# Patent

## Title
Enzyme cascade methods for E-TRACE assay signal amplification

## Abstract

The disclosure also relates to novel methods for detection of biological targets using amplification steps in conjunction with conversion of functional groups attached to a transitional metal complex, resulting in quantifiable electrochemical signal at two unique potentials, E°1 and E°2.

## Background
CROSS REFERENCE TO RELATED APPLICATIONS
This application claims the benefit of priority to U.S. Provisional Patent Application No. 61/584,563, filed Jan. 9, 2012, the entire disclosures of which are hereby incorporated by reference in their entirety.


FIELD OF THE INVENTION
The invention relates to novel compositions and methods for the detection of biological targets using amplification steps in conjunction with conversion of functional groups attached to a transitional metal complex, resulting in quantifiable electrochemical signal at two unique potentials, E°1 and E°2. In particular, the methods of the invention utilize enzyme-triggered redox altering chemical elimination (E-TRACE) reaction.
BACKGROUND OF THE INVENTION
The electromotive force (EMF) is the maximum potential difference between two electrodes of a galvanic or voltaic cell, where the standard hydrogen electrode is on the left-hand side for the following cell:
















1



2


Pt Electrode
H2
Aqueous Electrolyte
10−3M Fe(ClO4)3
Pt




Solution
10−3M Fe(ClO4)2









The EMF is called the electrode potential of the electrode placed on the right-hand side in the graphical scheme of the cell, but only when the liquid junction between the solutions can be neglected or calculated, or if it does not exist at all.

The electrode potential of the electrode on the right-hand side (often called the oxidation-reduction potential) is given by the Nernst equation

EFe3+/Fe2+=EFe3+Fe2+0+(RT/F)ln(aFe3+/aFe2+)

This relationship follows from equation (2.21) when (μFe3−0−μFe2+0)/F is set equal to EFe3+/Fe2+0 and the pH and ln pH2 are equal to zero. In the subscript of the symbol for the electrode potential the symbols for the oxidized and reduced components of the oxidation-reduction system are indicated. With more complex reactions it is particularly recommended to write the whole reaction that takes place in the right-hand half of the cell after symbol E (the ‘half-cell’ reaction); thus, in the present case

EFe3+/Fe2+≡E(Fe3+e=Fe2+)

Quantity EFe3+/Fe2+0 is termed the standard electrode potential. It characterizes the oxidizing or reducing ability of the component of oxidation-reduction systems. With more positive standard electrode potentials, the oxidized form of the system is a stronger oxidant and the reduced form is a weaker reductant. Similarly, with a more negative standard potential, the reduced component of the oxidation-reduction system is a stronger reductant and the oxidized form a weaker oxidant.
The standard electrode E°, in its standard usage in the Nernst equation, equation (1-2) is described as:




  E
  =
  
    
      E
      0
    
    +
    
      
        
          2.3
          ⁢
          RT
        
        
          n
          ⁢
          
            
          
          ⁢
          F
        
      
      ⁢
      log
      ⁢
      
        
          
            C
            0
          
          ⁡
          
            (
            
              0
              ,
              t
            
            )
          
        
        
          
            C
            R
          
          ⁡
          
            (
            
              0
              ,
              t
            
            )
          
        
      
    
  




where E0 is the standard potential for the redox reaction, R is the universal gas constant (8.314 JK−1 mol−1), T is the Kelvin temperature, n is the number of electrons transferred in the reaction, and F is the Faraday constant (96,487 coulombs). On the negative side of E0, the oxidized form thus tends to be reduced, and the forward reaction (i.e., reduction) is more favorable. The current resulting from a change in oxidation state of the electroactive species is termed the faradaic.

Previous work describes using conversion of functional groups attached to a transitional metal complex resulting in quantifiable electrochemical signal at two unique potentials, E°1 and E°2. See for example, U.S. Patent Publication Nos. US 2011 0033869 and US 2012-0181186, all herein incorporated by reference in their entirety. The methods generally comprise binding an analyte within a sandwich of binding ligands which may have a functional tag, on a solid support other than the electrode. After target binding, a peroxide generating moiety or an intermediary enzyme and substrate are added which generates hydrogen peroxide. The redox active complex is bound to an electrode and comprises a peroxide sensitive moiety (PSM). The peroxide generated from the enzyme system reacts with the PSM, removing a self-immolative moiety (SIM) and converting functional groups attached to a transitional metal complex resulting in quantifiable electrochemical signal at two unique potentials, E°1 and E°2.
SUMMARY OF THE INVENTION
The present invention provides composition and methods for the detection of target analytes using amplification methods to enhance catalytically electrochemical signal from the conversion of functional groups attached to a transitional metal complex resulting in quantifiable electrochemical signal at two unique potentials, E°1 and E°2. In particular, the present invention discloses the advantages of combining the amplification steps. In one aspect, the invention provides compositions and methods for the detection of target analyte in a test sample. Thus, the invention provides a first solid support comprising an electrode comprising: a self-assembled monolayer (SAM). (ii) a covalently attached electroactive active moiety (EAM) comprising a transition metal complex comprising a self-immolative moiety (SIM) and a peroxide sensitive moiety (PSM), wherein said EAM has a first E0 and a self-assembled monolayer (SAM). The capture binding ligand that binds the analyte, is on a second solid support other than the electrode.
In one embodiment a small molecule target, adenosine triphopsphate (ATP) can be detected utilizing an enzymatic amplification system. The ATP, along with glycerol, acts as a substrate for Glycerol Kinase (GK), generating Adenosine Diphosphate (ADP) and glycerol-3-phosphate. The ADP byproduct and phosphocreatine act as substrates for Creatine Kinase (CK) which transfers the phosphate group from phosphocreatine to ADP to regenerate ATP and Creatine. The ATP is then utilized to generate another glycerol-3-phosphate by Glycerol Kinase. Thus the ATP/ADP cycling allows multiple glycerol-3-phosphate molecules to be generated for one starting molecule of ATP. The glycerol-3-phosphate then is oxidized to form H2O2 and glycerone phosphate by Glycerol-3-Phosphate Oxidase (G3PO). Therefore H2O2 is generated in a manner dependent on the starting ATP concentration but results in a concentration of H2O2 orders of magnitude higher.
In one embodiment, the disclosure provides methods for detecting a target analyte in a test sample, said method comprising:

    
    
        (a) contacting a target specific enzyme, a recycling enzyme and a peroxide-generating enzyme with said target sample under conditions wherein a peroxide is generated in the presence of said target analyte to form an assay mixture;
        (b) contacting the assay mixture with a first solid support comprising an electrode comprising a covalently attached electroactive moiety (EAM) having a first E0, said EAM comprising a transition metal complex comprising a self-immolative moiety (SIM) and a peroxide sensitive moiety (PSM), wherein said peroxide reacts with said PSM to release said SIM from said EAM and result in said EAM having a second E0;
        (c) measuring the electrochemical properties of said EAM at the first E0 and at the second E0; and
        (d) detecting for the presence or concentration of said target analyte from said electrochemical properties.
    
    


In one embodiment of the disclosure any preceding embodiment is where said electrode further comprises a self-assembled monolayer (SAM). In another embodiment of the disclosure any preceding embodiment is where the target analyte is a small molecule.
In one embodiment of the disclosure said target analyte is reduced Nicotinamide Adenine Dinucleotide (NADH). In another embodiment, said recycling enzyme is Alcohol Dehydrogenase (ADH), said target specific enzyme is NADH Oxidase, and said peroxide generating enzyme is NADH oxidase.
In one embodiment of the disclosure said target analyte is Adenosine Triphosphate (ATP). In another embodiment, said target specific enzyme is Glycerol Kinase (GK), said recycling enzyme is Creatine Kinase (CK) or Glycerol 3-Phosphate Dehydrogenase (GPDH), and said peroxide generating enzyme is Glycerol-3-Phosphate Oxidase (G3PO).
In one embodiment of the disclosure any preceding embodiment is where the target analyte is testosterone.
In one embodiment of the disclosure any preceding embodiment is where said EAM comprises a transition metal. In one embodiment, said transition metal is chosen from the group consisting of iron, ruthenium and osmium.
In one embodiment of the disclosure any preceding embodiment is said EAM is chosen from the group consisting of ferrocene and substituted ferrocene.
In another embodiment a small molecule target, adenosine triphosphate (ATP) can be detected utilizing a different enzymatic amplification system. The ATP, along with glycerol, acts as a substrate for Glycerol Kinase (GK), generating Adenosine Diphosphate (ADP) and glycerol-3-phosphate. The glycerol-3-phosphate then is oxidized to form H2O2 and glycerone phosphate by Glycerol-3-Phosphate Oxidase (G3PO). The glycerone phosphate is then reduced by Glycerol-3-phosphate Dehyrodgenase (GPDH) utilizing NADH, regenerating glycerol-3-phosphate which in turn is re-oxidized by G3PO generating another molecule of H2O2. Therefore H2O2 is generated in a manner dependent on the starting ATP concentration but results in a concentration of H2O2 orders of magnitude higher.
In one embodiment a small molecule target, reduced Nicotinamide Adenine Dinucleotide (NADH) can be detected utilizing an enzymatic amplification system. The NADH, acts as a substrate for NADH oxidase (NAOX), generating NAD+ and H2O2. The NAD+ byproduct and ethanol act as substrates for alcohol dehydrogenase (ADH) which produces acetaldehyde and regenerates NADH. The NADH is then re-oxidized by NADH oxidase generating another H2O2. Thus the NADH/NAD+ cycling allows multiple NADH molecules to be generated from one starting molecule of NADH. Therefore H2O2 is generated in a manner dependent on the starting NADH concentration but results in a concentration of H2O2 orders of magnitude higher.
In one embodiment, the disclosure provides methods for detecting a target analyte in a test sample, said method comprising:

    
    
        (a) contacting said test sample with a first complex comprising a labeled target analyte pre-bound to a binding ligand, with said test sample under conditions wherein said target analyte from said test sample, if present, displaces said labeled target from said first complex forming a second complex, wherein said labeled target analyte is labeled with a first member of a specific binding pair;
        (b) contacting said second complex with an intermediary enzyme of a peroxide generating system comprising a labeled linker forming a third complex, wherein said labeled linker is labeled with a second member of said specific binding pair;
        (c) isolating said third complex;
        (d) contacting said third complex with a substrate for said intermediary enzyme of peroxide-generating system under conditions such that product(s) are generated to form a first assay mixture;
        (e) contacting a peroxide-generating enzyme and optionally a recycling enzyme with first assay mixture under conditions wherein peroxide is generated to form a second assay mixture;
        (f) contacting the second assay mixture with a first solid support comprising an electrode comprising a covalently attached electroactive moiety (EAM) having a first E0, said EAM comprising a transition metal complex comprising a self-immolative moiety (SIM) and a peroxide sensitive moiety (PSM), wherein said peroxide reacts with said PSM to release said SIM from said EAM and result in said EAM having a second E0;
        (g) measuring the electrochemical properties of said EAM at the first E0 and at the second E0; and
        (h) detecting for the presence or the concentration of said target analyte from said electrochemical properties.
    
    


As used in this disclosure, the term “isolating” or “isolate” means separating the particular components from others through any suitable means including Physical separation or purification.
In one embodiment of the disclosure, said specific binding pair is biotin/streptavidin. In another embodiment of the disclosure, said binding ligand is attached to a second solid support. In yet another embodiment of the disclosure, said second solid support is chosen from the group consisting of microparticles, magnetic microparticles, beads, and microchannels.
In one embodiment of the disclosure any preceding embodiment is where said electrode further comprises a self-assembled monolayer (SAM). In another embodiment of the disclosure any preceding embodiment is where the target analyte is a small molecule.
In one embodiment of the disclosure said product(s) is a substrate for said peroxide generating enzyme. In another embodiment of the disclosure method further comprises the presence of a substrate for said peroxide generating enzyme and wherein said product(s) is a cofactor for said peroxide-generating enzyme. In yet another embodiment said recycling enzyme is included to recycle said cofactor.
In one embodiment of the disclosure any preceding embodiment is wherein said intermediary enzyme of a peroxide generating system is alkaline phosphatase (AP) or any other dephosphorylating enzyme.
In another embodiment of the disclosure any preceding embodiment is where said peroxide-generating enzyme is selected from the group consisting of D-amino acid oxidase (DAAO), or any flavin dependent oxidoreductase enzyme.
In another embodiment of the disclosure any preceding embodiment is where said peroxide-generating enzyme is NADH Oxidase and said optional recycling enzyme is Alcohol Dehydrogenase (ADH).
In one embodiment of the disclosure any preceding embodiment is where the target analyte is testosterone.
In another embodiment of the disclosure any preceding embodiment is where said first binding ligand and said second binding ligand are independently chosen from the group consisting of monoclonal antibodies, fragments of monoclonal antibodies, polyclonal antibodies, fragments of polyclonal antibodies, proteins, and peptides.
In one embodiment of the disclosure any preceding embodiment is where said EAM comprises a transition metal. In one embodiment, said transition metal is chosen from the group consisting of iron, ruthenium and osmium.
In one embodiment of the disclosure any preceding embodiment is said EAM is chosen from the group consisting of ferrocene and substituted ferrocene.
In one embodiment a small molecule target, (e.g., testosterone) can be detected utilizing a competition based assay. The sample is added to a preformed first complex comprising a binding ligand and a bound biotinylated target molecule attached to a solid support. Target molecule in sample displaces a proportion of the prebound biotinylated target molecule in a concentration dependent manner forming a second complex. Sample is then washed away, retaining both first and second complexes attached to solid support. A streptavidin linker tagged with an intermediary enzyme of a peroxide generating system e.g., Alkaline phosphatase (AP) is added binding only to the biotinylated targets of first complexes forming a third complex. Substrate for intermediary enzyme (e.g., FADP, NADP), oxidase enzyme (e.g., D-amino acid oxidase, NADH oxidase) and, optionally cycling enzymes (Alcohol Dehyrodgenase) are added to the complexes and H2O2 is generated. The signal output is only dependent on the number of third complexes and is inversely proportional to the concentration of target in the test sample. The higher the signal measured the lower the concentration of target molecule in the test sample.
In another embodiment a small molecule target, (e.g., testosterone) can be detected utilizing a competition based assay. The sample is added to a preformed first complex comprising a binding ligand attached to a solid support, a bound biotinylated target molecule, and an intermediary enzyme of a peroxide generating system tag (e.g., Alkaline Phosphatase) attached via a streptavidin linker to the biotinylated target. Target molecule in sample displaces a proportion of the prebound biotinylated target molecule in a concentration dependent manner forming a second complex. Sample is then washed away, retaining complexed binding ligands. Substrate for intermediary enzyme (e.g., FADP, NADP), oxidase enzyme (e.g., D-amino acid oxidase, NADH oxidase) and, optionally cycling enzymes (Alcohol Dehyrodgenase) are added to the complexes and H2O2 is generated. The signal output is only dependent on the number of first complexes and inversely proportional to the concentration of target in the test sample. The higher the signal measured the lower the concentration of target molecule in the test sample.
In another embodiment a small molecule target, (e.g., testosterone) can be detected utilizing a competition based assay. The sample is added to a preformed first complex comprising a binding ligand attached to a solid support, a bound biotinylated target molecule, and an intermediary enzyme of a peroxide generating system tag (e.g., Alkaline Phosphatase) attached via a streptavidin linker to the biotinylated target. Target molecule in sample displaces a proportion of the prebound biotinylated target molecule in a concentration dependent manner forming a second complex. Supernatant, containing displaced biotinylated target labeled with streptavidin and intermediary enzyme, is removed. Substrate for intermediary enzyme (e.g., FADP, NADP), oxidase enzyme (e.g., D-amino acid oxidase, NADH oxidase) and, optionally cycling enzymes (Alcohol Dehyrodgenase) are added to the supernatant and H2O2 is generated. The signal output is only dependent on the amount of biotinylated target displaced in the supernatant and is directly proportional to the concentration of target in the test sample. The higher the signal measured the higher the concentration of target molecule in the test sample.
In another embodiment a small molecule target, (e.g., testosterone) can be detected utilizing a competition based assay. The sample is added to a binding ligand attached to a solid support. Target molecule in sample binds capture ligand forming a first complex. Sample is washed away. A bound biotinylated target molecule is introduced and displaces target molecule forming a second complex. The biotinylated target molecule may optionally have and an intermediary enzyme of a peroxide generating system tag (e.g., Alkaline Phosphatase) attached via a streptavidin linker. Remaining unbound biotinylated target is washed away. Optionally, an intermediary enzyme of a peroxide generating system tag (e.g., Alkaline Phosphatase) attached to a streptavidin linker is added if not precomplexed with biotinylated target in previous step. Optionally, wash away excess intermediary enzyme. Substrate for intermediary enzyme (e.g., FADP, NADP), oxidase enzyme (e.g., D-amino acid oxidase, NADH oxidase) and optionally cycling enzymes (Alcohol Dehyrodgenase) are added to the complexes and H2O2 is generated. The signal output is only dependent on the number of second complexes and inversely proportional to the concentration of target in the test sample. The higher the signal measured the lower the concentration of target molecule in the test sample.
In one embodiment, the disclosure provides methods for detecting a target analyte in a test sample, said method comprising:

    
    
        (a) contacting a first binding ligand with said test sample under conditions wherein said first binding ligand binds said target analyte, if present, in said test sample to form a first complex;
        (b) contacting said first complex with a second binding ligand under conditions wherein said first complex and said second binding ligand bind to form a second complex, wherein said second binding ligand comprises an intermediary enzyme of a peroxide-generating system;
        (c) isolating said second complex;
        (d) contacting said second complex with a substrate for said intermediary enzyme of peroxide-generating system under conditions such that products are generated to form a first assay mixture;
        (e) contacting a peroxide-generating enzyme and optionally a recycling enzyme with a first assay mixture under conditions wherein peroxide is generated to form a second assay mixture;
        (f) contacting the second assay mixture with a first solid support comprising an electrode comprising a covalently attached electroactive moiety (EAM) having a first E0, said EAM comprising a transition metal complex comprising a self-immolative moiety (SIM) and a peroxide sensitive moiety (PSM), wherein said peroxide reacts with said PSM to release said SIM from said EAM and result in said EAM having a second E0;
        (g) measuring the electrochemical properties of said EAM at the first E0 and at the second E0; and
        (h) detecting for the presence or the concentration of said target analyte from said electrochemical properties.
    
    


In one embodiment of the disclosure, the target analyte is a protein. In another embodiment of the disclosure, said binding ligand is attached to a second solid support. In yet another embodiment of the disclosure, said second solid support is chosen from the group consisting of microparticles, magnetic microparticles, beads, and microchannels.
In one embodiment of the disclosure any preceding embodiment is where said electrode further comprises a self-assembled monolayer (SAM). In another embodiment of the disclosure any preceding embodiment is where the target analyte is a small molecule.
In one embodiment of the disclosure said product(s) is a substrate for said peroxide generating enzyme. In another embodiment of the disclosure method further comprises the presence of a substrate for said peroxide generating enzyme and wherein said product(s) is a cofactor for said peroxide-generating enzyme. In yet another embodiment said recycling enzyme is included to recycle said cofactor.
In one embodiment of the disclosure any preceding embodiment is wherein said intermediary enzyme of a peroxide generating system is alkaline phosphatase (AP) or any other dephosphorylating enzyme.
In another embodiment of the disclosure any preceding embodiment is where said peroxide-generating enzyme is selected from the group consisting of D-amino acid oxidase (DAAO), or any flavin dependent oxidoreductase enzyme.
In another embodiment of the disclosure any preceding embodiment is where said peroxide-generating enzyme is NADH Oxidase and said optional recycling enzyme is Alcohol Dehydrogenase (ADH).
In another embodiment of the disclosure any preceding embodiment is where said first binding ligand and said second binding ligand are independently chosen from the group consisting of monoclonal antibodies, fragments of monoclonal antibodies, polyclonal antibodies, fragments of polyclonal antibodies, proteins, and peptides.
In one embodiment of the disclosure any preceding embodiment is where said EAM comprises a transition metal. In one embodiment, said transition metal is chosen from the group consisting of iron, ruthenium and osmium.
In one embodiment of the disclosure any preceding embodiment is said EAM is chosen from the group consisting of ferrocene and substituted ferrocene.
In one embodiment a protein target can be detected utilizing a sandwich based assay. The sample is added to a first binding ligand attached to a solid support. Target molecule in sample binds capture ligand forming a first complex. Test sample and excess first binding ligand are washed away. A second capture ligand comprising an intermediary enzyme of a peroxide generating system tag is added to first complex. Second binding ligand binds target on first complex forming a second complex. Excess second binding ligand is washed away. Substrate for intermediary enzyme (e.g., FADP, NADP), oxidase enzyme (e.g., D-amino acid oxidase, NADH oxidase) and optionally cycling enzymes (Alcohol Dehyrodgenase) are added to the complexes and H2O2 is generated. The signal output is directly proportional to the concentration of target in the test sample. The higher the signal measured the higher the concentration of target molecule in the test sample.
In another aspect, the invention provides compositions comprising (a) a first solid support comprising an electrode comprising: (i) a self-assembled monolayer (SAM); (ii) a covalently attached electroactive active moiety (EAM) comprising a transition metal complex comprising a self-immolative moiety and a peroxide sensitive moiety (PSM), wherein said first EAM has a first E0; and (b) a second solid support comprising of a peroxide-generating enzyme that generates peroxide in the presence of a substrate for said peroxide-generating enzyme.
In one embodiment the reaction mechanism for representative ferrocene-based EAMs that undergo a peroxide-triggered change in apparent formal potential (E-TRACE) follow the following steps:

    a) starting ferrocenyl EAM that contains an electron-withdrawing carbamate-linked boronate ester-substituted ligand; and
    b) reaction with peroxide leads to an electron-donating amino ligand on the ferrocene which results in a distinct the redox potential from starting species.





BRIEF DESCRIPTION OF THE DRAWINGS
FIG. 1. illustrates structure of electroactive molecule (EAM) 1 and mechanism of peroxide-induced ligand dissociation. The change in ligand electronics is responsible for the shift in redox potential.
FIG. 2. illustrates the synthetic scheme of one of the embodiments of the invention as depicted in FIG. 1.
FIG. 3. shows solution CV data for EAM 1 and a control compound following H2O2 induced cleavage of the POM ligand. The change in EU following the self-immolative process is 331 mV. Experiments were run in THF with TBAClO4 (150 mM) supporting electrolyte using a carbon working electrode, Ag/AgCl reference electrode, and a Pt wire counter electrode.
FIG. 4. shows overlaid cyclic voltammograms from a SAM of EAM 1 before (dotted) and after solid incubation with 1 mM hydrogen peroxide in NaHCO3 buffer (pH 8.5) for 10 min, followed by a 5-min wash in Na2CO3 buffer (pH 10.1; lower peaks). Supporting electrolyte was 1M LiClO4, silver quasi reference electrode, platinum wire counter electrode. Scan rate was 10000 mV/s.
FIG. 5. shows overlaid cyclic voltammograms from a SAM of EAM 1 before (dotted) and after (solid) incubation with 1 mM glucose and 100 uM glucose oxidase in NaHCO3 buffer (pH 8.5) for 10 min, followed by a 5 min wash in Na2CO3 buffer (pH 10.1). Supporting electrolyte was 1M LiClO4, silver quasi reference electrode, platinum wire counter electrode. Scan rate was 10000 mV/s.
FIG. 6. Illustrates a sample self-immolative spacer groups based on substituted quinone methides.
FIG. 7. shows cyclic voltamogram for SAM of EAM 1 following antibody sandwich formation with human cardiac troponin I (10 ng/mL) before (dotted) and after (solid) incubation with glucose for 10 min. Inset shows the peak at −0.10V magnified.
FIG. 8. depicts a variety of self-immolative moieties which find use in the present invention. “PSM” stands for “peroxide sensitive moiety” and “EAM” stands for “electroactive moiety”. As is shown in the figures, a variety of monomeric self-immolative moieties (sometimes referred to herein as “SIM”) can be used; Figure XA depicts a first type of self-immolative moiety, which relies on the PSM contributing an —OH group upon contact with peroxide, resulting a phenol-based linker that releases from the EAM. n can be an integer of 1 or higher, with from 1 to 5 finding particular use in the invention. m is an integer of at least one; as will be appreciated by those in the art, m will depend on the transitional metal complex used and the number of positions in the EAM; for example, when a metallocene such as ferrocene is used, there can be up to 5 PSM-SIMs per cyclopentadienyl ring, with at least one of the positions on one of the rings being used for attachment to the electrode. Figures B, C and D show multimers of SIMs. X can be —NH— or —O—.
FIG. 9. depicts additional peroxide sensitive moieties. Figure A depicts the PSB ether (parasiletanylbenzyl) moiety and Figure B depicts the pentafluorophenylsulfonate (PFPS) moiety. As shown in Figure (next), there can be more than one self-immolative moiety per EAM and/or more than one PSM-SIM per EAM. As for the boron containing PSMs, there can be multiple PSB ethers or PFPS moieties per EAM as well.
FIG. 10. depicts a ferrocene that has R groups. The moiety shown has the attachment linker and the self-immolative moiety and the peroxide sensitive moiety on different rings, although as described herein, they can be on the same ring. In addition, any or all of the R groups can be an additional -SIM-PSM substituent, as well as traditional substituents (alkyl (including substituted alkyl, heteroalkyl, cyclic alkyl, etc.), aryl (including substituted aryl and heteroaryl), etc.).
FIG. 11 is similar to FIG. 1 in showing the reaction mechanism for a representative ferrocene based EAM that undergoes a peroxide-triggered change in the apparent formal potential. (A) is the starting ferrocenyl EAM that contains an electron-withdrawing carbamate-linked boronate ester-substituted ligand. (B) Shows that the reaction with peroxide leads to an electron-donating amino ligand on the ferrocene which changes the redox potential (E0).
FIG. 12 shows example Cyclic Voltammagrams of typical response prior to and after reaction of hydrogen peroxide with electro-active moiety (EAM) on a self-assembled monolayer.
FIG. 13. illustrates typical dose response to hydrogen peroxide titration reaction on a E-TRACE modified self-assembled monolayer (SAM).
FIG. 14. shows cascade signal amplification schematic for NADH detection via E-TRACE.
FIG. 15. shows cascade signal amplification schematic for ATP detection via E-TRACE.
FIG. 16. shows cascade signal amplification strategies for AP-based cascade amplification for small molecules. A competitive assay is described based on the displacement of biotinylated small molecules. The peroxide generated is detected via E-TRACE.
FIG. 17. shows FADP-based cascade amplification for protein targets. The peroxide generated is detected via E-TRACE.
FIG. 18. shows NADP-based cascade amplification for protein targets. The peroxide generated is detected via E-TRACE.
FIG. 19. illustrates calibration curve for a serial dilution of NADH in buffer following the signal amplification for NADH with the E-TRACE assay. The limit of detection is improved one thousand fold from 3 uM using only NADH oxidase to 1 nM using the NADH/NAD cycling amplification approach using Alcohol Dehydrogenase.
FIG. 20. illustrates calibration curve for a serial dilution of ATP in buffer following the signal amplification for ATP with the E-TRACE assay. The limit of detection is improved nearly one thousand fold from 1 uM using Glycerol Kinase/Glycerol3-Phosphate oxidase to the 3 nM using the ATP/ADP cycling amplification approach with Creatine Kinase.
FIG. 21. shows a typical calibration curve expected for a serial dilution of a small molecule using a competitive assay that utilizes the cascade signal amplification approach.
FIG. 22. A. illustrates calibration curve for a serial dilution of cTnI in serum following the FADP-based cascade amplification E-TRACE assay. The limit of detection is improved many fold from a 100 ng/mL using the unamplified approach to 3 pg/mL using the amplified approach. B. Correlation study measuring levels of cTnI in clinical samples using the E-TRACE assay approach comparing it to the data provided from a clinical immunoanalyzer.
FIG. 23. A. illustrates calibration curve for a serial dilution of thyroid stimulating hormone in serum following the FADP-based cascade amplification E-TRACE assay. B. Correlation study measuring levels of TSH clinical samples using the E-TRACE assay approach comparing it to the data provided from a clinical immunoanalyzer.
FIG. 24. illustrates a calibration curve obtained using the NADP-based cascade amplification for a serial dilution of Alkaline Phosphatase.



