Abstract:
A kit and method for detection of a target in a sample. An assay mixture provided in the kit and used in the method includes a first probe with a first antibody recognizing a first epitope of the target and conjugated to an RNA oligonucleotide; a second probe with a second antibody recognizing a second epitope of the target and conjugated to a DNA oligonucleotide; a reverse primer with a first region complimentary to the RNA oligonucleotide and a second region complimentary to the DNA oligonucleotide; and a reverse transcriptase that creates a DNA transcription product from the RNA oligonucleotide using the reverse primer only if the RNA oligonucleotide and the DNA oligonucleotide are in close proximity. If the target is present in the sample, the reverse primer binds the RNA oligonucleotide and the DNA oligonucleotide to bring the RNA oligonucleotide and the DNA oligonucleotide in close proximity.

Description:
CROSS-REFERENCE TO RELATED APPLICATIONS 
     This application claims priority to U.S. Provisional Patent Application Ser. No. 61/825,615, filed on May 21, 2013, and entitled “Methods And Systems For Quantitative Fluorescence-Based Detection Of Molecules And Proteins,” the entire disclosure of which is incorporated herein by reference. 
    
    
     BACKGROUND 
     1. Field of Invention 
     The present invention relates to methods and systems for the identification of biological threats, and, more particularly, to a novel fluorescence-based assay for the detection of molecules and proteins. 
     2. Background of Art 
     There is a continued need for innovative approaches for the identification of biological threats, including Staphylococcal enterotoxin B (SEB), among many others. SEB is a protein produced by the bacterium  Staphylococcus aureus  that acts as a potent enterotoxin. While SEB is the toxin most commonly associated with food poisoning, it is also classified as a potential biological weapon as it is very stable, easily aerosolized, and causes great harm and incapacitation (including death) upon inhalation. The harmful effects of SEB are due to its ability to induce a massive and nonspecific activation of the immune system causing a toxic shock due to the high concentrations of cytokines released into the body. SEB, considered a superantigen, is toxic because of its ability to bind to and crosslink/activate immune cells. Therefore, SEB toxicity is not due to any inherent enzymatic activity. Specifically, the toxicity of SEB is associated with two defined binding sites located on the surface of the SEB protein itself; one binding site for the T-cell receptor (TCR) and the other for the major histocompatibility complex (MHC) class II. 
     Existing assays available for SEB detection are based on Enzyme Linked Immunosorbent Assays (“ELISA”) technology. Quantitative forms of these ELISA-based detection assays are complex, time consuming and more suited for laboratory analysis. Fieldable versions of the ELISA-based assays, commonly referred to as hand-held assays (“HHA”), are not quantitative and have limited sensitivity. Additionally, all these assays are only capable of detecting the presence of SEB, without giving any indication of toxin activity/toxicity. 
     Accordingly, there is a continued need for methods and systems that quickly and effectively identify the biological toxin and provide quantitative information about the toxin activity/toxicity. 
     BRIEF SUMMARY 
     In accordance with the foregoing objects and advantages, methods and systems are provided for detecting molecules and proteins, such as biological toxins, and providing quantitative information pertaining to molecule/protein concentration and/or toxin activity/toxicity. 
     According to an embodiment is provided a quantitative one-step “activity” assay that can be performed inside or outside of a laboratory environment, and which can determine the threat level of an exposure or attack, including but not limited to the detection and activity of Staphylococcal enterotoxin B (“SEB”). The assay, which can be called the Proximity Activated PCR Assay (“PAPA”), for example, is a novel and simple-to-use detection assay that can identify and quantify any molecule or protein. This new technology incorporates the detection specificity of antibody binding with an initiation step that requires reverse transcriptase Polymerase Chain Reaction (“PCR”) and precise oligonucleotide interactions that are dependent on proximity/distance to activate a quantitative fluorescence-based PCR signal amplification reaction. According to an embodiment, the assay can be quickly run on any fluorescence-based PCR amplification platform in the lab or field. 
     According to one embodiment, the PAPA overcomes the complexities associated with developing an assay to detect and identify SEB toxin activity. SEB toxicity is a consequential result of binding events that over-excite the immune system, and not associated with a specific product produced. To detect SEB activity, there was a need to utilize a molecular binding-based assay for detection. The crucial cross-linking binding sites on SEB for the TCR and MHC class II molecule have been mapped and therefore the toxic activity of an SEB molecule can be determined by verifying the presence of the TCR and MHC class II binding sites on the SEB molecule. To detect the toxic potential of a single SEB molecule, the PAPA requires dual antibody binding event utilizing available monoclonal antibodies that bind to the epitopes of the TCR and MHC class II binding sites. Any mutation in either of these binding sites, which would prevent dual antibody binding, would also make the SEB molecule non-toxic; as it would be unable to cross-link the TCR and the MHC class II molecule on cells within the immune system. Therefore, utilizing two distinct antibody clones that bind to different sites on the same molecule is an important component of the PAPA design. 
     While a dual antibody binding event on an SEB molecule can determine its toxicity, it was also necessary to determine a way to associate a successful dual antibody binding event to the generation of measureable signal. One technology that utilizes antibody binding to a molecule in order to generate a signal are ELISAs. Sandwich ELISAs utilize two antibodies to the same molecule; one to capture the molecule to an assay plate and the other to bind to the “captured” molecules in order to detect and quantify the amount of molecule present. This detection typically utilizes enzymes that react with chromogenic reporter substrates to produce a change in color that is used as a signal. While ELISAs produce useful information, they are time consuming (5 to 6 hours), require multiple wash and incubation steps, and are typically designed for lab based experimentation. Therefore, ELISA based technology would not satisfy the requirement of a quantitative assay that must be simple and easy to perform outside of a lab environment. 
     Another commonly used method of detecting a dual antibody binding event is Förster/fluorescence resonance energy transfer (“FRET”) technology. In typical FRET assays, different chromophores are attached to each antibody. When these antibodies come in close proximity to each other, energy is transferred from one chromophore to the other chromophore. The output of FRET can either be a gain of a fluorescence signal (if two appropriate chromophores are utilized) or a loss in fluorescence signal (if a chromophore and a “quencher” are utilized). Unfortunately, antibody based FRET technology would not be useful in a system for detecting SEB since the signal produced from FRET is typically weak and requires either a high degree of amplification or a situation where many FRET based interaction are occurring in order to be measurable and quantitative. Additionally, the use of antibodies would require multiple incubation and wash steps (3-4 hours) as non-specific FRET interactions may occur if the two antibodies come in close contact within the solution. Consequently, a simple FRET based assay would not work for a quantitative assay that must be simple and easy to perform outside of a lab environment. 
