second antibody to the serum antigen will be used for detection.

Capture and detection antibodies can be replaced with antibody mimetics if desired. Antibody mimetics are generally substantially smaller than antibody molecules. This can be taken advantage of to increase the likelihood of capture and thus sensitivity, by attaching multiple copies of the antibody mimetic to the nanopore, generally via flexible linkers.

Finally, as above, the immunodetection reactions can be performed either directly on the nanopore array, or in solution in a microfluidic chip and then inserted into the membrane of the array for detection.

Example <NUM>: Multiplexing and Quantitation of Target Molecules. By definition the nanopore ionic current measurements are at the single molecule level, assuming that a single nanopore is inserted into the membrane above each sensor. With different antibodies (for different target biomarkers) attached to different nanopores, assuming no cross-reactivity of either the capture or detection antibody with other than the desired antigen, the system can be set up for multiplexing, quantitation or both. For example, using separate flow cells covering different portions of the chip, nanopores with a different capture antibody (for a specific target biomarker) can be placed in each flow cell, resulting in separate regions of the chip each with their own capture antibody. The same sample would then be added to each flow cell, so that specific antigens in the sample would attach to the specific capture antibodies. In the third step, the tagged detection antibody could be added to all the flow cells or to just the flow cell containing the capture antibody for the same antigenic protein or other antigen. With separate flow cells, each detection antibody can be labeled with the same tag.

In an alternative scheme to maximize the ability to quantitate antigen ratios, illustrated in <FIG>, an equimolar mixture of capture antibody-bound nanopores (each for a different target biomarker) can be flowed over the entire chip. Then the sample containing antigens and an equimolar mixture of the tagged detection antibodies (for the same collection of target biomarkers), each with a unique tag, will be flowed over the chip. Because this nanopore-based approach is single molecule (digital), quantitation can be carried out by simply counting the number of sensors reporting the appropriate tag. Assuming the capture antibody-nanopores insert into the membranes with equal efficiency, and the antibodies have equal affinity for their respective antigenic targets, this approach will be highly quantitative. Thus if <NUM> sensors display currents indicative of tag <NUM>, <NUM> sensors display currents indicative of tag <NUM>, and <NUM> sensors display currents indicative of tag <NUM>, then one can assume with a reasonable level of confidence that the sample contains a <NUM>:<NUM>:<NUM> ratio of the antigenic biomarker targets <NUM>, <NUM> and <NUM>. If some of these assumptions are not correct, the system can be calibrated accordingly. For example, if some antibodies have a higher affinity, their fraction in the antibody mixture will be reduced proportionately.

An important consideration with all multiplexing methods is that the use of even just <NUM> distinguishable tags in two different steps can reveal up to <NUM> different features (e.g., representation of <NUM> analytes in <NUM> different tissues or <NUM> different functional or developmental states of the same tissue).

Example <NUM> (comparative Example): Alternative Protocol with Antibody Attached Near the Nanopore and Cleavable Linker between the Tag and <NUM>nd Antibody: One variation of the above approach comprises attachment of the antibody near the nanopore rather than directly to the nanopore. For instance, if microfabricated wells separate the sensors and associated membranes, the capture antibody may be attached directly to the surface of the well using traditional surface conjugation techniques. For instance the surface can be modified with a variety of reactive groups (amino, NHS ester or carboxylic acid, alkyne, tetrazine, biotin, etc.) and the antibody modified with partner reactive groups (carboxy, amino, azide, TCO, streptavidin, etc.). Coupling will be accomplished under conditions well known in the art. Alternatively, the capture antibody can be attached directly to the membrane, taking advantage of reactions between phosopholipids, artificial lipid polymers, or modified lipids with associated reacting chemical moieties on the antibody. In either case, it is highly unlikely that after incubating with the antigen and the detection antibody, tagged as described earlier, the position of the tag in the resulting surface or membrane-capture antibody-antigen-detection antibody-tag complex will be close enough to reach and extend into the nanopore channel. To overcome this obstacle, the tag can be attached to the <NUM>nd antibody through a cleavable linker. After cleavage, the tag is provided sufficient time to be drawn with the aid of the electric field into and through the nanopore channel. This may require a different concentration of electrolytes and a higher voltage than in the basic protocol.

The steps of this alternative protocol are thus as follows: (<NUM>) incubation of the derivatized chip or membrane surface, already containing embedded nanopores, with the appropriately derivatized capture antibody; (<NUM>) incubation of the chip with an antigen-containing sample; (<NUM>) incubation with the cleavably tagged detection antibody in an electrolyte solution; (<NUM>) cleavage of the cleavable linker with appropriate chemical or other cleavage agent to release the tag; and (<NUM>) application of a voltage across the membranes and measurement of the resulting ionic current: transient ionic current blockade indicative of tag entry into the nanopore channel will indicate binding of target antigen to the complex.