DETAILED DESCRIPTION OF THE INVENTION
U.S. patent application Ser. Nos. 13/653,931, 12/253,828, 12/253,875, 12/853,204, 61/332,565, 61/347,121, 61/394,458, 61/366,013 and 61/407,828 are all incorporated by reference in their entirety.
Overview
The sensitivities of E-TRACE assays for proteins, DNA, and small molecules may be exponentially enhanced through signal amplification strategies that rely on target-dependent enzyme cascades for generating hydrogen peroxide. FIG. 1a shows a general approach for cascade signal amplification based on an alkaline phosphatase (AP)-tagged sandwich immunocomplex with a protein target. A similar colorimetric assay has been reported previously.1 In this system AP catalyzes the dephosphorylation of FADP to yield FAD, an enzyme cofactor that turns “on” a dormant apo-D-amino acid oxidase (D-AAO). In turn, each active D-AAO generated oxidizes D-proline and produces hydrogen peroxide which is detected using the Ohmx E-TRACE technology, which is described in U.S. Patent Publication No. US 20120181186, filed Jan. 19, 2012 which claims the benefit of priority to U.S. provisional application Nos. 61/434,122, filed Jan. 19, 2011 and 61/523,679, filed Aug. 15, 2011 and Ser. No. 12/853,204, filed Aug. 9, 2010, which claims the benefit of priority to U.S. provisional application Nos. 61/232,339, filed Aug. 7, 2009, and in U.S. patent application Ser. No. 13/653,931, filed Oct. 17, 2012, all which are incorporated by reference in their entirety. An example protein target detected in this manner is shown in FIG. 1b, where a dilution series of cardiac troponin-I (cTnI) in serum is analyzed. The data suggest a detection limit in the low pg/mL regime is possible for cTnI in serum using this E-TRACE amplification assay.
The assay relies on the use of an electroactive moiety (“EAM”), which is attached to the electrode and comprises a self-immolative moiety, whose presence gives the EAM a first E0, whose absence, upon irreversible cleavage, gives the EAM a second E0. The electrode also contains capture binding ligands that will bind the target analyte upon its introduction. A soluble capture ligand is introduced, which also binds the target analyte and comprises a peroxide generating moiety, such as a glucose oxidase enzyme. Upon the addition of oxygen and a substrate for the peroxidase generating moiety (e.g., an oxygen saturated buffer and glucose, in the case of a glucose oxidase enzyme as the peroxidase generating moiety) peroxide is generated, attacking the self-immolative moiety and causing the removal of the self-immolative moiety from the EAM, which results in a change in the E0 of the EAM. This difference is detected, and if such a change occurs, it is an indication of the presence of the target analyte.
Thus, to determine whether a target analyte is present in the sample, the sample is applied to the detection electrode surface, optionally washed, and an oxidase enzyme-conjugated secondary binding ligand (for example, an antibody) that binds an alternative epitope of the target analyte is added, creating a “sandwich assay” format with the target. The surface is optionally washed, and treated with an oxygen-saturated buffer containing a high concentration of glucose. The presence of the substrate oxidase enzyme (sometimes referred to herein as “SOX”) on the surface results in the enzymatic creation of hydrogen peroxide in solution which diffuses to the monolayer surface and triggers a chemical elimination reaction (“self-immolative” reaction) in the immobilized EAMs. This irreversible elimination reaction changes the electronic environment of the EAM, for example by altering the “R” groups (e.g., substituent groups) of the transition metal complex, thus shifting the apparent formal potential of the EAM to a second E0 to signal the presence of the target.
Accordingly, the present invention provides methods and compositions for detecting target analytes in samples. The single measurement approach for detecting directly the percentage of glycated Hemoglobin is not affected by the amount of total Hemoglobin present in the sample. Since total Hemoglobin, can vary physiologically from 5-20 g/dL, a direct measurement of the same percentage of glycated Hemoglobin across this range is feasible with this approach.
Target Analytes
By “target analyte” or “analyte” or grammatical equivalents herein is meant any molecule, compound or particle to be detected. Target analytes bind to binding ligands (both capture and soluble binding ligands), as is more fully described below.
Suitable analytes include organic and inorganic molecules, including biomolecules. In a preferred embodiment, the analyte may be an environmental pollutant (including pesticides, insecticides, toxins, etc.); a chemical (including solvents, polymers, organic materials, etc.); therapeutic molecules (including therapeutic and abused drugs, antibiotics, etc.); biomolecules (including hormones, cytokines, proteins, lipids, carbohydrates, cellular membrane antigens and receptors (neural, hormonal, nutrient, and cell surface receptors) or their ligands, etc); whole cells (including procaryotic (such as pathogenic bacteria) and eukaryotic cells, including mammalian tumor cells); viruses (including retroviruses, herpesviruses, adenoviruses, lentiviruses, etc.); and spores; etc.
In some embodiments, the target analyte is a protein. As will be appreciated by those in the art, there are a large number of possible proteinaceous target analytes that may be detected using the present invention. By “proteins” or grammatical equivalents herein is meant proteins, oligopeptides and peptides, derivatives and analogs, including proteins containing non-naturally occurring amino acids and amino acid analogs, and peptidomimetic structures. The side chains may be in either the (R) or the (S) configuration. In a preferred embodiment, the amino acids are in the (S) or L configuration. As discussed below, when the protein is used as a binding ligand, it may be desirable to utilize protein analogs to retard degradation by sample contaminants.
Suitable protein target analytes include, but are not limited to, (1) immunoglobulins, particularly IgEs, IgGs and IgMs, and particularly therapeutically or diagnostically relevant antibodies, including but not limited to, for example, antibodies to human albumin, apolipoproteins (including apolipoprotein E), human chorionic gonadotropin, cortisol, α-fetoprotein, thyroxin, thyroid stimulating hormone (TSH), antithrombin, antibodies to pharmaceuticals (including antieptileptic drugs (phenyloin, primidone, carbariezepin, ethosuximide, valproic acid, and phenobarbitol), cardioactive drugs (digoxin, lidocaine, procainamide, and disopyramide), bronchodilators (theophylline), antibiotics (chloramphenicol, sulfonamides), antidepressants, immunosuppresants, abused drugs (amphetamine, methamphetamine, cannabinoids, cocaine and opiates) and antibodies to any number of viruses (including orthomyxoviruses, (e.g. influenza virus), paramyxoviruses (e.g., respiratory syncytial virus, mumps virus, measles virus), adenoviruses, rhinoviruses, coronaviruses, reoviruses, togaviruses (e.g. rubella virus), parvoviruses, poxviruses (e.g. variola virus, vaccinia virus), enteroviruses (e.g. poliovirus, coxsackievirus), hepatitis viruses (including A, B and C), herpesviruses (e.g. Herpes simplex virus, varicella zoster virus, cytomegalovirus, Epstein Barr virus), rotaviruses, Norwalk viruses, hantavirus, arenavirus, rhabdovirus (e.g. rabies virus), retroviruses (including HIV, HTLV I and II), papovaviruses (e.g. papillomavirus), polyomaviruses, and picornaviruses, and the like), and bacteria (including a wide variety of pathogenic and non pathogenic prokaryotes of interest including Bacillus; Vibrio, e.g. V. cholerae; Escherichia, e.g. Enterotoxigenic E. coli, Shigella, e.g. S. dysenteriae; Salmonella, e.g. S. typhi; Mycobacterium e.g. M. tuberculosis, M. leprae; Clostridium, e.g. C. botulinum, C. tetani, C. difficile, C. perfringens; Cornyebacterium, e.g. C. diphtheriae; Streptococcus, S. pyogenes, S. pneumoniae; Staphylococcus, e.g. S. aureus; Haemophilus, e.g. H. influenzae; Neisseria, e.g. N. meningitidis, N. gonorrhoeae; Yersinia, e.g. G. lamblia, Y. pestis, Pseudomonas, e.g. P. aeruginosa, P. putida; Chlamydia, e.g. C. trachomatis; Bordetella, e.g. B. pertussis; Treponema, e.g. T. palladium; and the like); (2) enzymes (and other proteins), including but not limited to, enzymes used as indicators of or treatment for heart disease, including creatine kinase, lactate dehydrogenase, aspartate amino transferase, troponin T, myoglobin, fibrinogen, cholesterol, triglycerides, thrombin, tissue plasminogen activator (tPA); pancreatic disease indicators including amylase, lipase, chymotrypsin and trypsin; liver function enzymes and proteins including cholinesterase, bilirubin, and alkaline phosphotase; aldolase, prostatic acid phosphatase, terminal deoxynucleotidyl transferase, and bacterial and viral enzymes such as HIV protease; (3) hormones and cytokines (many of which serve as ligands for cellular receptors) such as erythropoietin (EPO), thrombopoietin (TPO), the interleukins (including IL-1 through IL-17), insulin, insulin-like growth factors (including IGF-1 and -2), epidermal growth factor (EGF), transforming growth factors (including TGF-α and TGF-β), human growth hormone, transferrin, epidermal growth factor (EGF), low density lipoprotein, high density lipoprotein, leptin, VEGF, PDGF, ciliary neurotrophic factor, prolactin, adrenocorticotropic hormone (ACTH), calcitonin, human chorionic gonadotropin, cotrisol, estradiol, follicle stimulating hormone (FSH), thyroid-stimulating hormone (TSH), leutinzing hormone (LH), progeterone, testosterone; and (4) other proteins (including α-fetoprotein, carcinoembryonic antigen CEA.
In addition, any of the biomolecules for which antibodies may be detected may be detected directly as well; that is, detection of virus or bacterial cells, therapeutic and abused drugs, etc., may be done directly.
Suitable target analytes include carbohydrates, including but not limited to, markers for breast cancer (CA15-3, CA 549, CA 27.29), mucin-like carcinoma associated antigen (MCA), ovarian cancer (CA125), pancreatic cancer (DE-PAN-2), and colorectal and pancreatic cancer (CA 19, CA 50, CA242).
Targets include small molecules such as glucose or cholesterol or ATP, FADP, NADH and other metabolites, or hormones such as testosterones etc, or proteins such as thyroid stimulating hormone, troponin I etc.
In one embodiment, a single measurement method for determining the proportion of target analyte in a sample can be performed according to the methods described herein by an electrochemical measurement using the enzyme-triggered redox altering chemical elimination (E-TRACE) reaction, or a standard immunoassay optical test detecting H2O2 in solution and is described in the following steps:
Step 1: Modification with Primary Antibody:
The surface of the electrochemical platform is modified to include the sensing molecule (EAM) for the E-TRACE detection of peroxide. Additionally a second solid support is modified with a capture probe. This capture probe, e.g., antibody, binds selectively and equivalently to all variant types of target (e.g., hemoglobin including hemoglobin and glycated hemoglobin). As defined herein, the terms “binds selectively” means binding to a predetermined target (e.g. total hemoglobin including hemoglobin A1c) and “binds equivalently” mean non-preferentially to both the protein (e.g., hemoglobin) and the glycated protein (e.g., hemoglobin A1c).
Step 2: Addition of Target:
Target can be small molecule or protein. In certain embodiments, the primary binding occurs and is assumed to saturate nearly all binding sites on the surface of the secondary support. The importance of this is that samples with different total target concentrations will still yield a representative proportion of the target analyte bound to the surface.
Step 3: Addition of Detection Antibody:
In certain embodiments, the secondary antibody is introduced to the surface and only binds to the immobilized target analyte. This means the ELISA-like sandwich complex only forms on sites occupied by target analyte and not on sites occupied by non-target (e.g., non-glycated hemoglobin).
Step 4: Signal Transduction and Detection:
The anti-target antibody that selectively binds to target is labeled with an intermediary enzyme of a peroxide generating system, e.g., an oxidase enzyme (SOx). The intermediary enzyme label, generates a product that is a cofactor or substrate for an oxidase enzyme which produces hydrogen peroxide. The hydrogen peroxide generated reacts with the electrochemical surface of the electrochemical platform to provide an electrochemical signal.
The amount of signal is directly correlated to the number of sandwich complexes, which in turn is dependent on how much Target immobilized on the surface. Since the amount of immobilized Target is directly dependent on the percentage of Target to total hemoglobin in the original sample, the signal observed provides an assessment of the ratio (percentage) of hemoglobin Target to total hemoglobin.
For HbTarget, one of the binding ligands, either the capture binding ligand or the soluble binding ligand has specificity for the glycated form of hemoglobin. That is, in one embodiment, the capture binding ligand can bind either form of hemoglobin; after washing the surface, a soluble binding ligand that has specificity only for the glycated form (i.e. HbTarget) with the peroxide-generating moiety is added. Alternatively, the capture binding ligand has specificity for Hb1Ac over other forms of hemoglobin, and a soluble capture ligand without such specificity can be used after appropriate washing of the surface. This approach can be used for other target analytes where detection of either the glycated or nonglycated form is desired. As will be appreciated by those in the art, there are also target analytes for which detection of both forms is desired, and in those embodiments, using binding ligands that do not have specificity for one or the other is used.
This single-measurement detection of Target coupled to an electro-active SAM provides a less complex means for determining the proportion of Target to total hemoglobin in a sample. It offers the advantages of not needing to perform two measurements, as well as eliminating optical measurements, multiple antibody pairs, or percentage calculation algorithms, that introduces further error, based on two separate measurements for Target and total hemoglobin.
Target analytes of the disclosure may be labeled. Thus, by “labeled target analyte” herein is meant a target analyte that is labeled with a member of a specific binding pair.
Samples
The target analytes are generally present in samples. As will be appreciated by those in the art, the sample solution may comprise any number of things, including, but not limited to, bodily fluids (including, but not limited to, blood, urine, serum, lymph, saliva, anal and vaginal secretions, perspiration and semen, of virtually any organism, with mammalian samples being preferred and human samples being particularly preferred); environmental samples (including, but not limited to, air, agricultural, water and soil samples); plant materials; biological warfare agent samples; research samples, purified samples, raw samples, etc.; as will be appreciated by those in the art, virtually any experimental manipulation may have been done on the sample. Some embodiments utilize target samples from stored (e.g. frozen and/or archived) or fresh tissues. Paraffin-embedded samples are of particular use in many embodiments, as these samples can be very useful, due to the presence of additional data associated with the samples, such as diagnosis and prognosis. Fixed and paraffin-embedded tissue samples as described herein refers to storable or archival tissue samples. Most patient-derived pathological samples are routinely fixed and paraffin-embedded to allow for histological analysis and subsequent archival storage.
Solid Supports
The target analytes are detected using solid supports comprising electrodes. By “substrate” or “solid support” or other grammatical equivalents herein is meant any material that can be modified to contain discrete individual sites appropriate of the attachment or association of capture ligands. Suitable substrates include metal surfaces such as gold, electrodes as defined below, glass and modified or functionalized glass, fiberglass, teflon, ceramics, mica, plastic (including acrylics, polystyrene and copolymers of styrene and other materials, polypropylene, polyethylene, polybutylene, polyimide, polycarbonate, polyurethanes, TeflonTM, and derivatives thereof, etc.), GETEK (a blend of polypropylene oxide and fiberglass), etc, polysaccharides, nylon or nitrocellulose, resins, silica or silica-based materials including silicon and modified silicon, carbon, metals, inorganic glasses and a variety of other polymers, with printed circuit board (PCB) materials being particularly preferred.
The present system finds particular utility in array formats, i.e. wherein there is a matrix of addressable detection electrodes (herein generally referred to “pads”, “addresses” or “micro-locations”). By “array” herein is meant a plurality of capture ligands in an array format; the size of the array will depend on the composition and end use of the array. Arrays containing from about 2 different capture substrates to many thousands can be made.
In a preferred embodiment, the detection electrodes are formed on a substrate. In addition, the discussion herein is generally directed to the use of gold electrodes, but as will be appreciated by those in the art, other electrodes can be used as well. The substrate can comprise a wide variety of materials, as outlined herein and in the cited references.
In general, preferred materials include printed circuit board materials. Circuit board materials are those that comprise an insulating substrate that is coated with a conducting layer and processed using lithography techniques, particularly photolithography techniques, to form the patterns of electrodes and interconnects (sometimes referred to in the art as interconnections or leads). The insulating substrate is generally, but not always, a polymer. As is known in the art, one or a plurality of layers may be used, to make either “two dimensional” (e.g. all electrodes and interconnections in a plane) or “three dimensional” (wherein the electrodes are on one surface and the interconnects may go through the board to the other side or wherein electrodes are on a plurality of surfaces) boards. Three dimensional systems frequently rely on the use of drilling or etching, followed by electroplating with a metal such as copper, such that the “through board” interconnections are made. Circuit board materials are often provided with a foil already attached to the substrate, such as a copper foil, with additional copper added as needed (for example for interconnections), for example by electroplating. The copper surface may then need to be roughened, for example through etching, to allow attachment of the adhesion layer.
Accordingly, in a preferred embodiment, the present invention provides biochips (sometimes referred to herein “chips”) that comprise substrates comprising a plurality of electrodes, preferably gold electrodes. The number of electrodes is as outlined for arrays. Each electrode preferably comprises a self-assembled monolayer as outlined herein. In a preferred embodiment, one of the monolayer-forming species comprises a capture ligand as outlined herein. In addition, each electrode has an interconnection, that is attached to the electrode at one end and is ultimately attached to a device that can control the electrode. That is, each electrode is independently addressable.
Finally, the compositions of the invention can include a wide variety of additional components, including microfluidic components and robotic components (see for example U.S. Pat. Nos. 6,942,771 and 7,312,087 and related cases, both of which are hereby incorporated by reference in its entirety), and detection systems including computers utilizing signal processing techniques (see for example U.S. Pat. No. 6,740,518, hereby incorporated by reference in its entirety).
Electrodes
The solid supports of the invention comprise electrodes. By “electrodes” herein is meant a composition, which, when connected to an electronic device, is able to sense a current or charge and convert it to a signal. Preferred electrodes are known in the art and include, but are not limited to, certain metals and their oxides, including gold; platinum; palladium; silicon; aluminum; metal oxide electrodes including platinum oxide, titanium oxide, tin oxide, indium tin oxide, palladium oxide, silicon oxide, aluminum oxide, molybdenum oxide (Mo206), tungsten oxide (WO3) and ruthenium oxides; and carbon (including glassy carbon electrodes, graphite and carbon paste). Preferred electrodes include gold, silicon, carbon and metal oxide electrodes, with gold being particularly preferred.
The electrodes described herein are depicted as a flat surface, which is only one of the possible conformations of the electrode and is for schematic purposes only. The conformation of the electrode will vary with the detection method used.
The electrodes of the invention are generally incorporated into biochip cartridges and can take a wide variety of configurations, and can include working and reference electrodes, interconnects (including “through board” interconnects), and microfluidic components. See for example U.S. Pat. No. 7,312,087, incorporated herein by reference in its entirety. In addition, the biochips generally include a working electrode with the components described herein, a reference electrode, and a counter/auxiliary electrode.
The biochip cartridges include substrates comprising the arrays of biomolecules, and can be configured in a variety of ways. For example, the chips can include reaction chambers with inlet and outlet ports for the introduction and removal of reagents. In addition, the cartridges can include caps or lids that have microfluidic components, such that the sample can be introduced, reagents added, reactions done, and then the sample is added to the reaction chamber comprising the array for detection.
Self Assembled Monolayers
The electrodes comprise a self assembled monolayer (“SAM”). By “monolayer” or “self-assembled monolayer” or “SAM” herein is meant a relatively ordered assembly of molecules spontaneously chemisorbed on a surface, in which the molecules are oriented approximately parallel to each other and roughly perpendicular to the surface. Each of the molecules includes a functional group that adheres to the surface, and a portion that interacts with neighboring molecules in the monolayer to form the relatively ordered array. A “mixed” monolayer comprises a heterogeneous monolayer, that is, where at least two different molecules make up the monolayer. As outlined herein, the use of a monolayer reduces the amount of non-specific binding of biomolecules to the surface, and, in the case of nucleic acids, increases the efficiency of oligonucleotide hybridization as a result of the distance of the oligonucleotide from the electrode. Thus, a monolayer facilitates the maintenance of the target enzyme away from the electrode surface. In addition, a monolayer serves to keep charge carriers away from the surface of the electrode. Thus, this layer helps to prevent electrical contact between the electrodes and the ReAMs, or between the electrode and charged species within the solvent. Such contact can result in a direct “short circuit” or an indirect short circuit via charged species which may be present in the sample. Accordingly, the monolayer is preferably tightly packed in a uniform layer on the electrode surface, such that a minimum of “holes” exist. The monolayer thus serves as a physical barrier to block solvent accessibility to the electrode.
In some embodiments, the monolayer comprises conductive oligomers, and in particular, conductive oligomers are generally used to attach the EAM to the electrode surface, as described below. By “conductive oligomer” herein is meant a substantially conducting oligomer, preferably linear, some embodiments of which are referred to in the literature as “molecular wires”. By “substantially conducting” herein is meant that the oligomer is capable of transferring electrons at 100 Hz. Generally, the conductive oligomer has substantially overlapping π-orbitals, i.e. conjugated π-orbitals, as between the monomeric units of the conductive oligomer, although the conductive oligomer may also contain one or more sigma (σ) bonds. Additionally, a conductive oligomer may be defined functionally by its ability to inject or receive electrons into or from an associated EAM. Furthermore, the conductive oligomer is more conductive than the insulators as defined herein. Additionally, the conductive oligomers of the invention are to be distinguished from electroactive polymers, that themselves may donate or accept electrons.
A more detailed description of conductive oligomers is found in WO/1999/57317, herein incorporated by reference in its entirety. In particular, the conductive oligomers as shown in Structures 1 to 9 on page 14 to 21 of WO/1999/57317 find use in the present invention. In some embodiments, the conductive oligomer has the following structure:




In addition, the terminus of at least some of the conductive oligomers in the monolayer is electronically exposed. By “electronically exposed” herein is meant that upon the placement of an EAM in close proximity to the terminus, and after initiation with the appropriate signal, a signal dependent on the presence of the EAM may be detected. The conductive oligomers may or may not have terminal groups. Thus, in a preferred embodiment, there is no additional terminal group, and the conductive oligomer terminates with a terminal group; for example, such as an acetylene bond. Alternatively, in some embodiments, a terminal group is added, sometimes depicted herein as “Q”. A terminal group may be used for several reasons; for example, to contribute to the electronic availability of the conductive oligomer for detection of EAMs, or to alter the surface of the SAM for other reasons, for example to prevent non-specific binding. For example, there may be negatively charged groups on the terminus to form a negatively charged surface such that when the target analyte is nucleic acid such as DNA or RNA, the nucleic acid is repelled or prevented from lying down on the surface, to facilitate hybridization. Preferred terminal groups include —NH, —OH, —COOH, and alkyl groups such as —CH3, and (poly)alkyloxides such as (poly)ethylene glycol, with —OCH2CH2OH, —(OCH2CH2O)2H, —(OCH2CH2O)3H, and —(OCH2CH2O)4H being preferred.
In one embodiment, it is possible to use mixtures of conductive oligomers with different types of terminal groups. Thus, for example, some of the terminal groups may facilitate detection, and some may prevent non-specific binding.
In some embodiments, the electrode further comprises a passivation agent, preferably in the form of a monolayer on the electrode surface. For some analytes the efficiency of analyte binding (i.e. hybridization) may increase when the binding ligand is at a distance from the electrode. In addition, the presence of a monolayer can decrease non-specific binding to the surface (which can be further facilitated by the use of a terminal group, outlined herein. A passivation agent layer facilitates the maintenance of the binding ligand and/or analyte away from the electrode surface. In addition, a passivation agent serves to keep charge carriers away from the surface of the electrode. Thus, this layer helps to prevent electrical contact between the electrodes and the electron transfer moieties, or between the electrode and charged species within the solvent. Such contact can result in a direct “short circuit” or an indirect short circuit via charged species which may be present in the sample. Accordingly, the monolayer of passivation agents is preferably tightly packed in a uniform layer on the electrode surface, such that a minimum of “holes” exist. Alternatively, the passivation agent may not be in the form of a monolayer, but may be present to help the packing of the conductive oligomers or other characteristics.
The passivation agents thus serve as a physical barrier to block solvent accessibility to the electrode. As such, the passivation agents themselves may in fact be either (1) conducting or (2) nonconducting, i.e. insulating, molecules. Thus, in one embodiment, the passivation agents are conductive oligomers, as described herein, with or without a terminal group to block or decrease the transfer of charge to the electrode. Other passivation agents which may be conductive include oligomers of —(CF2)n—, —(CHF)n— and —(CFR)n—. In a preferred embodiment, the passivation agents are insulator moieties.
In some embodiments, the monolayers comprise insulators. An “insulator” is a substantially nonconducting oligomer, preferably linear. By “substantially nonconducting” herein is meant that the rate of electron transfer through the insulator is slower than the rate of electron transfer through the conductive oligomer. Stated differently, the electrical resistance of the insulator is higher than the electrical resistance of the conductive oligomer. It should be noted however that even oligomers generally considered to be insulators, such as —(CH2)16 molecules, still may transfer electrons, albeit at a slow rate.
In some embodiments, the insulators have a conductivity, S, of about 10−7Ω-1 cm−1 or lower, with less than about 10−8Ω−1 cm−1 being preferred. Gardner et al., Sensors and Actuators A 51 (1995) 57-66, incorporated herein by reference.
Generally, insulators are alkyl or heteroalkyl oligomers or moieties with sigma bonds, although any particular insulator molecule may contain aromatic groups or one or more conjugated bonds. By “heteroalkyl” herein is meant an alkyl group that has at least one heteroatom, i.e. nitrogen, oxygen, sulfur, phosphorus, silicon or boron included in the chain. Alternatively, the insulator may be quite similar to a conductive oligomer with the addition of one or more heteroatoms or bonds that serve to inhibit or slow, preferably substantially, electron transfer. In some embodiments the insulator comprises C6-C16 alkyl.
The passivation agents, including insulators, may be substituted with R groups as defined herein to alter the packing of the moieties or conductive oligomers on an electrode, the hydrophilicity or hydrophobicity of the insulator, and the flexibility, i.e. the rotational, torsional or longitudinal flexibility of the insulator. For example, branched alkyl groups may be used. In addition, the terminus of the passivation agent, including insulators, may contain an additional group to influence the exposed surface of the monolayer, sometimes referred to herein as a terminal group (“TG”). For example, the addition of charged, neutral or hydrophobic groups may be done to inhibit non-specific binding from the sample, or to influence the kinetics of binding of the analyte, etc. For example, there may be charged groups on the terminus to form a charged surface to encourage or discourage binding of certain target analytes or to repel or prevent from lying down on the surface.
The length of the passivation agent will vary as needed. Generally, the length of the passivation agents is similar to the length of the conductive oligomers, as outlined above. In addition, the conductive oligomers may be basically the same length as the passivation agents or longer than them, resulting in the binding ligands being more accessible to peroxide.
The monolayer may comprise a single type of passivation agent, including insulators, or different types.
Suitable insulators are known in the art, and include, but are not limited to, —(CH2)n—, —(CRH)n—, and —(CR2)n—, ethylene glycol or derivatives using other heteroatoms in place of oxygen, i.e. nitrogen or sulfur (sulfur derivatives are not preferred when the electrode is gold). In some embodiments, the insulator comprises C6 to C16 alkyl.
In some embodiments, the electrode is a metal surface and need not necessarily have interconnects or the ability to do electrochemistry.
Electroactive Moieties
In addition to the SAMs, the electrodes comprise an EAM. By “electroactive moiety (EAM)” or “transition metal complex” or “redox active molecule” or “electron transfer moiety (ETM)” herein is meant a metal-containing compound which is capable of reversibly or semi-reversibly transferring one or more electrons. It is to be understood that electron donor and acceptor capabilities are relative; that is, a molecule which can lose an electron under certain experimental conditions will be able to accept an electron under different experimental conditions.
It is to be understood that the number of possible transition metal complexes is very large, and that one skilled in the art of electron transfer compounds will be able to utilize a number of compounds in the present invention. By “transitional metal” herein is meant metals whose atoms have a partial or completed shell of electrons. Suitable transition metals for use in the invention include, but are not limited to, cadmium (Cd), copper (Cu), cobalt (Co), palladium (Pd), zinc (Zn), iron (Fe), ruthenium (Ru), rhodium (Rh), osmium (Os), rhenium (Re), platinium (Pt), scandium (Sc), titanium (Ti), Vanadium (V), chromium (Cr), manganese (Mn), nickel (Ni), Molybdenum (Mo), technetium (Tc), tungsten (W), and iridium (Ir). That is, the first series of transition metals, the platinum metals (Ru, Rh, Pd, Os, Ir and Pt), along with Fe, Re, W, Mo and Tc, find particular use in the present invention. Metals that find use in the invention also are those that do not change the number of coordination sites upon a change in oxidation state, including ruthenium, osmium, iron, platinum and palladium, with osmium, ruthenium and iron being especially useful. Generally, transition metals are depicted herein (or in incorporated references) as TM or M.
The transitional metal and the coordinating ligands form a metal complex. By “ligand” or “coordinating ligand” (depicted herein or in incorporated references in the figures as “L”) herein is meant an atom, ion, molecule, or functional group that generally donates one or more of its electrons through a coordinate covalent bond to, or shares its electrons through a covalent bond with, one or more central atoms or ions.
In some embodiments, small polar ligands are used; suitable small polar ligands, generally depicted herein as “L”, fall into two general categories, as is more fully described herein. In one embodiment, the small polar ligands will be effectively irreversibly bound to the metal ion, due to their characteristics as generally poor leaving groups or as good sigma donors, and the identity of the metal. These ligands may be referred to as “substitutionally inert”. Alternatively, as is more fully described below, the small polar ligands may be reversibly bound to the metal ion, such that upon binding of a target analyte, the analyte may provide one or more coordination atoms for the metal, effectively replacing the small polar ligands, due to their good leaving group properties or poor sigma donor properties. These ligands may be referred to as “substitutionally labile”. The ligands preferably form dipoles, since this will contribute to a high solvent reorganization energy.
Some of the structures of transitional metal complexes are shown below:




L are the co-ligands, that provide the coordination atoms for the binding of the metal ion. As will be appreciated by those in the art, the number and nature of the co-ligands will depend on the coordination number of the metal ion. Mono-, di- or polydentate co-ligands may be used at any position. Thus, for example, when the metal has a coordination number of six, the L from the terminus of the conductive oligomer, the L contributed from the nucleic acid, and r, add up to six. Thus, when the metal has a coordination number of six, r may range from zero (when all coordination atoms are provided by the other two ligands) to four, when all the co-ligands are monodentate. Thus generally, r will be from 0 to 8, depending on the coordination number of the metal ion and the choice of the other ligands.
In one embodiment, the metal ion has a coordination number of six and both the ligand attached to the conductive oligomer and the ligand attached to the nucleic acid are at least bidentate; that is, r is preferably zero, one (i.e. the remaining co-ligand is bidentate) or two (two monodentate co-ligands are used).
As will be appreciated in the art, the co-ligands can be the same or different. Suitable ligands fall into two categories: ligands which use nitrogen, oxygen, sulfur, carbon or phosphorus atoms (depending on the metal ion) as the coordination atoms (generally referred to in the literature as sigma (σ) donors) and organometallic ligands such as metallocene ligands (generally referred to in the literature as pi (π) donors, and depicted herein as Lm). Suitable nitrogen donating ligands are well known in the art and include, but are not limited to, cyano (C≡N), NH2; NHR; NRR′; pyridine; pyrazine; isonicotinamide; imidazole; bipyridine and substituted derivatives of bipyridine; terpyridine and substituted derivatives; phenanthrolines, particularly 1,10-phenanthroline (abbreviated phen) and substituted derivatives of phenanthrolines such as 4,7-dimethylphenanthroline and dipyridol[3,2-a:2′,3′-c]phenazine (abbreviated dppz); dipyridophenazine; 1,4,5,8,9,12-hexaazatriphenylene (abbreviated hat); 9,10-phenanthrenequinone diimine (abbreviated phi); 1,4,5,8-tetraazaphenanthrene (abbreviated tap); 1,4,8,11-tetra-azacyclotetradecane (abbreviated cyclam) and isocyanide. Substituted derivatives, including fused derivatives, may also be used. In some embodiments, porphyrins and substituted derivatives of the porphyrin family may be used. See for example, Comprehensive Coordination Chemistry, Ed. Wilkinson et al., Pergammon Press, 1987, Chapters 13.2 (pp 73-98), 21.1 (pp. 813-898) and 21.3 (pp 915-957), all of which are hereby expressly incorporated by reference.
As will be appreciated in the art, any ligand donor(1)-bridge-donor(2) where donor (1) binds to the metal and donor(2) is available for interaction with the surrounding medium (solvent, protein, etc) can be used in the present invention, especially if donor(1) and donor(2) are coupled through a pi system, as in cyanos (C is donor(1), N is donor(2), pi system is the CN triple bond). One example is bipyrimidine, which looks much like bipyridine but has N donors on the “back side” for interactions with the medium. Additional co-ligands include, but are not limited to cyanates, isocyanates (—N═C═O), thiocyanates, isonitrile, N2, O2, carbonyl, halides, alkoxyide, thiolates, amides, phosphides, and sulfur containing compound such as sulfino, sulfonyl, sulfoamino, and sulfamoyl.
In some embodiments, multiple cyanos are used as co-ligand to complex with different metals. For example, seven cyanos bind Re(III); eight bind Mo(IV) and W(IV). Thus at Re(III) with 6 or less cyanos and one or more L, or Mo(IV) or W(IV) with 7 or less cyanos and one or more L can be used in the present invention. The EAM with W(IV) system has particular advantages over the others because it is more inert, easier to prepare, more favorable reduction potential. Generally that a larger CN/L ratio will give larger shifts.
Suitable sigma donating ligands using carbon, oxygen, sulfur and phosphorus are known in the art. For example, suitable sigma carbon donors are found in Cotton and Wilkenson, Advanced Organic Chemistry, 5th Edition, John Wiley & Sons, 1988, hereby incorporated by reference; see page 38, for example. Similarly, suitable oxygen ligands include crown ethers, water and others known in the art. Phosphines and substituted phosphines are also suitable; see page 38 of Cotton and Wilkenson.
The oxygen, sulfur, phosphorus and nitrogen-donating ligands are attached in such a manner as to allow the heteroatoms to serve as coordination atoms.
In some embodiments, organometallic ligands are used. In addition to purely organic compounds for use as redox moieties, and various transition metal coordination complexes with δ-bonded organic ligand with donor atoms as heterocyclic or exocyclic substituents, there is available a wide variety of transition metal organometallic compounds with .pi.-bonded organic ligands (see Advanced Inorganic Chemistry, 5th Ed., Cotton & Wilkinson, John Wiley & Sons, 1988, chapter 26; Organometallics, A Concise Introduction, Elschenbroich et al., 2nd Ed., 1992, VCH; and Comprehensive Organometallic Chemistry II, A Review of the Literature 1982-1994, Abel et al. Ed., Vol. 7, chapters 7, 8, 10 & 11, Pergamon Press, hereby expressly incorporated by reference). Such organometallic ligands include cyclic aromatic compounds such as the cyclopentadienide ion [C5H5 (−1)] and various ring substituted and ring fused derivatives, such as the indenylide (−1) ion, that yield a class of bis(cyclopentadieyl)metal compounds, (i.e. the metallocenes); see for example Robins et al., J. Am. Chem. Soc. 104:1882-1893 (1982); and Gassman et al., J. Am. Chem. Soc. 108:4228-4229 (1986), incorporated by reference. Of these, ferrocene [(C5H5)2Fe] and its derivatives are prototypical examples which have been used in a wide variety of chemical (Connelly et al., Chem. Rev. 96:877-910 (1996), incorporated by reference) and electrochemical (Geiger et al., Advances in Organometallic Chemistry 23:1-93; and Geiger et al., Advances in Organometallic Chemistry 24:87, incorporated by reference) electron transfer or “redox” reactions. Metallocene derivatives of a variety of the first, second and third row transition metals are potential candidates as redox moieties that are covalently attached to either the ribose ring or the nucleoside base of nucleic acid. Other potentially suitable organometallic ligands include cyclic arenes such as benzene, to yield bis(arene)metal compounds and their ring substituted and ring fused derivatives, of which bis(benzene)chromium is a prototypical example. Other acyclic π-bonded ligands such as the allyl(−1) ion, or butadiene yield potentially suitable organometallic compounds, and all such ligands, in conduction with other .pi.-bonded and .delta.-bonded ligands constitute the general class of organometallic compounds in which there is a metal to carbon bond. Electrochemical studies of various dimers and oligomers of such compounds with bridging organic ligands, and additional non-bridging ligands, as well as with and without metal-metal bonds are potential candidate redox moieties in nucleic acid analysis.
When one or more of the co-ligands is an organometallic ligand, the ligand is generally attached via one of the carbon atoms of the organometallic ligand, although attachment may be via other atoms for heterocyclic ligands. Preferred organometallic ligands include metallocene ligands, including substituted derivatives and the metalloceneophanes (see page 1174 of Cotton and Wilkenson, supra). For example, derivatives of metallocene ligands such as methylcyclopentadienyl, with multiple methyl groups being preferred, such as pentamethylcyclopentadienyl, can be used to increase the stability of the metallocene. In a preferred embodiment, only one of the two metallocene ligands of a metallocene are derivatized.
As described herein, any combination of ligands may be used. Preferred combinations include: a) all ligands are nitrogen donating ligands; b) all ligands are organometallic ligands; and c) the ligand at the terminus of the conductive oligomer is a metallocene ligand and the ligand provided by the nucleic acid is a nitrogen donating ligand, with the other ligands, if needed, are either nitrogen donating ligands or metallocene ligands, or a mixture.
As a general rule, EAM comprising non-macrocyclic chelators are bound to metal ions to form non-macrocyclic chelate compounds, since the presence of the metal allows for multiple proligands to bind together to give multiple oxidation states.
In some embodiments, nitrogen donating proligands are used. Suitable nitrogen donating proligands are well known in the art and include, but are not limited to, NH2; NHR; NRR′; pyridine; pyrazine; isonicotinamide; imidazole; bipyridine and substituted derivatives of bipyridine; terpyridine and substituted derivatives; phenanthrolines, particularly 1,10-phenanthroline (abbreviated phen) and substituted derivatives of phenanthrolines such as 4,7-dimethylphenanthroline and dipyridol[3,2-a:2′,3′-c]phenazine (abbreviated dppz); dipyridophenazine; 1,4,5,8,9,12-hexaazatriphenylene (abbreviated hat); 9,10-phenanthrenequinone diimine (abbreviated phi); 1,4,5,8-tetraazaphenanthrene (abbreviated tap); 1,4,8,11-tetra-azacyclotetradecane (abbreviated cyclam) and isocyanide. Substituted derivatives, including fused derivatives, may also be used. It should be noted that macrocylic ligands that do not coordinatively saturate the metal ion, and which require the addition of another proligand, are considered non-macrocyclic for this purpose. As will be appreciated by those in the art, it is possible to covalent attach a number of “non-macrocyclic” ligands to form a coordinatively saturated compound, but that is lacking a cyclic skeleton.
In some embodiments, a mixture of monodentate (e.g., at least one cyano ligand), bi-dentate, tri-dentate, and polydentate ligands can be used in the construction of EAMs.
Of particular use in the present invention are EAMs that are metallocenes, and in particular ferrocenes, which have at least a first self-immolative moiety attached, although in some embodiments, more than one self-immolative moiety is attached as is described below (it should also be noted that other EAMs, as are broadly described herein, with self-immolative moieties can also be used). In some embodiments, when more than one self-immolative moiety is attached to a ferrocene, they are all attached to one of the cyclopentydienyl rings. In some embodiments, the self-immolative moieties are attached to different rings. In some embodiments, it is possible to saturate one or both of the cyclopentydienyl rings with self-immolative moieties, as long as one site is used for attachment to the electrode.
In some embodiments, the EAMs comprise substituted 1,1′-ferrocenes. Ferrocene is air-stable. It can be easily substituted with both capture ligand and anchoring group. Upon binding of the target protein to the capture ligand on the ferrocene which will not only change the environment around the ferrocene, but also prevent the cyclopentadienyl rings from spinning, which will change the energy by approximately 4 kJ/mol. WO/1998/57159; Heinze and Schlenker, Eur. J. Inorg. Chem. 2974-2988 (2004); Heinze and Schlenker, Eur. J. Inorg. Chem. 66-71 (2005); and Holleman-Wiberg, Inorganic Chemistry, Academic Press 34th Ed, at 1620, all incorporated by reference.




In some other embodiments, the EAMs comprise 1,3-disubstituted ferrocenes. While 1,3-disubstituted ferrocenes are known (see, Bickert et al., Organometallics 1984, 3, 654-657; Farrington et al., Chem. Commun. 2002, 308-309; Pichon et al., Chem. Commun. 2004, 598-599; and Steurer et al., Organometallics 2007, 26, 3850-3859), electrochemical studies of this class of molecules in SAMs have not been reported in the literature. In contrast to 1,1′-disubstituted ferrocenes where cyclopentadienyl (Cp) ring rotation can place both Cp substituents in an eclipsed conformation, 1,3-disubstituted ferrocene regioisomers provide a molecular architecture that enforces a rigid geometry between these Cp groups. Thus, 1,3-disubstituted ferrocenes that possess an anchoring group, such as an organosulfur group for gold anchoring, and a capture ligand such as a receptor group, protein capture ligands and/or enzyme-reactive moieties are suited for SAM-based electrochemical biosensing applications where the receptor is displayed at the solution/SAM interface with limited degrees of freedom (see FIG. 1, where X is an anchoring group and Y can comprise a capture ligand). Representative examples of 1,3-disubstituted ferrocenes are shown in FIG. 12, such as compounds 1-5. An example of a 1,3-disubstituted ferrocene for attaching both anchoring and capture ligands is shown below:




A series of 1,3-disubstituted ferrocene derivatives (1-4) were synthesized with different functional moieties and organosulfur anchoring groups for SAM formation on gold, and are shown below.




Additional ferrocene EAMs suitable for use in methods of disclosure are disclosed in U.S. patent application Ser. No. 13/667,713, filed Nov. 2, 2012, which claims the benefit of U.S. Provisional Application No. 61/555,945, filed Nov. 4, 2011, all which are expressly incorporated by reference in their entirety.
In addition, EAMs generally have an attachment moiety for attachment of the EAM to the conductive oligomer which is used to attach the EAM to the electrode. In general, although not required, in the case of metallocenes such as ferrocenes, the self-immolative moiety(ies) are attached to one of the cyclopentydienyl rings, and the attachment moiety is attached to the other ring, as is generally depicted in FIG. 1, although attachment to the same ring can also be done. As will be appreciated by those in the art, any combination of self-immolative moieties and at least one attachment linker can be used, and on either ring.
In addition to the self-immolative moiety(ies) and the attachment moiety(ies), the ferrocene can comprise additional substituent groups, which can be added for a variety of reasons, including altering the E0 in the presence or absence of at least the self-immolative group. Suitable substituent groups, frequently depicted in associated and incorporated references as “R” groups, are recited in U.S. patent application Ser. No. 12/253,828, filed Oct. 17, 2008; U.S. patent application Ser. No. 12/253,875, filed Oct. 17, 2008; U.S. Provisional Patent Application No. 61/332,565, filed May 7, 2010; U.S. Provisional Patent Application No. 61/347,121, filed May 21, 2010; and U.S. Provisional Patent Application No. 61/366,013, filed Jul. 20, 2010, hereby incorporated by reference.
In some embodiments, such as depicted below, the EAM does not comprise a self-immolative moiety, in the case where the peroxide-sensitive moiety is attached directly to the EAM and provides a change in E0 when the peroxide-sensitive moiety is exposed to peroxide. As shown below, one embodiment allows the peroxide-sensitive moiety to be attached directly to the EAM (in this case, a ferrocene), such that the ferrocene has a first E0 when the pinacol boronate ester moiety is attached, and a second E0 when removed, e.g., in the presence of the peroxide.