     Accordingly, in one aspect, a method for detection of a target in a sample, the method comprising the steps of: providing an assay mixture comprising: (i) a first probe comprising a first antibody recognizing a first epitope of the target, the first antibody conjugated to an RNA oligonucleotide; (ii) a second probe comprising a second antibody recognizing a second epitope of the target, the second antibody conjugated to a DNA oligonucleotide; (iii) a reverse primer, wherein the reverse primer comprises a first region complimentary to the RNA oligonucleotide, and a second region complimentary to the DNA oligonucleotide; and (iv) a reverse transcriptase, wherein the reverse transcriptase creates a DNA transcription product from the RNA oligonucleotide using the reverse primer only if the RNA oligonucleotide and the DNA oligonucleotide are in close proximity; adding the sample to the assay mixture to create a reaction mixture; incubating the reaction mixture for a predetermined period of time under conditions suitable for reverse transcription by the reverse transcriptase; and analyzing the reaction mixture for the presence of the DNA transcription product of the RNA oligonucleotide; wherein when the target is present in the sample, and the first antibody is interacting with the first epitope, and the second antibody is interacting with the second epitope, the first region of the reverse primer binds the RNA oligonucleotide and the second region of the reverse primer binds the DNA oligonucleotide to bring the RNA oligonucleotide and the DNA oligonucleotide in close proximity; and wherein the presence of the DNA transcription product indicates the presence of the target in the sample. 
     In some embodiments, the first antibody is conjugated to the 5′ end of the RNA oligonucleotide. 
     In some embodiments, the second antibody is conjugated to the 3′ end of the DNA oligonucleotide. 
     In some embodiments, the first region of the reverse primer is complimentary to the 3′ end of the RNA oligonucleotide. 
     In some embodiments, the first region of the reverse primer comprises up to approximately eight nucleotides. 
     In some embodiments, the second region of the reverse primer is complimentary to the 5′ end of the DNA oligonucleotide. 
     In some embodiments, the assay mixture further comprises: (i) a DNA polymerase; (ii) a forward primer complimentary to at least a portion of the DNA transcription product and (iii) a detection probe comprising an oligonucleotide complimentary to at least a portion of the DNA transcription product, and further comprising a fluorophore at one end of the oligonucleotide and a quencher at the opposite end of the oligonucleotide; and further comprising the steps of: inactivating the reverse transcriptase; and incubating the reaction mixture for a predetermined period of time under conditions suitable for qPCR. 
     In some embodiments, the method includes the step of incubating the sample with an antibody prior to the step of adding the sample to the assay mixture. 
     In some embodiments, the assay mixture further comprises a modified DNA oligonucleotide complimentary to at least a portion of the RNA oligonucleotide. 
     In some embodiments, the modification is selected from the group consisting of a 3′ spacer, a 3′ chain terminator, a 3′ fluorochrome, and combinations thereof. 
     In some embodiments, the assay mixture further comprises a detection probe comprising an oligonucleotide complimentary to at least a portion of the RNA oligonucleotide. 
     In one aspect, a method for detection of a target in a sample, the method comprising the steps of; providing an assay mixture comprising: (i) a first probe comprising a first antibody recognizing a first epitope of the target, the first antibody conjugated to the 5′ end of an RNA oligonucleotide; (ii) a second probe comprising a second antibody recognizing a second epitope of the target, the second antibody conjugated to the 3′ end of a DNA oligonucleotide; (iii) a reverse primer, wherein the reverse primer comprises a first region complimentary to 3′ end of the RNA oligonucleotide, and a second region complimentary to the 5′ end of the DNA oligonucleotide; (iv) a reverse transcriptase, wherein the reverse transcriptase creates a DNA transcription product from the RNA oligonucleotide using the reverse primer only if the RNA oligonucleotide and the DNA oligonucleotide are in close proximity; (v) a DNA polymerase; (vi) a forward primer complimentary to at least a portion of a DNA transcription product; and (vii) a detection probe comprising an oligonucleotide complimentary to at least a portion of the DNA transcription product, and further comprising a fluorophore at one end of the oligonucleotide and a quencher at the opposite end of the oligonucleotide; adding the sample to the assay mixture to create a reaction mixture; incubating the reaction mixture for a predetermined period of time under conditions suitable for reverse transcription by the reverse transcriptase; inactivating the reverse transcriptase; and incubating the reaction mixture for a predetermined period of time under conditions suitable for qPCR; wherein when the target is present in the sample, and the first antibody is interacting with the first epitope, and the second antibody is interacting with the second epitope, the first region of the reverse primer binds the RNA oligonucleotide and the second region of the reverse primer binds the DNA oligonucleotide to bring the RNA oligonucleotide and the DNA oligonucleotide in close proximity. 
     In some embodiments, the method includes the step of analyzing the reaction mixture for the presence of the DNA transcription product of the RNA oligonucleotide, wherein the presence of the DNA transcription product indicates the presence of the target in the sample. 
     In some embodiments, the method includes the step of analyzing the reaction mixture for fluorescence from the detection probe, wherein the presence of fluorescence from the detection probe indicates the presence of the target in the sample. 
     In one aspect, a kit for detection of a target in a sample, including: an as say mixture comprising: (i) a first probe comprising a first antibody recognizing a first epitope of the target, the first antibody conjugated to an RNA oligonucleotide; (ii) a second probe comprising a second antibody recognizing a second epitope of the target, the second antibody conjugated to a DNA oligonucleotide; (iii) a reverse primer, wherein the reverse primer comprises a first region complimentary to the RNA oligonucleotide, and a second region complimentary to the DNA oligonucleotide; and (iv) a reverse transcriptase. 
     In some embodiments, one or more components of the assay mixture are stored separately from the remainder of the components prior to use of the assay mixture. 
     In some embodiments, the assay mixture further comprises: (i) a DNA polymerase; (ii) a forward primer complimentary to at least a portion of the DNA transcription product and (iii) a detection probe comprising an oligonucleotide complimentary to at least a portion of the DNA transcription product, and further comprising a fluorophore at one end of the oligonucleotide and a quencher at the opposite end of the oligonucleotide. 
     In some embodiments, the first antibody is conjugated to the 5′ end of the RNA oligonucleotide. 
     In some embodiments, the second antibody is conjugated to the 3′ end of the DNA oligonucleotide. 
     In some embodiments, the first region of the reverse primer is complimentary to the 3′ end of the RNA oligonucleotide. 
     In some embodiments, the first region of the reverse primer comprises up to approximately eight nucleotides. 
     In some embodiments, the second region of the reverse primer is complimentary to the 5′ end of the DNA oligonucleotide. 
     In some embodiments, the assay mixture further comprises a modified DNA oligonucleotide complimentary to at least a portion of the RNA oligonucleotide. In some embodiments, the modification is selected from the group consisting of a 3′ spacer, a 3′ chain terminator, a 3′ fluorochrome, and combinations thereof. 
     In some embodiments, the assay mixture further comprises a detection probe comprising an oligonucleotide complimentary to at least a portion of the RNA oligonucleotide. 
    