As with the basic protocol, wash steps to remove prior unbound or unconjugated molecules will be carried out as needed between steps. To greatly improve the likelihood that tags will be captured by the nanopore, many copies of the same capture antibody can be used to decorate the surface or membrane in the vicinity of the nanopore, or the capture antibodies can be clustered on beads attached to the surface. It is also important in these circumstances to have rapid sensing, since the tags will pass through the nanopore channels at high speeds (in the order of nanoseconds to hundreds of nanoseconds depending on e.g., the nature of the tag, ion composition of the buffer, and the applied voltage).

A variety of cleavable groups that can be placed in linkers have been described, for each of which specific and protein compatible cleavage agents exist. Examples have been described involving biomarker sensing with nanopores (<CIT>), where cleavable linkers have been designed and placed in a variety of molecules for assorted purposes including sequencing by synthesis using fluorescent tags and anchors (<CIT>), attachment of biotin to primers for enrichment of ternary complexes (<CIT>), etc. Importantly, sulfhydryl or other groups that undergo cleavage with reducing agents should be avoided, as these groups can affect immunoglobulin (antibody) subunits, potentially altering their binding properties so that they no longer bind with sufficient affinity to the antigens. Other cystine (linked cysteine)-containing proteins can be similarly affected by reducing reagents. <FIG> includes examples of cleavable linkers that can be used to attach tags to antibodies or other molecules for the protocols described herein.

Example <NUM>: Additional Methods for Detecting Multiple Target Molecules: In this variation (<FIG>), a specific tag is attached to the capture antibody for a given target molecule. Different specific tags are attached to capture antibodies for different target molecules. The nanopore-tagged capture antibody conjugates are flowed over the array, where nanopores bearing different tagged capture antibodies will insert randomly into membranes in different sites on the chip, at approximately their ratio in the solution. The tags are attached to the capture antibody via a cleavable linker (examples of cleavable groups are presented in <FIG>). A voltage is applied across the membranes. After obtaining recordings at each position to establish which capture antibodies are associated with each position in the array, the tags are then cleaved as described previously (<CIT>). Isolated antigenic biomarkers present in the sample, which are pre-labeled with a general purpose nanopore detectable tag (different from any of the specific ones that were attached to the capture antibodies), are flowed over the chips, and bind to the appropriate capture antibody. A voltage is again applied across the membranes, and new current readings obtained. The presence of a blockade current due to the general purpose antigen tag is indicative of antigen binding. Since it is already known which capture antibody is present at that site on the chip from the first recording, the specific antigen that has bound can be determined. Thus, at each position on the array for which the specific capture antibody that was present due to the first recording is known, the second recording indicates binding of antigen, and counting all such cases (presence of both a specific and a general tag current) indicates the relative amounts of different antigens in the sample. An alternative method (not illustrated) would be the use of a non-cleavable tag on the capture antibody. In this case, subsequent binding of the antigen with its general tag would result in a competition for entry of the general and specific tags in the channel of the nanopore with repetitive voltage applications (pulses) across the membrane. The current traces for a given well would present as a mixture of blockades due to the specific tag and the general tag, in contrast to the initial recording with just the specific tag current blockade. Thus instead of a switch from specific tag blockade to general tag blockade, this variation would present as a switch from specific tag blockade to a mixture of specific and general tag blockades.

The preparation of the nanopore with capture antibody and cleavable tag is illustrated in <FIG> and <FIG>. First a cleavable trifunctional linker, NHS ester-Azo-TCO/PEG3-Maleimide, is synthesized (<FIG>). TCO is first coupled to Fmoc protected lysine, which can be further coupled to an Azo Linker via carboxylic acid activation and amide bond formation. Removal of the Fmoc group allows one more coupling step with maleimide NHS ester. The subsequent activation of the azo linker acid affords NHS ester-Azo-TCO/PEG3-Maleimide. Next the nanopore-capture antibody-cleavable tag conjugate is prepared (<FIG>). The above cleavable trifunctional linker, NHS ester-Azo-TCO/PEG3-Maleimide, is reacted with amino-Tag yielding a Tag-Azo-TCO/PEG3-Maleimide conjugate, which can readily react with Tetrazine modified capture antibody through TCO-Tetrazine addition. The resulting Tag-Azo-Capture Antibody-Maleimide conjugate is further reacted with α-hemolysin-SH via thiol-ene addition, affording the Nanopore-Cleavable Tag-Capture Antibody conjugate in which the Tag can be removed by Azo reduction and cleavage upon sodium dithionite treatment.