Self-Immolative Moieties
The EAMs of the invention include at least one self-immolative moiety that is covalently attached to the EAM such that the EAM has a first E0 when it is present and a second E0 when it has been removed as described below.
The term “self-immolative spacer” refers to a bifunctional chemical moiety that is capable of covalently linking two chemical moieties into a normally stable tripartate molecule. The self-immolative spacer is capable of spontaneously separating from the second moiety if the bond to the first moiety is cleaved. In the present invention, the self-immolative spacer links a peroxide sensitive moiety, e.g., a boron moiety, to the EAM. Upon exposure to peroxide, the boron moiety is removed and the spacer falls apart, as generally depicted in FIG. 1. Generally speaking, any spacer where irreversible repetitive bond rearrangement reactions are initiated by an electron-donating alcohol functional group (i.e. quinone methide motifs) can be designed with boron groups serving as triggering moieties that generate alcohols under oxidative conditions. Alternatively, the boron moiety can mask a latent phenolic oxygen in a ligand that is a pro-chelator for a transition metal. Upon oxidation, the ligand is transformed and initiates EAM formation in the SAM. For example, a sample chelating ligand is salicaldehyde isonicotinoyl hydrazone that binds iron.
As will be appreciated by those in the art, a wide variety of self-immolative moieties may be used with a wide variety of EAMs and peroxide sensitive moieties. Self-immolative linkers have been described in a number of references, including US Publication Nos. 20090041791; 20100145036 and U.S. Pat. Nos. 7,705,045 and 7,223,837, all of which are expressly incorporated by reference in their entirety, particularly for the disclosure of self-immolative spacers.
A few self-immolative linkers of particular use in the present invention are shown in FIG. 6. The self-immolative spacer can comprise a single monomeric unit or polymers, either of the same monomers (homopolymers) or of different monomers (heteropolymers). Alternatively, the self-immolative spacer can be a neighboring group to an EAM in a SAM that changes the environment of the EAM following cleavage analogous to the chemistry as recited in previous application “Electrochemical Assay for the Detection of Enzymes”, U.S. Ser. No. 12/253,828, PCT/US2008/080363, hereby incorporated by reference.
Peroxide Sensitive Moieties
The self-immolative spacers join the peroxide sensitive moieties (PSMs, sometimes referred to herein as POMs) and the EAMs of the invention. In general, a peroxide sensitive moiety is one containing boron as depicted in FIG. 1.
For example, the figures herein depict the use of ferrocene derivatives, where the peroxide triggers a change from a benzyl carbamate with a p-substituted pinacol borate ester to an amine. This self-eliminating group has been described previously for generating amine-functionalized florophores in the presence of hydrogen peroxide (Sella, E.; Shabat, D. Self-immolative dendritic probe for the direct detection of triacetone triperoxide. Chem. Commun. 2008, 5701-5703; and Lo, L.-Cl; Chu, C.-Y. Development of highly selective and sensitive probes for hydrogen peroxide. Chem. Commun. 2003, 2728-2729 both of which are incorporated by reference. Other such groups (aryl borate esters and arylboronic acids) are also described in Sella and Lo. In addition, ferrocenylamines are known to exhibit redox behavior at lower potentials (−150 mV) as compared to their corresponding carbamate derviatives (see Sagi et al., Amperometric Assay for Aldolase Activity; Antibody-Catalyzed Ferrocenylamine Formation. Anal. Chem. 2006, 78, 1459-1461, incorporated by reference herein).
Capture and Soluble Binding Ligands
In addition to SAMs and EAMs, in some embodiments, the electrodes comprise capture binding ligands. By “binding ligand” or “binding species” herein is meant a compound that is used to probe for the presence of the target analyte and that will bind to the target analyte. In general, for most of the embodiments described herein, there are at least two binding ligands used per target analyte molecule; a “capture” or “anchor” binding ligand that is attached to the detection surface, and a soluble binding ligand, that binds independently to the target analyte, and either directly or indirectly comprises at least one label such as a SOX. By “capture binding ligand” herein is meant a binding ligand that binds the target analyte that is attached to the electrode surface that binds the target analyte. By “soluble binding ligand” herein is meant a binding ligand that is in solution that binds the target analyte at a different site than the capture binding ligand.
As will be appreciated by those in the art, the composition of the binding ligand will depend on the composition of the target analyte. Binding ligands for a wide variety of analytes are known or can be readily found using known techniques. For example, when the analyte is a protein, the binding ligands include proteins (particularly including antibodies or fragments thereof (FAbs, etc.)) or small molecules.
In general, antibodies are useful as both capture and soluble binding ligands.
The soluble binding ligand also comprises a peroxide generating moiety such as an enzyme that generates peroxide. As defined herein, the term “peroxide generating system” or “peroxide-generating system” means one or more enzymes that directly generates a peroxide from its substrate and/or an intermediary enzyme that generates an intermediate, e.g., a cofactor or pre-substrate, for another enzyme that in turn generates a peroxide. In one example, a peroxide generating moiety may be an enzyme that generates peroxide, e.g., “peroxide generating enzyme”. A wide variety of such enzymes are known, including glucose oxidase, acyl CoA oxidases, alcohol oxidases, aldehyde oxidases, etc. A wide variety of suitable oxidase enzymes are known in the art (see any glucose oxidase enzyme classified as EC 1.1.3.4, including, but not limited to, glucose oxidase, D-amino acid oxidase (DAAO) and choline oxidase). Glucose oxidase enzymes from a wide variety of organisms are well known, including bacterial, fungal and animal (including mammalian), including, but not limited to, Aspergillus species (e.g. A. niger), Penicillum species, Streptomyces species, mouse, etc.). Also of use are acyl CoA oxidases, classified as EC 1.3.3.6.
By the term “an intermediary enzyme” herein is meant an enzyme that generates a product that is a substrate or a cofactor for another enzyme such as another intermediary enzyme or a peroxide-generating enzyme. For instance, the soluble binding ligand may contain an enzyme, such as alkaline phosphatase (AP), that catalyzes the generation of a necessary cofactor from a phosphorylated precursor for a soluble apo-oxidase enzyme (i.e., FADP converted to FAD which binds to apo-DAAO) which in turn generates peroxide by reaction with substrate. This strategy enables cascade amplification of target binding events if the concentrations of apo-enzyme, phosphorylated cofactor, and oxidase enzyme substrate are high with respect to the surface immobilized target.
As defined herein, the term “target specific enzyme” herein is meant an enzyme, e.g., Glycerol Kinase, that is specific for a target analyte, e.g. ATP.
As defined herein, the term “recycling enzyme” herein is meant an enzyme that regenerates or recycles a necessary substrate of another enzyme such as the generation of NADH from NAD+.
Generally, the capture binding ligand allows the attachment of a target analyte to the detection surface, for the purposes of detection. In one embodiment, the binding is specific, and the binding ligand is part of a binding pair. By “specifically bind” herein is meant that the ligand binds the analyte, with specificity sufficient to differentiate between the analyte and other components or contaminants of the test sample. By “specific binding pair” herein is meant a complimentary pair of binding ligands such as an antibody/antigen and receptor/ligand. The binding should be sufficient to allow the analyte to remain bound under the conditions of the assay, including wash steps to remove non-specific binding. In some embodiments, for example in the detection of certain biomolecules, the binding constants of the analyte to the binding ligand will be at least about 10−4 to 10−9 M−1, with at least about 10−5 to 10−9 being preferred and at least about 10−7 to 10−9 M−1 being particularly preferred.
Binding ligands to a wide variety of analytes are known or can be readily found using known techniques. For example, when the analyte is a single-stranded nucleic acid, the binding ligand is generally a substantially complementary nucleic acid. Alternatively, as is generally described in U.S. Pat. Nos. 5,270,163, 5,475,096, 5,567,588, 5,595,877, 5,637,459, 5,683,867, 5,705,337, and related patents, hereby incorporated by reference, nucleic acid “aptamers” can be developed for binding to virtually any target analyte. Similarly the analyte may be a nucleic acid binding protein and the capture binding ligand is either a single-stranded or double-stranded nucleic acid; alternatively, the binding ligand may be a nucleic acid binding protein when the analyte is a single or double-stranded nucleic acid. When the analyte is a protein, the binding ligands include proteins (particularly including antibodies or fragments thereof (FAbs, etc.)), small molecules, or aptamers, described above. Preferred binding ligand proteins include antibodies and peptides. As will be appreciated by those in the art, any two molecules that will associate, preferably specifically, may be used, either as the analyte or the binding ligand. Suitable analyte/binding ligand pairs include, but are not limited to, antibodies/antigens, receptors/ligand, proteins/nucleic acids; nucleic acids/nucleic acids, enzymes/substrates and/or inhibitors, carbohydrates (including glycoproteins and glycolipids)/lectins, carbohydrates and other binding partners, proteins/proteins; and protein/small molecules. These may be wild-type or derivative sequences.
The capture binding ligands (e.g. a capture antibody) can be covalently coupled to the electrode (usually through an attachment linker) or bound tightly but not covalently; for example, using biotin/streptavidin reactions (e.g. biotin on the surface of the SAM, streptavin-conjugated capture ligand such as an antibody, or vice versa), bound via a nucleic acid reaction (for example, the capture ligand can have a nucleic acid (“Watson”) and the surface can have a complementary nucleic acid (“Crick”), bound using protein G binding to the Fc fragment of the antibody, etc.
It should also be noted that the invention described herein can also be used as a sensor for the illicit explosive triacetone triperoxide (TATP).
Anchor Groups
The present invention provides compounds including the EAM (optionally attached to the electrode surface with a conductive oligomer), the SAM, and the capture binding ligands on the electrode surface. Generally, in some embodiments, these moieties are attached to the electrode using anchor group. By “anchor” or “anchor group” herein is meant a chemical group that attaches the compounds of the invention to an electrode.
As will be appreciated by those in the art, the composition of the anchor group will vary depending on the composition of the surface to which it is attached. In the case of gold electrodes, both pyridinyl anchor groups and thiol based anchor groups find particular use.
The covalent attachment of the conductive oligomer may be accomplished in a variety of ways, depending on the electrode and the conductive oligomer used. Generally, some type of linker is used, as depicted below as “A” in Structure 1, where X is the conductive oligomer, and the hatched surface is the electrode:




In this embodiment, A is a linker or atom. The choice of “A” will depend in part on the characteristics of the electrode. Thus, for example, A may be a sulfur moiety when a gold electrode is used. Alternatively, when metal oxide electrodes are used, A may be a silicon (silane) moiety attached to the oxygen of the oxide (see for example Chen et al., Langmuir 10:3332-3337 (1994); Lenhard et al., J. Electroanal. Chem. 78:195-201 (1977), both of which are expressly incorporated by reference). When carbon based electrodes are used, A may be an amino moiety (preferably a primary amine; see for example Deinhammer et al., Langmuir 10:1306-1313 (1994)). Thus, preferred A moieties include, but are not limited to, silane moieties, sulfur moieties (including alkyl sulfur moieties), and amino moieties.
In some embodiments, the electrode is a carbon electrode, i.e. a glassy carbon electrode, and attachment is via a nitrogen of an amine group. A representative structure is depicted in Structure 15 of US Patent Application Publication No. 20080248592, hereby incorporated by reference in its entirety but particularly for Structures as described therein and the description of different anchor groups and the accompanying text. Again, additional atoms may be present, i.e. linkers and/or terminal groups.
In Structure 16 of US Patent Application Publication No. 20080248592, hereby incorporated by reference as above, the oxygen atom is from the oxide of the metal oxide electrode. The Si atom may also contain other atoms, i.e. be a silicon moiety containing substitution groups. Other attachments for SAMs to other electrodes are known in the art; see for example Napier et al., Langmuir, 1997, for attachment to indium tin oxide electrodes, and also the chemisorption of phosphates to an indium tin oxide electrode (talk by H. Holden Thorpe, CHI conference, May 4-5, 1998).
In one preferred embodiment, indium-tin-oxide (ITO) is used as the electrode, and the anchor groups are phosphonate-containing species.
1). Sulfur Anchor Groups
Although depicted in Structure 1 as a single moiety, the conductive oligomer may be attached to the electrode with more than one “A” moiety; the “A” moieties may be the same or different. Thus, for example, when the electrode is a gold electrode, and “A” is a sulfur atom or moiety, multiple sulfur atoms may be used to attach the conductive oligomer to the electrode, such as is generally depicted below in Structures 2, 3 and 4. As will be appreciated by those in the art, other such structures can be made. In Structures 2, 3 and 4 the A moiety is just a sulfur atom, but substituted sulfur moieties may also be used.
Thus, for example, when the electrode is a gold electrode, and “A” is a sulfur atom or moiety, such as generally depicted below in Structure 6, multiple sulfur atoms may be used to attach the conductive oligomer to the electrode, such as is generally depicted below in Structures 2, 3 and 4. As will be appreciated by those in the art, other such structures can be made. In Structures 2, 3 and 4, the A moiety is just a sulfur atom, but substituted sulfur moieties may also be used.




It should also be noted that similar to Structure 4, it may be possible to have a conductive oligomer terminating in a single carbon atom with three sulfur moieties attached to the electrode.
In another aspect, the present invention provide anchor comprise conjugated thiols. Some exemplary complexes with conjugated thiol anchors are shown in FIG. 10. In some embodiments, the anchor comprises an alkylthiol group. Some of the examples are shown in FIGS. 10A and 4B. The two compounds depicts in FIG. 10B are based on carbene and 4-pyridylalanine, respectively.
In another aspect, the present invention provides conjugated multipodal thio-containing compounds that serve as anchoring groups in the construction of electroactive moieties for analyte detection on electrodes, such as gold electrodes. That is, spacer groups (which can be attached to EAMs, ReAMCs, or an “empty” monolayer forming species) are attached using two or more sulfur atoms. These mulitpodal anchor groups can be linear or cyclic, as described herein.
In some embodiments, the anchor groups are “bipodal”, containing two sulfur atoms that will attach to the gold surface, and linear, although in some cases it can be possible to include systems with other multipodalities (e.g. “tripodal”). Such a multipodal anchoring group display increased stability and/or allow a greater footprint for preparing SAMs from thiol-containing anchors with sterically demanding headgroups.
In some embodiments, the anchor comprises cyclic disulfides (“bipod”). Although in some cases it can be possible to include ring system anchor groups with other multipodalities (e.g. “tripodal”). The number of the atoms of the ring can vary, for example from 5 to 10, and also includes multicyclic anchor groups, as discussed below
In some embodiments, the anchor groups comprise a [1,2,5]-dithiazepane unit which is seven-membered ring with an apex nitrogen atom and a intramolecular disulfide bond as shown below:




In Structure (IIIa), it should also be noted that the carbon atoms of the ring can additionally be substituted. As will be appreciated by those in the art, other membered rings are also included. In addition, multicyclic ring structures can be used, which can include cyclic heteroalkanes such as the [1,2,5]-dithiazepane shown above substituted with other cyclic alkanes (including cyclic heteroalkanes) or aromatic ring structures. In some embodiments, the anchor group and part of the spacer has the structure shown below