    
     
       BRIEF DESCRIPTION OF THE DRAWINGS 
       The present invention will be more fully understood and appreciated by reading the following Detailed Description in conjunction with the accompanying drawings, in which: 
         FIG. 1  is a diagrammatic representation of the assay components of the fluorescence-based assay in accordance with an embodiment; 
         FIG. 2  is a diagrammatic representation of antibodies (conjugated with an oligonucleotide) binding to molecular target in accordance with an embodiment; 
         FIG. 3  is a diagrammatic representation of a primer simultaneously binding to a short segment on the RNA-Left Arm element and a short segment on the DNA-Right arm element, which occurs when the two elements are brought together in close proximity after antibodies bind to molecular target, in accordance with an embodiment; 
         FIG. 4  is a diagrammatic representation of reverse transcriptase synthesizing a single stranded DNA molecule from the RNA-Left Arm template, according to an embodiment; 
         FIG. 5  is a diagrammatic representation of a first cycle of qPCR reaction, in which DNA polymerase synthesizes DNA from the reverse-transcribed DNA template and excises fluorophore from a probe, in accordance with an embodiment; 
         FIG. 6  is a diagrammatic representation of a second cycle of qPCR reaction, in accordance with an embodiment; 
         FIG. 7  is a graph of a qPCR reaction in accordance with an embodiment including variations of the Reverse Primers (with differing degrees of nucleotide overlap, from 0 to 8 bp, with the RNA-Left Arm) and preparations of the Left and Right Arms not conjugated to antibodies; 
         FIG. 8  is a graph of a qPCR reaction analyzing the use of PAPA to detect insulin in accordance with an embodiment; 
         FIG. 9  is a graph of a qPCR reaction analyzing the use of PAPA to detect IL-2 in accordance with an embodiment; 
         FIG. 10A  is a graph of a qPCR reaction analyzing the use of PAPA to detect active SEB toxin compared to inactive SEB toxoid in accordance with an embodiment; 
         FIG. 10B  is a graph of a qPCR reaction analyzing the use of PAPA and control isotype antibodies to detect active SEB toxin or inactive SEB toxoid in accordance with an embodiment; and 
         FIG. 11  is a graph of a qPCR reaction analyzing the use of PAPA with CAPs and COMP Probe (to reduce background) to detect insulin in accordance with an embodiment. 
     
    
    