This format is flexible, and thus would not be limited to detecting a particular category of target molecule (a protein, a nucleic acid, a small molecule, etc.) on a given chip. It would be feasible to simultaneously detect protein and DNA biomarkers, for instance, by the use of appropriate combinations of antibodies, aptamers (Lakhin et al <NUM>) or other molecules for specific binding of these biomarkers.

In an exemplary embodiment of Example <NUM>, the capture antibodies and detection antibodies can be directed against a multiplicity of cancer markers comprising PSA, MUC-<NUM>, carcinoembryonic antigen, CA-<NUM> and estrogen receptor (Gam <NUM>, Mueller et al <NUM>).

Example <NUM>: Method for Detecting Multiple Viral Antibodies: Just as one can use cleavable tags and multiple capture antibodies with cleavable tags for multiplexing of target molecules (Example <NUM>), multiple types of viral antibodies in serum can be detected using cleavable tags and viral antigens as capture reagents. In this case, this method can be adapted for quantitation of one type or multiple types of viral antibodies, by prior labeling of the viral particles or viral proteins bound to the nanopores (via methods similar to those described for attaching antibodies or beads to the nanopore) with a cleavable tag specific for the antigen. The nanopores with the attached tagged antigens are then inserted into membranes, one per sensor on an array chip. Upon applying a voltage across the membranes, the tag will be captured by its respective nanopore, to generate a specific ionic current blockade signal. This will reveal which antigen is attached to the nanopore in each position. After the first detection step, the tags are cleaved. Then the nanopore array chip is incubated with the serum or serum protein extract to capture the viral antibodies, either non-specifically tagged ones as in <FIG>, or untagged viral antibodies followed by non-specifically tagged secondary antibodies as in <FIG>. A voltage is again applied across the membranes and the non-specific tag signals detected. Detection of a signal at this step will reveal the presence of the viral antibody, for which this nanopore is specific, as determined by the initial tag detection. Versions in which the first tag is attached not to the antigen on the nanopore, but to a position in the vicinity of the nanopore, such as the well surface or membranes, can also be envisioned but in this case the initial tag will be cleaved and detected transiently as it flows through the nanopore.

Example <NUM>: Sample Multiplexing: In example <NUM> and <NUM>, multiplexing and quantitation of antigens was described. However, the protocol also can be developed to compare multiple samples on the same chip. In the simplest version, the basic protocol of example <NUM>, with antibody <NUM> (capture antibody) attached to the nanopore and tagged antibody <NUM> (detection antibody) is performed, but with samples from different tissues, treatments or patients are loaded into separate flowcells in equal amounts.

An approach has been previously described involving generalized tagging of any or all proteins or other antigenic targets in each sample, each sample with a different tag that can be distinguished in a nanopore (<CIT>). In this case, there is no tagged detection antibody. A single capture antibody is attached to all the nanopores in the array, and then an equimolar mixture of the differentially tagged samples is added to the chip.

A variation of this approach is disclosed herein, which combines sample and antigen multiplexing. In this approach, a capture antibody specific for a given antigenic target is attached to the nanopore. A multiplicity of such antibodies is used for different antigens of interest, one of which will bind by chance to each nanopore. Next a set of several samples, each labeled with a unique cleavable tag that binds to the multiplicity of proteins or other targets present in the sample, are mixed together in equal amounts and added to the chip. After cleavage, the current attributable to this tag passing through the nanopore channel at each position on the array determines the sample from which the attached antigen was derived. Next, a detection antibody specific for a given antigen with a unique distinguishable nanopore tag is added to the array. A multiplicity of such differentially tagged specific antibodies is used and applied to the chip in equimolar amounts, adjusted as necessary according to the predetermined antibody affinities. Depending on whether capture antibodies <NUM> are directly attached to the nanopore or -in a manner not part of the invention- attached to the surface near the nanopore, the tag on sample detection antibodies <NUM> can be non-cleavable or cleavable, respectively. The ionic currents associated with this second set of tags will determine the specific antigen bound at each nanopore position on the array.

Claim 1:
A method for detecting the presence of a compound of interest in a sample, which comprises:
a) binding a capture compound or multiple copies of said capture compound for the compound of interest to a nanopore;
b) inserting the nanopore into an electrically resistive barrier;
c) contacting the capture compound or multiple copies of said capture compound with the sample containing the compound of interest under conditions permitting the compound of interest to attach to the capture compound;
d) contacting the compound of interest with a tagged compound or multiple copies of said tagged compound under conditions permitting the tagged compound to attach to the compound of interest, wherein the tagged compound comprises at least one tag;
e) contacting the nanopore with an electrolyte solution and applying a voltage across the electrically resistive barrier; and
f) measuring the electronic signal change across the pore resulting from at least one tag of the tagged compound entering the nanopore,
thereby detecting the presence of the compound of interest.