The “R” group herein can be any substitution group, including a conjugated oligophenylethynylene unit with terminal coordinating ligand for the transition metal component of the EAM.
The anchors are synthesized from a bipodal intermediate (I) (the compound as formula III where R═I), which is described in Li et al., Org. Lett. 4:3631-3634 (2002), herein incorporated by reference. See also Wei et al, J. Org, Chem. 69:1461-1469 (2004), herein incorporated by reference.
The number of sulfur atoms can vary as outlined herein, with particular embodiments utilizing one, two, and three per spacer.
As will be appreciated by those in the art, the compositions of the invention can be made in a variety of ways, including those outlined below and in U.S. patent application Ser. No. 12/253,828, filed Oct. 17, 2008; U.S. patent application Ser. No. 12/253,875, filed Oct. 17, 2008; U.S. Provisional Patent Application No. 61/332,565, filed May 7, 2010; U.S. Provisional Patent Application No. 61/347,121, filed May 21, 2010; U.S. Provisional Patent Application No. 61/366,013, filed Jul. 20, 2010. In some embodiments, the composition are made according to methods disclosed in of U.S. Pat. Nos. 6,013,459, 6,248,229, 7,018,523, 7,267,939, U.S. patent application Ser. No. 09/096,593 and 60/980,733, and U.S. Provisional Application No. 61/087,102, filed on Aug. 7, 2008, all are herein incorporated in their entireties for all purposes.
Applications
The systems of the invention find use in the detection of a variety of target analytes, as outlined herein. In some embodiments, “sandwich” type assays are used, as are generally depicted in FIGS. 11-13. In other embodiments, for example for the detection of particular metabolites such as ATP and NADH, other formats are used.
In some embodiments, for example in “sandwich” type formats, the target analyte, contained within a test sample, is added to the electrode with the PSM-SIM-EAM mixture, a capture binding ligand, and optionally a SAM. This addition is followed by an optional washing step and the addition of the soluble binding ligand, although as will be appreciated by those in the art, these additions can be done simultaneously or the solution binding ligand can be added to the sample containing the target analyte prior to addition to the chip. The surface is again optionally washed, and the substrate for the peroxide sensitive moiety, e.g. glucose, is added under conditions that if present, peroxide is generated and the SIM is cleaved.
In some embodiments, for example when there is a specific peroxidase-generating enzyme that uses a metabolite of interest (e.g. a target analyte or target metabolite), as depicted in FIGS. 12 and 13, the system takes on different configurations. For example, in FIG. 12, the electrode, generally with a SAM, contains at least two species: (1) an EAM with a self-immolative moiety, depicted in FIG. 12 as a ferrocene-based derivative (although as described herein and as will be appreciated by those in the art, other EAMs can be used); and (2) an attached peroxidase-generating enzyme, in this case, as depicted, NADH oxidase. As outlined herein, the peroxidase-generating enzyme can be attached to the electrode surface in a number of different ways. The attachment can be “direct” when the enzyme is attached to the terminus of a monolayer forming species, as is generally outlined in PCT/US2008/080379, using a coupling chemistry. Alternatively, and as depicted in FIG. 12, the enzyme can be attached using a number of “sandwich” type attachments, for example using a monolayer species with a biotin attached, a streptavidin and a biotin-labeled enzyme.
In some embodiments, these two species can be attached as a single moiety to the electrode surface, for example as generally depicted in Structure 7 of U.S. Pat. No. 7,595,153, hereby incorporated by reference in its entirety and specifically for the schematics of attachment configurations.
These conditions are generally physiological conditions. Generally a plurality of assay mixtures is run in parallel with different concentrations to obtain a differential response to the various concentrations. Typically, one of these concentrations serves as a negative control, i.e., at zero concentration or below the level of detection. In addition, any variety of other reagents may be included in the screening assay. These include reagents like salts, neutral proteins, e.g. albumin, detergents, etc. which may be used to facilitate optimal binding and/or reduce non-specific or background interactions. Also reagents that otherwise improve the efficiency of the assay, such as protease inhibitors, nuclease inhibitors, anti-microbial agents, etc., may be used. The mixture of components may be added in any order that provides for the requisite binding.
[The generation of peroxidase results in the loss of the PGM-SIM component of the complex, resulting the a change in the E0 of the EAM. In some embodiments, the E0 of the EAM changes by at about 20 mV, 30 mV, 40 mV, 50 mV, 75 mV, 80 mV, 90 mV to 100 mV, some embodiments resulting in changes of 200, 300 or 500 mV being achieved. In some embodiments, the changes in the E0 of the EAM is a decrease. In some embodiments, the changes in the E0 of the EAM is an increase.
Electron transfer is generally initiated electronically, with voltage being preferred. Precise control and variations in the applied potential can be via a potentiostat and either a three electrode system (one reference, one sample and one counter electrode) or a two electrode system (one sample and one counter electrode). This allows matching of applied potential to peak electron transfer potential of the system which depends in part on the choice of redox active molecules and in part on the conductive oligomer used.
Detection
Electron transfer between the redox active molecule and the electrode can be detected in a variety of ways, with electronic detection, including, but not limited to, amperommetry, voltammetry, capacitance and impedance being preferred. These methods include time or frequency dependent methods based on AC or DC currents, pulsed methods, lock in techniques, and filtering (high pass, low pass, band pass). In some embodiments, all that is required is electron transfer detection; in others, the rate of electron transfer may be determined.
In some embodiments, electronic detection is used, including amperommetry, voltammetry, capacitance, and impedance. Suitable techniques include, but are not limited to, electrogravimetry; coulometry (including controlled potential coulometry and constant current coulometry); voltametry (cyclic voltametry, pulse voltametry (normal pulse voltametry, square wave voltametry, differential pulse voltametry, Osteryoung square wave voltametry, and coulostatic pulse techniques); stripping analysis (aniodic stripping analysis, cathiodic stripping analysis, square wave stripping voltammetry); conductance measurements (electrolytic conductance, direct analysis); time dependent electrochemical analyses (chronoamperometry, chronopotentiometry, cyclic chronopotentiometry and amperometry, AC polography, chronogalvametry, and chronocoulometry); AC impedance measurement; capacitance measurement; AC voltametry, and photoelectrochemistry.
In some embodiments, monitoring electron transfer is via amperometric detection. This method of detection involves applying a potential (as compared to a separate reference electrode) between the electrode containing the compositions of the invention and an auxiliary (counter) electrode in the test sample. Electron transfer of differing efficiencies is induced in samples in the presence or absence of target analyte.
The device for measuring electron transfer amperometrically involves sensitive current detection and includes a means of controlling the voltage potential, usually a potentiostat. This voltage is optimized with reference to the potential of the redox active molecule.
In some embodiments, alternative electron detection modes are utilized. For example, potentiometric (or voltammetric) measurements involve non faradaic (no net current flow) processes and are utilized traditionally in pH and other ion detectors. Similar sensors are used to monitor electron transfer between the redox active molecules and the electrode. In addition, other properties of insulators (such as resistance) and of conductors (such as conductivity, impedance and capicitance) could be used to monitor electron transfer between the redox active molecules and the electrode. Finally, any system that generates a current (such as electron transfer) also generates a small magnetic field, which may be monitored in some embodiments.
It should be understood that one benefit of the fast rates of electron transfer observed in the compositions of the invention is that time resolution can greatly enhance the signal to noise results of monitors based on electronic current. The fast rates of electron transfer of the present invention result both in high signals and stereotyped delays between electron transfer initiation and completion. By amplifying signals of particular delays, such as through the use of pulsed initiation of electron transfer and “lock in” amplifiers of detection, orders of magnitude improvements in signal to noise may be achieved.
In some embodiments, electron transfer is initiated and detected using direct current (DC) techniques. As noted above, the first E0 of the redox active molecule before and the second E0 of the reacted redox active molecule afterwards will allow the detection of the analyte. As will be appreciated by those in the art, a number of suitable methods may be used to detect the electron transfer.
In some embodiments, electron transfer is initiated using alternating current (AC) methods. A first input electrical signal is applied to the system, preferably via at least the sample electrode (containing the complexes of the invention) and the counter electrode, to initiate electron transfer between the electrode and the second electron transfer moiety. Three electrode systems may also be used, with the voltage applied to the reference and working electrodes. In this embodiment, the first input signal comprises at least an AC component. The AC component may be of variable amplitude and frequency. Generally, for use in the present methods, the AC amplitude ranges from about 1 mV to about 1.1 V, with from about 10 mV to about 800 mV being preferred, and from about 10 mV to about 500 mV being especially preferred. The AC frequency ranges from about 0.01 Hz to about 10 MHz, with from about 1 Hz to about 1 MHz being preferred, and from about 1 Hz to about 100 kHz being especially preferred
In some embodiments, the first input signal comprises a DC component and an AC component. That is, a DC offset voltage between the sample and counter electrodes is swept through the electrochemical potential of the second electron transfer moiety. The sweep is used to identify the DC voltage at which the maximum response of the system is seen. This is generally at or about the electrochemical potential of the redox active molecule. Once this voltage is determined, either a sweep or one or more uniform DC offset voltages may be used. DC offset voltages of from about 1 V to about +1.1 V are preferred, with from about 500 mV to about +800 mV being especially preferred, and from about 300 mV to about 500 mV being particularly preferred. On top of the DC offset voltage, an AC signal component of variable amplitude and frequency is applied. If the redox active molecule has a low enough solvent reorganization energy to respond to the AC perturbation, an AC current will be produced due to electron transfer between the electrode and the redox active molecule.
In some embodiments, the AC amplitude is varied. Without being bound by theory, it appears that increasing the amplitude increases the driving force. Thus, higher amplitudes, which result in higher overpotentials give faster rates of electron transfer. Thus, generally, the same system gives an improved response (i.e. higher output signals) at any single frequency through the use of higher overpotentials at that frequency. Thus, the amplitude may be increased at high frequencies to increase the rate of electron transfer through the system, resulting in greater sensitivity. In addition, as noted above, it may be possible to the first and second E0 of the redox active molecules, molecules on the basis of the rate of electron transfer, which in turn can be used either to distinguish the two on the basis of frequency or overpotential.
In some embodiments, measurements of the system are taken at least two separate amplitudes or overpotentials, with measurements at a plurality of amplitudes being preferred. As noted above, changes in response as a result of changes in amplitude may form the basis of identification, calibration and quantification of the system.
In some embodiments, the AC frequency is varied. At different frequencies, different molecules respond in different ways. As will be appreciated by those in the art, increasing the frequency generally increases the output current. However, when the frequency is greater than the rate at which electrons may travel between the electrode and the redox active molecules, higher frequencies result in a loss or decrease of output signal. At some point, the frequency will be greater than the rate of electron transfer through even solvent inhibited redox active molecules, and then the output signal will also drop.
In addition, the use of AC techniques allows the significant reduction of background signals at any single frequency due to entities other than the covalently attached nucleic acids, i.e. “locking out” or “filtering” unwanted signals. That is, the frequency response of a charge carrier or redox active molecule in solution will be limited by its diffusion coefficient. Accordingly, at high frequencies, a charge carrier may not diffuse rapidly enough to transfer its charge to the electrode, and/or the charge transfer kinetics may not be fast enough. This is particularly significant in embodiments that do not utilize a passavation layer monolayer or have partial or insufficient monolayers, i.e. where the solvent is accessible to the electrode. As outlined above, in DC techniques, the presence of “holes” where the electrode is accessible to the solvent can result in solvent charge carriers “short circuiting” the system. However, using the present AC techniques, one or more frequencies can be chosen that prevent a frequency response of one or more charge carriers in solution, whether or not a monolayer is present. This is particularly significant since many biological fluids such as blood contain significant amounts of redox active molecules which can interfere with amperometric detection methods.
In some embodiments, measurements of the system are taken at least two separate frequencies, with measurements at a plurality of frequencies being preferred. A plurality of frequencies includes a scan. In a preferred embodiment, the frequency response is determined at least two, preferably at least about five, and more preferably at least about ten frequencies.
Signal Processing
After transmitting the input signal to initiate electron transfer, an output signal is received or detected. The presence and magnitude of the output signal will depend on the overpotential/amplitude of the input signal; the frequency of the input AC signal; the composition of the intervening medium, i.e. the impedance, between the electron transfer moieties; the DC offset; the environment of the system; and the solvent. At a given input signal, the presence and magnitude of the output signal will depend in general on the solvent reorganization energy required to bring about a change in the oxidation state of the metal ion. Thus, upon transmitting the input signal, comprising an AC component and a DC offset, electrons are transferred between the electrode and the redox active molecule, when the solvent reorganization energy is low enough, the frequency is in range, and the amplitude is sufficient, resulting in an output signal.
In some embodiments, the output signal comprises an AC current. As outlined above, the magnitude of the output current will depend on a number of parameters. By varying these parameters, the system may be optimized in a number of ways.
In general, AC currents generated in the present invention range from about 1 femptoamp to about 1 milliamp, with currents from about 50 femptoamps to about 100 microamps being preferred, and from about 1 picoamp to about 1 microamp being especially preferred.
Apparatus
The present invention further provides apparatus for the detection of analytes using AC detection methods. The apparatus includes a test chamber which has at least a first measuring or sample electrode, and a second measuring or counter electrode. Three electrode systems are also useful. The first and second measuring electrodes are in contact with a test sample receiving region, such that in the presence of a liquid test sample, the two electrodes may be in electrical contact.
In yet another embodiment, the first measuring electrode comprises a redox active complex, covalently attached via a spacer, and preferably via a conductive oligomer, such as are described herein. Alternatively, the first measuring electrode comprises covalently attached redox active molecules and binding ligands.
The apparatus further comprises a voltage source electrically connected to the test chamber; that is, to the measuring electrodes. Preferably, the voltage source is capable of delivering AC and DC voltages, if needed.
In an embodiment, the apparatus further comprises a processor capable of comparing the input signal and the output signal. The processor is coupled to the electrodes and configured to receive an output signal, and thus detect the presence of the target analyte.
EXAMPLES
Example 1
General Methods and Materials. Unless otherwise noted, all synthetic manipulations were performed under a dry argon atmosphere using standard Schlenk techniques. For reaction media, solvents were dried over neutral alumina via the Dow-Grubbs solvent system1 acquired from Glass Contours (Laguna Beach, Calif.). These solvents were deoxygenated with argon prior to use. Reactions were monitored by TLC using EMD precoated aluminum plates (silica gel 60, F254, EMD Chemicals, Inc., Gibbstown, N.J.). Spots were visualized by one of the following methods: iodine vapor, exposure to UV light, or staining with phosphomolybdic acid followed by heating. Flash chromatography was carried out on silica (silica gel 60 particle size: 40-63 μm; Sorbent Technologies, Atlanta, Ga.) under a positive pressure of laboratory air. 1H NMR and proton-decoupled 13C NMR spectra were recorded on a Bruker Avance III spectrometer (499.37 MHz for 1H, 125.58 MHz for 13C) and were processed with Bruker TOPSPIN 2.1 software. High-resolution mass spectrometry (HRMS) was obtained using an Agilent 6210 time-of-flight (TOF) LC/MS instrument using electrospray ionization (ESI) or atmospheric pressure photoionization (APPI) methods.
Chloroform-d1 was purchased from Cambridge Isotope Laboratories. Compound 2 and p-pinacolborate benzyl alcohol were synthesized as described previously (Bertin, P. A.; Meade, T. J. Tetrahedron Lett. 2009, 50, 5409-5412; Sella, E.; Shabat, D. Chem. Commun. 2008, 5701-5703, both of which are expressly incorporated by reference). All other reagents were purchased from commercial sources and used without further purification unless otherwise noted.
Compound 3.
To a solution of compound 2 (0.500 g, 1.2 mmol) and triethylamine (0.25 mL, 1.8 mmol) in tetrahydrofuran (15 mL) was added diphenylphosphoryl azide (DPPA) (0.285 mL, 1.32 mmol). The reaction was stirred at rt for 1.5 hours and concentrated under reduced pressure. The crude residue was purified by column chromatography (methanol:ethyl acetate:dichloromethane 0.5:1.5:8) to yield the title compound as a red/orange solid (0.460 g, 1.04 mmol, 87%). 1H NMR, 13C{1H} NMR, and HRMS were consistent with the title compound.
Compound 4.
A solution of compound 3 (0.460 g, 1.04 mmol) in toluene (20 mL) was vigorously degassed with Ar and heated to 100° C. for 1.5 hours, p-pinacolborate benzyl alcohol (0.268 g, 1.14 mmol) and dibutyltin-dilaurate (DBTL) (0.018 mL, 0.03 mmol) were added and the reaction maintained at 100° C. for an additional 2 hours. The reaction was concentrated under reduced pressure and the crude residue purified by column chromatography (diethyl ether:ethyl acetate:dichloromethane, 1:2:2) to yield the title compound as a pale orange solid (0.480 g, 0.741 mmol, 71%). 1H NMR, 13C{1H} NMR, and HRMS were consistent with the title compound.
Compound 5.
A solution of compound 4 (0.135 g, 0.209 mmol) in dichloromethane (5 mL) was cooled in an ice bath. Trifluoroacetic acid:dichloromethane (1:1 v/v, 5 mL) was added dropwise over 5 min. After 15 min, the ice bath was removed and the reaction warmed to room temperature. After 45 min, the volatiles were removed in vacuo to yield the trifluoroacetate salt of the title compound as a brown/orange solid (quantitative). 1H NMR, 13C{1H} NMR, and HRMS were consistent with the title compound.
Compound 1.
To a solution of 11-mercaptoundecanoic acid (0.045 g, 0.206 mmol) and HATU (0.078 g, 0.206 mmol) in dichloromethane:N,N-dimethylformamide (1:1 v/v, 5 mL) was added compound 5 (0.105 g, 0.159 mmol) and diisopropylethylamine (0.083 mL, 0.477 mmol). The reaction was stirred at room temperature for 2 hours. The reaction mixture was diluted into ethyl acetate (150 mL) and washed with brine (3×50 mL). The organic phase was dried over Na2SO4, filtered, and concentrated to crude residue that was purified by column chromatography (methanol:ethyl acetate:dichloromethane, 0.5:1.5:8) to yield the title compound as a yellow solid (0.035 g, 0.047 mmol, 30%). 1H NMR, 13C{1H} NMR, and HRMS were consistent with the title compound.
Electrochemistry.
Cyclic voltammetry was carried out with a CHI model 660A electrochemical analyzer (CHI Instruments Inc.) in THF with 0.15 M n-Bu4NClO4 supporting electrolyte (0.5 mL) using a three electrode system of SAM-modified gold as the working electrode, a Ag/AgCl wire reference electrode, and a platinum wire counter electrode (Bioanalytical Systems). Model compound (green) was prepared by treating compound 4 with hydrogen peroxide. The results are shown in FIG. 3.
Example 2
Measurement of a Quantifiable Electrochemical Signal at Two Unique Potentials, E°1 and E°2, as a Result of Direct Addition of H2O2 
A. Purpose
The goal of this study was to test the effect of 5-minute and 10-minute H2O2 incubation times on a diluted SAM of EAM 1 (PB25—49) washed at pH 10.1 and incubated at pH 8.5. H2O2 would decompose the Ferrocene on the EAM into a new derivative which would show up at a new potential.
B. Materials
