     DETAILED DESCRIPTION 
     In contrast to ELISA and FRET, PAPA—a new type of Oligonucleotide Linked Immunosorbent Assay (“OLISA”)—is capable of detecting a dual antibody binding event by producing a strong signal while avoiding multiple wash and incubation steps. See, for example,  FIGS. 1 through 6 . 
     According to an embodiment, the assay consists of two distinct antibody clones (Antibody-1 denoted by numeral  10  and Antibody-2 denoted by numeral  20 ) that recognize two different epitopes on the same molecule (See  FIG. 1 ). Each of the antibody clones are conjugated or “linked” to oligonucleotides of a specified sequence and type. Antibody-1 is conjugated to an RNA oligonucleotide at its 5′ end, referred to as the RNA-left arm  30 . Antibody-2 is conjugated to a DNA oligonucleotide at its 3′ end, referred to as the DNA-right arm  40 . Also included in the assay mix is a DNA reverse primer  50  that is complimentary to the 5′ end of the DNA right arm, with the exception of the 3′ end of the DNA reverse primer that possesses a 1 to 8 (the number is dependent on the assay conditions) complimentary nucleotide bases to the 3′ end of the RNA-left arm (See  FIGS. 1-3 ). 
     According to one embodiment, the number of overlapping complimentary bases at the 3′ end of the DNA reverse primer which joins the RNA-left arm to the DNA-right arm is a critical element of the assay. Since so few nucleotide bases are involved in this interaction, the energy required to break this bond between the RNA-left arm to the DNA-right arm held together by the DNA reverse primer is minimal, and therefore would not normally occur in solution/suspension. However, when the RNA-left arm and DNA-right arm are brought into close proximity to each other, such as when bound together on the same molecule (See  FIG. 2 ), the interaction becomes much more favorable. Therefore, when held in close proximity, the RNA-left arm and DNA-right arm can be held together with the DNA reverse primer (See  FIG. 3 ). 
     According to an embodiment, a reverse transcriptase  60  such as M-MLV, or a hot-start reverse transcriptase, among others, is used for the detection of the dual antibody binding event (See  FIG. 1 ). This reverse transcriptase uses the DNA reverse primer and the RNA-left arm to create a DNA single stranded complimentary copy  70  of the RNA-left arm sequence (See  FIG. 4 ). This DNA copy is only created when the RNA-left arm and DNA-right arm are joined together by the DNA reverse primer (with a minimized overlap to the RNA-left arm which cannot initiate the reaction in solutions lacking the target molecule), and thus the DNA copy is only created when Antibody-1 and Antibody-2 are joined together on the same molecule (See  FIG. 4 ). Both the antibody binding and reverse transcriptase steps would occur at or near body temperature (including, but not limited to 37° C. to 42° C.), depending on the assay conditions. According to an embodiment, the reverse transcriptase step will only be allowed to occur for one cycle, and therefore the number of reverse-transcribed DNA copies made will be dependent on the number of molecules present onto which both Antibody-1 and Antibody-2 can bind. This makes the PAPA a quantitative assay. 
     According to an embodiment, other components are utilized in the assay mix in order to quantify the number of reverse-transcribed DNA copies via a quantitative fluorescence PCR method. For example, these components could include a DNA polymerase  80  with 5′ exo-nuclease activity, a DNA forward primer  90  complimentary to the 3′ end of the reverse-transcribed DNA, and a DNA probe  100  with a fluorophore and a quencher at opposite ends that is complimentary to the reverse-transcribed DNA (See  FIG. 1 ). To perform quantitative PCR, the temperature is initially raised to 95° C. At this temperature, the DNA polymerase  80 , such as a Hot-start DNA polymerase, is activated and non-heat stable proteins, such as the Reverse Transcriptase  60  and Antibody-1 and Antibody-2 are inactivated. Due to the inactivation of the reverse transcriptase and antibodies, no new reverse-transcribed DNA copies can be made. After this step, normal qPCR protocols can be followed. Temperatures are sequentially changed from the annealing (50-65° C.), to the elongation (55-72° C.), to the denaturation (95° C.) phases for each PCR cycle. During every cycle, a fluorescent signal is generated due to the separation of the fluorophore and quencher on a probe that is bound to a DNA template being transcribed by the DNA polymerase with 5′exo-nuclease activity (See  FIGS. 5-6 ). The fluorescence signals increase throughout the PCR cycles until the signal exceeds a threshold, called the threshold cycle (“Ct”). The threshold cycle, or the cycle at which the fluorescence threshold is reached, is relative to the amount of starting material/Reverse-transcribed DNA copies/target molecules. Therefore, the PAPA is as quantifiable as a qPCR assay. In addition to the Ct value, the maximum fluorescence output of the assay can be used to quantify the amount of starting material/reverse-transcribed DNA copies/target molecules in the assay. 
     According to an embodiment, other components can be added to the assay to reduce background signals within the PAPA. One such set of components, for example, would prevent the non-specific binding of DNA oligonucleotides to the RNA oligonucleotides. This can be accomplished by utilizing modified DNA oligonucleotides that possess a complimentary sequence to that of the RNA oligonucleotide. The modification on the DNA oligonucleotide would prevent the DNA nucleotide from being extended (i.e. used as a primer) by the DNA or RNA polymerase (reverse transcriptase). This modified DNA oligonucleotide is referred to as a “CAP”. The CAP can be of any length, as long as it maintains the ability to bind to the RNA oligonucleotide. Examples of modifications that prevent the CAP from being utilized as a primer include but are not limited to 3′ spacers (such as C3 spacer), 3′ chain terminators (such as dideoxcytidine or dideoxyguanine), and 3′ fluorochromes (such as fluorescein). In addition to CAPs, a qPCR probe can also be used to prevent the non-specific binding of DNA oligonucleotides to the RNA oligonucleotide if this probe was designed to be complimentary to a section. This type of blocking qPCR probe is referred to as a “COMP Probe”. 
     According to an embodiment, in order to design a PAPA specific for the detection of unique molecules a few details should be considered. If possible, it should be determined where the two different antibodies bind to on the specified molecule. It is important to determine the orientation of one antibody to the other in order to correctly establish the antibody that should be conjugated with the RNA-left arm vs. the DNA-right arm. If not, a series of experiments may be performed to establish the correct orientation. Another consideration is the distance between the antibody binding sites on the specified molecule. Distance is a factor in that the RNA-left arm needs to be close enough to the DNA-right arm to allow for an overlap to occur. This distance can be compensated for by varying the length of the DNA-right arm (at its 3′end) as long as the complementary sequence for the DNA reverse primer is not affected. Another important factor to consider is minimizing the possibility of “heterodimer” interactions from the various sequences with the Left-RNA template. These interactions have the potential to cause “false-positive” signals (i.e. a positive signal in the absence of a dual-antibody binding event) if the RNA template is primed with a heterodimer sequence (a nucleotide sequence that is not associated with the 3-prime end of the reverse primer) that binds near the 3-prime end of the RNA template. The strength of these non-ideal interactions will be affected by the assay conditions and can be determined through experimental testing. 
     According to yet another embodiment, there may be an initial antibody block step, such as with an isotype antibody, prior to the addition of the PAPA reagents. An additional wash step may or may not be included. 
     According to an embodiment, all the components for the PAPA can be added at once without the need for buffer changes, washes, or incubation steps, which sets it apart from many other assays. Similar OLISA technologies, such as the Proximity Ligation Assay (“PLA”) and the exonuclease enabled Proximity Extension Assay (“PEA”) require multiple wash and incubation steps to produce the positive signals in their laboratory tests. Due to their time consuming and difficult set-up, these technologies are not suited for fieldable applications. Additionally, since fluorochromes are used for the detection signal, the PAPA has the potential to be multiplexed, where more than one molecule or protein can be detected per assay. 
     Accordingly, the PAPA is a simple and easy to use one-step technology that can be designed to detect and quantify the presence of any molecule in a sample following analysis on any fluorescent PCR-based platform. According to one embodiment, in assays for SEB the SEB-PAPA is designed to detect and identify the toxic potential of SEB molecules found in unknown samples. 
     Example 1 
     A methodological procedure for developing and testing a PAPA test using kanamycin resistance gene sequence. Although the kanamycin resistance gene sequence is utilized for the primers, templates, and probes in this version of the PAPA, use of this sequence is not mandatory. Other sequences, and other selective mechanisms, are possible. 
     As an initial step, the development of the PAPA requires determination of the number of overlapping nucleotides between the reverse primer and RNA-Left Arm required to produce a positive signal in solution (i.e., without the requirement of being in close proximity caused by binding of the associated antibody to the target). This can be accomplished, for example, utilizing an assay comprising the reagents listed or described in  FIG. 1 . According to one variation, the RNA-Left Arm and DNA-Right Arm will not be linked to or associated with an antibody. According to another variation, the RNA-Left Arm and DNA-Right Arm are linked to or associated with an antibody (including but not limited to the antibody that each element will be linked to in the final, field-deployed assay), but no target is introduced. Without target, the antibodies should not themselves cause the RNA-Left Arm and DNA-Right Arm elements to come into close proximity. According to an embodiment, nucleotide overlaps of 0, 1, 2, 3, 4, 5, 6, 7, and 8 can be utilized to promote the interaction between the RNA-Left Arm and the DNA-Right Arm. See, for example, the sequences listed in TABLE 1. Depending on the assay conditions (i.e. reaction temperature, annealing/elongation times, etc) and components (i.e. salts, enzyme concentration, contaminants, etc), the number of nucleotide overlaps required for the assay to produce a signal with and without a dual antibody binding event will vary. According to one embodiment, the assay can initially be tested in the context of simple qPCR and Reverse Transcriptase PCR, using conditions with a full RNA template or a shortened Left-RNA template (requiring a nucleotide overlap to produce a signal). 
     According to yet another embodiment, the assay can be modified or made more specific by utilizing one or more oligonucleotide sequences with modified bases. For example, the assay can be designed to utilize oligonucleotides containing isoguanine (iso-dG) and 5′-methylisocytosine (iso-dC), which form specific bonds since iso-dG and iso-dC are unique and only form iso-dG/iso-dC or iso-dC/iso-dG bonds. Another example is the use of hybrid RNA/DNA oligonucleotide sequences. Many other examples of modified oligos are possible in order to increase or otherwise alter specificity in the assay. 
     To determine the minimal degree of overlap required to produce a positive signal in a Reverse Transcriptase driven PCR reaction, an assay was set up using preparations of the Left-RNA Arm and Right-DNA Arm in which the “arms” were not conjugated to detection antibodies ( FIG. 2 ). The assay consisted of Forward Primer 2 (500 nM), Probe 2 (100 nM), RNA-Left Arm (not conjugated to an antibody; 1.2×10 7  molecules per reaction), DNA-Right Arm 5 (not conjugated to an antibody; 500 nM), Hot-start DNA polymerase (0.025 units per uL), Reverse Transcriptase (M-MLV; 1 unit per uL), DNA polymerase/Reverse Transcriptase buffer mix, and different versions of the Reverse Primers (with differing degrees of nucleotide overlap, from 0 to 8 bp, with the RNA-Left Arm; 500 nM). The reaction was performed with a 5 minute initial Reverse Transcriptase step at 37° C., followed by 94° C. hot start/denaturing step (4 minutes), and then 55 cycles of 94° C. (15 seconds) to 55° C. (30 seconds) in the Rotor-Gene Q qPCR instrument. Based on the results, when Reverse Primers with 6, 7 or 8 bp overlapping nucleotides are used, positive signals are generated in solution in the absence of antibody binding events ( FIG. 7 ). Additionally, no signals are generated when Reverse Primers with 0, 2, 3, 4 or 5 bp overlapping nucleotides are used ( FIG. 7 ). Therefore, antibody binding events would be required in these conditions to generate a signal when Reverse Primers with 2, 3, 4 or 5 bp overlapping nucleotides are used. 
     
       
         
               
             
               
               
             
           
               
                 TABLE 1 
               
             
             
               
                   
               
               
                 Oligonucleotides utilized for PAPA testing 
               
               
                 according to an embodiment. 
               
             
          
           
               
                 Oligonucleotide 
                 Oligonucleotide Sequence 
               
               
                 Name 
                 (5′ to 3′) 
               
               
                   
               
               
                 Kan For 1 
                 CGAGTGATTTTGATGACGAGCGT 
               
               
                   
                 (SEQ ID NO: 1) 
               
               
                   
               
               
                 Kan For 2 
                 AGTGATTTTGATGACGAGCGTAA 
               
               
                   
                 (SEQ ID NO: 2) 
               
               
                   
               
               
                 Kan For 3 
                 CGAGTGATTTTGATGACGA 
               
               
                   
                 (SEQ ID NO: 3) 
               
               
                   
               
               
                 Kan Right 1 
                 ACCGGATTCAGTCGTCACTCATGGTGATTTC 
               
               
                 DNA Temp 
                 (SEQ ID NO: 4) 
               
               
                   
               
               
                 Kan Right 2 
                 ACCGGATTCAGTCGTCACTCATGGTGA 
               
               
                 DNA Temp 
                 (SEQ ID NO: 5) 
               
               
                   
               
               
                 Kan Right 3 
                 ACCGGATTCAGTCGTCACTCATGGT 
               
               
                 DNA Temp 
                 (SEQ ID NO: 6) 
               
               
                   
               
               
                 Kan Right 4 
                 ACCGGATTCAGTCGTCACTCATGGTGGT 
               
               
                 DNA Temp 
                 (SEQ ID NO: 7) 
               
               
                   
               
               
                 Kan Right 5 
                 ACCGGATTCAGTCGTCACTCATAATTAA 
               
               
                 DNA Temp 
                 (SEQ ID NO: 8) 
               
               
                   
               
               
                 Kan Right 6 
                 ACCGGATTCAGTCGTCACTCATCCATAA 
               
               
                 DNA Temp 
                 (SEQ ID NO: 9) 
               
               
                   
               
               
                 Kan Right 7 
                 ACCGGATTCAGTCGTCACTCATATATAA 
               
               
                 DNA Temp 
                 (SEQ ID NO: 10) 
               
               
                   
               
               
                 Kan Rev 1-8 
                 CGACTGAATCCGGTGAGAATGG 
               
               
                 overlap 
                 (SEQ ID NO: 11) 
               
               
                   
               
               
                 Kan Rev 1-7  
                 ACGACTGAATCCGGTGAGAATG 
               
               
                 overlap 
                 (SEQ ID NO: 12) 
               
               
                   
               
               
                 Kan Rev 1-6 
                 GACGACTGAATCCGGTGAGAAT 
               
               
                 overlap 
                 (SEQ ID NO: 13) 
               
               
                   
               
               
                 Kan Rev 1-5 
                 TGACGACTGAATCCGGTGAGAA 
               
               
                 overlap 
                 (SEQ ID NO: 14) 
               
               
                   
               
               
                 Kan Rev 1-4 
                 GTGACGACTGAATCCGGTGAGA 
               
               
                 overlap 
                 (SEQ ID NO: 15) 
               
               
                   
               
               
                 Kan Rev 1-3 
                 AGTGACGACTGAATCCGGTGAG 
               
               
                 overlap 
                 (SEQ ID NO: 16) 
               
               
                   
               
               
                 Kan Rev 1-2 
                 GAGTGACGACTGAATCCGGTGA 
               
               
                 overlap 
                 (SEQ ID NO: 17) 
               
               
                   
               
               
                   
               
               
                 Kan Rev 1-1 
                 TGAGTGACGACTGAATCCGGTG 
               
               
                 overlap 
                 (SEQ ID NO: 18) 
               
               
                   
               
               
                 Kan Rev 1-0 
                 ATGAGTGACGACTGAATCCGGT 
               
               
                 overlap 
                 (SEQ ID NO: 19) 
               
               
                   
               
               
                 Kan Probe 1 
                 TGGCTGGCCTGTTGAACAAGTCTGGAAAGA 
               
               
                   
                 (SEQ ID NO: 20) 
               
               
                   
               
               
                 Kan Probe 2 
                 CTGGCCTGTTGAACAAGTCTGGAAAGAAATG 
               
               
                   
                 (SEQ ID NO: 21) 
               
               
                   
               
               
                 Kan Probe 3 
                 AATGGCTGGCCTGTTGAACAAGTCTGGA 
               
               
                   
                 (SEQ ID NO: 22) 
               
               
                   
               
               
                 Kan COMP 
                 TGGCTGGCCTGTTGAACAAGTCTGGAAAGA 
               
               
                 Probe 1 
                 (SEQ ID NO: 23) 
               
               
                   
               
               
                 Kan COMP 
                 CATTTCTTTCCAGACTTGTTCAACAGGCCAG 
               
               
                 Probe 2 
                 (SEQ ID NO: 24 
               
               
                   
               
               
                 Kan COMP 
                 AATGGCTGGCCTGTTGAACAAGTCTGGA 
               
               
                 Probe 3 
                 (SEQ ID NO: 25) 
               
               
                   
               
               
                 CAP 24 
                 GAGAATGGCAAAAGCTTATGCATT 
               
               
                   
                 (SEQ ID NO: 26) 
               
               
                   
               
               
                 CAP 20 
                 GAGAATGGCAAAAGCTTATG 
               
               
                   
                 (SEQ ID NO: 27) 
               
               
                   
               
               
                 CAP 28 
                 GAGAATGGCAAAAGCTTATGCATTTCTT 
               
               
                   
                 (SEQ ID NO: 28) 
               
               
                   
               
               
                 Kan Full 
                 CGAGUGAUUUUGAUGACGAGCGUAAUGGCUG 
               
               
                 RNA Temp 
                 GCCUGUUGAACAAGUCUGGAAAGAAAUGCAU 
               
               
                   
                 AAGCUUUUGCCAUUCUCACCGGAUUCAGUCG 
               
               
                   
                 UCACUCAU (SEQ ID NO: 29) 
               
               
                   
               
               
                 Kan Left 
                 CGAGUGAUUUUGAUGACGAGCGUAAUGGCUG 
               
               
                 RNA Temp 
                 GCCUGUUGAACAAGUCUGGAAAGAAAUGCAU 
               
               
                   
                 AAGCUUUUGCCAUUCUC (SEQ ID NO: 30) 
               
               
                   
               
             
          
         
       
     
     As a second step in PAPA testing, antibody binding studies utilizing antibodies conjugated to oligonucleotides can be performed to determine if close proximity can promote PCR. The experiment described above for the first step can be repeated, this time with the RNA-Left Arm and DNA-Right Arm elements conjugated to antibodies (preferably the antibodies that each element will be linked to in the final, field-deployed assay) and target will be introduced to the system. According to an embodiment (see Example 2), antibodies against human insulin from Mercodia (Mab 1 Anti-Insulin and Mab 2 Anti-Insulin) can be utilized, with human insulin (from Tocris) used as the target protein. These Mercodia anti-insulin antibodies have been reported to be successful in an antibody-based proximity ligation assay. 
     According to another embodiment (see Example 3), antibodies against mouse interleukin-2 (IL-2) from eBioscience (JES6-1A12 and JES6-5H4) can be utilized, with recombinant mouse IL-2 (from eBioscience) as the target protein in the PAPA. These eBioscience anti-insulin antibodies have been utilized in mouse IL-2 ELISA assays. 
     According to another embodiment (see Example 4), antibodies against SEB (2B33 and B87, both available from Santa Cruz Biotechnology) can be utilized with SEB toxin (from BEI resources) as the target protein in the PAPA. These antibodies target the SEB active (TCR and MHC class II) binding sites. The 2B33 antibody blocks MHC class II binding and the B87 antibody blocks TCR binding. 
     According to yet another embodiment, any antibody, aptamer or substance/protein/molecule that can specifically (or non-specifically) bind to a target protein or molecule and be conjugated to an oligonucleotide can be utilized in the PAPA. 
     According to an embodiment, initial studies use a RNA-Left Arm. Additionally, InnovaBiosciences will be utilized initially to conjugate the oligonucleotides to the antibodies. According to an embodiment, the antibodies and target are different from those described herein, and are instead another known or to-be-discovered antibody/antigen recognition pair. 
     Example 2 
     Experiment to test whether the PAPA can be utilized to detect insulin. Antibodies against human insulin (Mab 1 Anti-Insulin and Mab 2 Anti-Insulin) were obtained from Mercodia and conjugated to RNA (Kan Left RNA Temp) and DNA (Kan Right 5 DNA Temp) oligonucleotides by InnovaBiosciences. These sequences were chosen based on data from supporting experiments. Initial conjugations utilized a 2:1 oligo:antibody ratio. Mab 1 Anti-Insulin antibody was conjugated to the RNA oligo, making it the Anti-Insulin Left-RNA Arm. Mab 2 Anti-Insulin antibody was conjugated to the DNA oligo, making it the Anti-Insulin Right-DNA Arm. The assay consisted of Kan Forward Primer 2 (500 nM), Kan Probe 2 (100 nM), Anti-Insulin Left-RNA Arm (1.6×10 10  molecules per reaction), Anti-Insulin Right-DNA Arm (1.6×10 10  molecules per reaction), Hot-start DNA polymerase (0.025 units per uL), Reverse Transcriptase (M-MLV; 1 unit per uL), RNasin (0.4 units per uL), DNA polymerase/Reverse Transcriptase buffer mix, Kan Reverse Primers 1-3 (500 nM) and varying amounts of Insulin (0.116 or 1.16 ng) or H20 (control). The reaction was performed with a 1 hour initial Reverse Transcriptase step at 37° C., followed by 94° C. hot start/denaturing step (4 minutes), and then 55 cycles of 94° C. (15 seconds) to 55° C. (30 seconds) in the Rotor-Gene Q qPCR instrument in a total volume of 15 uL per reaction. The results are shown in  FIG. 8 . The Insulin PAPA is able to detect both concentrations of Insulin (0.116 and 1.16 ng) compared to the H20 samples, with lower Ct values and higher fluorescent outputs for the Insulin samples compared to the H20 samples. In addition, the highest concentrations of Insulin (1.16 ng) produced the lowest Ct values and highest fluorescent outputs, indicating that the assay results correlate to the amount of target added. 
     Example 3 
     Experiment to test whether the PAPA can be utilized to detect IL-2. Antibodies against mouse IL-2 (JES6-1A12 and JES6-5H4) were obtained from eBioscience and conjugated to RNA (Kan Left RNA Temp) and DNA (Kan Right 5 DNA Temp) oligonucleotides by InnovaBiosciences. These sequences were chosen based on data from supporting experiments. Initial conjugations utilized a 2:1 oligo:antibody ratio. The JES6-1A12 Anti-IL-2 antibody was conjugated to the RNA oligo, making it the Anti-IL-2 Left-RNA Arm. The JES6-5H4 Anti-IL-2 antibody was conjugated to the DNA olgio, making it the Anti-IL-2 Right-DNA Arm. The assay consisted of Kan Forward Primer 2 (500 nM), Kan Probe 2 (100 nM), Anti-IL-2 Left-RNA Arm (1.6×10 10  molecules), Anti-IL-2 Right-DNA Arm (1.6×10 10  molecules per reaction), Hot-start DNA polymerase (0.025 units per uL), Reverse Transcriptase (M-MLV; 1 unit per uL), RNasin (0.4 units per uL), DNA polymerase/Reverse Transcriptase buffer mix, Kan Reverse Primers 1-3 (500 nM) and varying amounts of IL-2 (0.20 or 2.0 ng) or H20 (control). The reaction was performed with a 1 hour initial Reverse Transcriptase step at 37° C., followed by 94° C. hot start/denaturing step (4 minutes), and then 55 cycles of 94° C. (15 seconds) to 55° C. (30 seconds) in the Rotor-Gene Q qPCR instrument in a total volume of 15 uL per reaction. The results are shown in  FIG. 9 . The IL-2 PAPA is able to detect both concentrations of IL-2 (0.20 and 2.0 ng) compared to the H20 samples, with lower Ct values and higher fluorescent outputs for the IL-2 samples compared to the H20 samples. In addition, the highest concentrations of IL-2 (2.0 ng) produced the lowest Ct values and highest fluorescent outputs, indicating that the assay results correlate to the amount of target added. 
     Example 4 
     Experiment to test whether the PAPA can be utilized to detect active SEB toxin versus inactive SEB toxoid. Antibodies against SEB (2B33 and B87) or an isotype control (eBioscience, Rat IgG2a) were conjugated to RNA (Kan Left RNA Temp) and DNA (Kan Right DNA Temp) oligonucleotides by InnovaBiosciences. These sequences were chosen based on data from supporting experiments. Initial conjugations utilized a 2:1 oligo:antibody ratio. The 2B33 Anti-SEB antibody was conjugated to the RNA oligo, making it the Anti-SEB Left-RNA Arm. The B87 Anti-SEB antibody was conjugated to the DNA olgio, making it the Anti-SEB Right-DNA Arm. For a control, the isotype antibody was also conjugated to the RNA and DNA oligos, making a Control Left-RNA Arm and Control Right-DNA Arm, respectively. The SEB assay consisted of Kan Forward Primer 2 (500 nM), Kan Probe 2 (100 nM), Anti-SEB Left-RNA Arm (1.6×10 10  molecules per reaction), Anti-SEB Right-DNA Arm (1.6×10 10  molecules per reaction), Hot-start DNA polymerase (0.025 units per uL), Reverse Transcriptase (M-MLV; 1 unit per uL), RNasin (0.4 units per uL), DNA polymerase/Reverse Transcriptase buffer mix, Kan Reverse Primers 1-3 (500 nM) and added SEB toxin (BEI, 200 ng), inactivated SEB toxoid (BEI, 200 ng) or H20 (control). The control assay consisted of the same components above, with the Control Arms being used in place of the SEB Arms. The reaction was performed with a 5 minute initial Reverse Transcriptase step at 37° C., followed by 94° C. hot start/denaturing step (4 minutes), and then 55 cycles of 94° C. (15 seconds) to 55° C. (30 seconds) in the BioRad CFX96 qPCR instrument in a total volume of 15 uL per reaction. The results are shown in  FIG. 10A  and  FIG. 10B . The SEB PAPA is able to detect the active SEB toxin samples compared to the H20 and inactive SEB toxoid samples, with lower Ct values and higher fluorescent outputs for the SEB toxin compared to the H20 and SEB toxoid samples ( FIG. 10A ). This indicates that the SEB PAPA is specific for active SEB toxin ( FIG. 10A ). The Control PAPA shows that there are no differences between SEB toxin samples compared to the H20 samples, with similar Ct values and fluorescent outputs, indicating that the SEB toxin is not detected in the Control PAPA ( FIG. 10B ). The SEB toxoid produces higher Ct values and lower fluorescent outputs, indicating that the SEB toxoid is also not detected in the Control PAPA ( FIG. 10B ). 
     Example 5 
     Experiment to test whether the PAPA with CAPs and COMP Probe can be utilized to detect insulin. Antibodies against human insulin (Mab 1 Anti-Insulin and Mab 2 Anti-Insulin) were obtained from Mercodia and conjugated to RNA (Kan Left RNA Temp) and DNA (Kan Right 5 DNA Temp) oligonucleotides by InnovaBiosciences. These sequences were chosen based on data from supporting experiments. Initial conjugations utilized a 2:1 oligo:antibody ratio. Mab 1 Anti-Insulin antibody was conjugated to the RNA oligo, making it the Anti-Insulin Left-RNA Arm. Mab 2 Anti-Insulin antibody was conjugated to the DNA olgio, making it the Anti-Insulin Right-DNA Arm. The assay consisted of Kan Forward Primer 2 (500 nM), Kan COMP Probe 2 (100 nM), CAP 20 (1.3 uM), Anti-Insulin Left-RNA Arm (1.6×10 10  molecules per reaction), Anti-Insulin Right-DNA Arm (1.6×10 10  molecules per reaction), Hot-start DNA polymerase (0.025 units per uL), Reverse Transcriptase (M-MLV; 1 unit per uL), RNasin (0.4 units per uL), DNA polymerase/Reverse Transcriptase buffer mix, Kan Reverse Primers 1-3 (500 nM) and varying amounts of Insulin (0.116 or 1.16 ng) or H20 (control). The reaction was performed with a 1 hour initial Reverse Transcriptase step at 37° C., followed by 94° C. hot start/denaturing step (4 minutes), and then 55 cycles of 94° C. (15 seconds) to 55° C. (30 seconds) in the Rotor-Gene Q qPCR instrument in a total volume of 15 uL per reaction. The results are shown in  FIG. 11 . The Insulin PAPA with CAPs and COMP Probe 2 is able to detect both concentrations of Insulin (0.116 and 1.16 ng) compared to the H20 samples, with lower Ct values and higher fluorescent outputs for the Insulin samples compared to the H20 samples. In addition, the highest concentrations of Insulin (1.16 ng) produced the lowest Ct values and highest fluorescent outputs, indicating that the assay results correlate to the amount of target added. Compared to the Insulin PAPA without CAPs and COMP Probe 2 ( FIG. 8 ), less background signal is produced when CAPs and COMP Probe 2 are present in the PAPA ( FIG. 11 ). 
     While various embodiments have been described and illustrated herein, those of ordinary skill in the art will readily envision a variety of other means and/or structures for performing the function and/or obtaining the results and/or one or more of the advantages described herein, and each of such variations and/or modifications is deemed to be within the scope of the embodiments described herein. More generally, those skilled in the art will readily appreciate that all parameters, dimensions, materials, and configurations described herein are meant to be exemplary and that the actual parameters, dimensions, materials, and/or configurations will depend upon the specific application or applications for which the teachings is/are used. Those skilled in the art will recognize, or be able to ascertain using no more than routine experimentation, many equivalents to the specific embodiments described herein. It is, therefore, to be understood that the foregoing embodiments are presented by way of example only and that, within the scope of the appended claims and equivalents thereto, embodiments may be practiced otherwise than as specifically described and claimed. Embodiments of the present disclosure are directed to each individual feature, system, article, material, kit, and/or method described herein. In addition, any combination of two or more such features, systems, articles, materials, kits, and/or methods, if such features, systems, articles, materials, kits, and/or methods are not mutually inconsistent, is included within the scope of the present disclosure.