BATCH #/






MATERIALS
Name
MW
Final C
Stock/Solvent
NOTES





















1. EAM for SAM:
PB25_49
MW = 747.57
0.1
mM
0.5 mg/0.5 mL EtOH
Stock: 0.5 mg


2. Diluent solutions for SAM
(C6S)2
MW = 234.47
0.5
mM
—
Stock C = 9.13x (4.56 mM stock)



(HO—C6S)2
MW = 266.47
0.5
mM
—
Stock C = 7.51x (3.75 mM stock)












3. Electrode testing solution:
1M LiClO4
MW = 106.39
1M
10.6 g/1 L H2O
Aqueous solution 1X


4. Hydrogen peroxide
Hydrogen
MW = 34.01
1M
57 μL/943 μL H2O 
Made fresh



peroxide (50.4%)

















5. Buffer
Na2CO3
MW = 105.99
100
mM
0.53 g/50 mL H2O
pH 10.1












6. Washing buffers
EtOH, nanopure
—
—
—
—



water, Na2CO3,







1M LiClO4






7. Electrodes:
Reference
Counter
Working
Wash and
—



electrode
electrode
Electrode
store




Quasi 1
Pt Wire
Au Chip
Rinse before
13 chips



reference

d = 0.25 um
and after each




(1M LiClO4)


use





Note:


All calculations were based on the equation below; Nanopure water was 18 megaohm water from a Millipore purification system.


with Molecular Weight (MW or FW) found usually on the product bottles, making sure units are correct.






  
    Concentration
    ⁡
    
      (
      
        M
        :
        
          mol
          L
        
      
      )
    
  
  =
  
    
      Weight
      ⁡
      
        (
        g
        )
      
    
    
      
        Volume
        ⁡
        
          (
          L
          )
        
      
      ×
      
        MolecularWeight
        ⁡
        
          (
          
            g
            mol
          
          )
        
      
    
  



EAM 1 structure:












C. Procedure

Day 1:
Wash and Assemble Chips
13 (12 for assay+1 for internal reference testing) chips were washed as follows: the chips were placed in glass jar with inserts, sonicated in 0.2% TWEEN 20 solution for 5 minutes, rinsed with nanopure water and ethanol, and then dried with Argon. The chips were then cleaned in a Plasma Cleaner for 10 minutes, and rinsed with ethanol and dried with Argon. Metal bases, gaskets, and PDMS stamps were hand washed with hand soap, rinsed with ethanol and air dried. Chips were assembled by placing the chip on the double sided tape on center of the metal base, PDMS stamp on the chip, gasket on the PDMS stamp, all clamped together with binder clips.
Prepare Experimental Stocks
EAM stock was prepared by combining the following into the EAM aliquot:

















Stocks
EAM
# Aliquots
Amount (mg ea)
MW
EtOH
THF
Final Conc.







A
PB25_49
1
0.5
747.57
500 μL
none
1.34 mM









Prepare SAM Solutions
SAM Solution was prepared by combining the following into separate glass vials:



















[EAM]
AMT

[D1]


[D2]
AMT
EtOH
Tot Vol.


mM
μL
D1
mM
AMT μL
D2
mM
μL
μL
μL







1.34
493
(C6S)2
4.56
723
(HOC6S)2
3.75
879
4505
6600









SAM Incubation
To chips 1-12, 500 μL of above prepared SAM solution was added, followed by overnight incubation. All chips were placed in plastic containers containing ethanol, sealed with parafilm (to avoid ethanol evaporation and drying of chips). The setup was covered with Aluminum foil.
Day 2:
Internal Reference Measurements:
A 1 mM solution of 1 1′ Ferrocene dimethanol was prepared in 1M LiClO4 solution. 1.3 mg of 1 1′ Ferrocene dimethanol were combined with 5 mL 1M LiClO4. MW 1 1′ Ferrocene dimethanol=246.09. 500 μL of 1 mM 1 1′ Ferrocene dimethanol solution was added to a clean chip. Quasi 1 reference and platinum counter electrodes were added to the system and CVs were recorded.
Initial Testing to Check for Proper SAM Formation on Chips:
After overnight incubation, the chips were removed from the incubation container. The SAM deposition solution was collected in a vial and dried to obtain recycled EAM for future use. After overnight incubation, chips 1 through 12 were washed by following the steps shown below:















Ethanol
8 times



Nanopure water
4 times



Testing buffer, 1M LiClO4
2 times









500 μL of 1M LiClO4 was added to chips 1, 3, 5, 6, 7, 9, 11, and 12, and then chip was plugged in the switchbox. Reference and counter electrodes were added to the EC system. The white alligator clip from the CHI 650C was connected to the reference electrode (Quasi 1), green clip to the working electrode and the red clip to the counter electrode (Platinum wire, flamed in advance, rinsed with EtOH and water).
The CHI 650C system was used to test all chips. For each test, six files were used: 10000 mV/s, 100 mV/s, 10000 mV/s long, multi CV (20 cycles) and ACV (forward and backward).
The multiplexer was used for testing all chips in this experiment.
After initial testing, chips 1 through 5 and 7 through 11 were washed as follows:















Nanopure water
8 times



100 mM Na2CO3 (pH 10.1)
2 times









Chips 6 and 12 were washed as follows:
















Nanopure water
8 times



100 mM NaHCO3 (pH 8.5)
2 times









Preparation of Different Concentrations of Hydrogen Peroxide:
Different concentrations of H2O2 solution were made in 100 mM Na2CO3 buffer (pH 10.1) immediately before use. Original stock of H2O2 was at 1M which was made by combining 57 μL of 50% H2O2 with 943 μL of nanopure water. This stock was left in the 4° C. fridge overnight to allow for muta-rotation. From there on the dilutions were made as shown below:














Final

Amount of




concentration
Ratio (previous
previous
Amount
Total


of
to final
concentration of
of buffer
volume


H2O2 (mM)
concentration)
H2O2 (μL)
(μL)
(μL)



















1
1:1000
2
1998
2000


0.1
1:10
200
1800
2000


0.01
1:10
200
1800
2000


0.001
1:10
200
1800
2000


0
—
0
2000
2000









Addition of Different Concentrations of H2O2 to the Chips and Testing:
The hydrogen peroxide solutions made were vortexed well. 500 μL of the respective hydrogen peroxide solutions was added to each chip (1-12) and the solution was mixed thoroughly. The incubation was carried out at room temperature for 5 minutes, while mixing the solution in between with pipette tips at 4:30, 2:30, and 0:30 times, and for 10 minutes, while mixing the solution in between with pipette tips at 7:30, 5:00, and 2:30 times. After the respective H2O, incubations, the chips were washed as follows:













Nanopure water
8 times


100 mM Na2CO3 (pH 10.1) or 100 mM NaHCO3 (pH 8.5)
2 times









Each well was incubated with 500 μL of their respective buffers for 5 minutes. After the chips were incubated with buffer, the chips were washed as follows:















Nanopure water
8 times



1M LiClO4
2 times









The switchbox was used for testing all chips as shown in steps VI d, e and f. After testing, the chips were washed, cleaned with ethanol and water and then disassembled.
Experiment Outline











Chip
Chip Name
















1
#1_2_H2O2_0uM_5min_pH10pt1


2
#2_2_H2O2_1uM_5min_pH10pt1


3
#3_2_H2O2_10uM_5min_pH10pt1


4
#4_2_H2O2_100uM_5min_pH10pt1


5
#5_2_H2O2_1mM_5min_pH10pt1


6
#6_2_H2O2_0uM_5min_pH8pt5


7
#7_2_H2O2_0uM_10min_pH10pt1


8
#8_2_H2O2_1uM_10min_pH10pt1


9
#9_2_H2O2_10uM_10min_pH10pt1


10
#10_2_H2O2_100uM_10min_pH10pt1


11
#11_2_H2O2_1mM_10min_pH10pt1


12
#11_2_H2O2_0uM_10min_pH8pt5


13
#11_3_post-H2O2_FcMe2









Example 3
ATP Amplification Protocol
ATP Full Dose Response Curve in Complete Lysis Buffer (0.5×HEPES)
Glycerol (2 mM), Glycerol kinase (GK, 1.33 U/mL), Glycerol 3-phosphate oxidase (G3PO-1.33 U/mL), Creatine kinase 18× (18 U/mL), Phosphocreatine (PC, 30 mM), ATP 0 nM-10 μM were used.
The following buffers were used: 0.5×HEPES (pH 7.4, 29 mM Maltoside), 1:200 benzonase, 1:2000 protease inhibitor, and 1:100 phosphatase inhibitor cocktail (0.5×), which was modified as follows: 2.5 mM NaF, 3 μM sodium orthovanadate, 500 μM sodium pyrophosphate decahydrate, 500 μM beta-Glycerolphosphate, and 2.5 mM NaN3 (added to the phosphatase inhibitor cocktail as a catalase inhibitor for H2O2).
ATP 0 nM-10 μM was prepared as follows: ATP serial dilutions were made 10-fold higher in nanopure water containing 10 mM MgCl2, such that the [MgCl2] in the final assay is 1 mM. Nanopure water containing 10 mM MgCl2 was used to reconstitute enzymes such as GK and G3PO. The following were the desired final assay concentration of each component:
GK 10 U/aliquot was prepared as follows: reconstituted in 250 μL of water containing 10 mM MgCl2—0.04 U/μL. 5 μL of 0.04 U/μL stock was taken and added to each well to a final assay concentration of 1.33 U/mL. (For 140 μL assay volume, 5 μL of GK was added for each data point)
G3PO 5 U/aliquot was prepared as follows: reconstituted in 125 μL buffer to 0.04 U/uL. 5 μL of 0.04 U/uL stock was taken and added to each well to a final assay concentration of 1.33 U/mL. 5 μL of G3PO was taken for total of 140 μL assay volume.
Creatine kinase at 350 U/mg was prepared as follows: 0.5 mg of CK was dissolved in 300 μL of 20% glycerol in water to give 0.58 U/μL. Then 5 μL of 0.58 U/μL stock was added to data point for 140 μL total assay volume.
Phosphocreatine (30 mM) was obtained by dissolving 574 mg of solid in 5 mL water, and taking 5 μL of that stock to each tube to make 140 μL total assay volume.
Glycerol (2 mM) was prepared by taking 22 μL of Glycerol stock and adding it to 4978 μL buffer to make a 5 mL total stock, and 5 μL of this 5 mL stock was added to each well to make 14 μL total volume.
5 μL of Benzonase stock was added to 1 mL of 0.5×HEPES, pH 7.4 buffer to give Benzonase: 1:200 in 0.5×HEPES buffer, pH 7.4.
Phosphatase inhibitor cocktail (modified, 1:100) was prepared as follows. 250 mM NaN3 was added to 5 mL (50×) phosphatase inhibitor cocktail solution such as that final concentration in 0.5× buffer was 2.5 mM NaN3. 1 μM of 1 M stock of Zn acetate was added to 100 μL of 50× Phosphatase inhibitor cocktail aliquot such as that the final concentration of Zn acetate in 0.5× lysis buffer is 100 μM. 10 μL of phosphatase inhibitor cocktail added to 0.5×HEPES, lysis buffer.
0.5 μL Protease inhibitor was added to 1 mL 0.5×HEPES, lysis buffer to give Protease inhibitor (1:2000 dilution) in 0.5×HEPES, pH 7.4.
Assay conditions constituted of 140 μL of each sample incubated for 2.5 hrs to be run in triplicates. The following components were added to the tube for 2.5 hrs incubation before putting them on chips for target testing:

    
    
        Upon incubation in 0.5×HEPES, pH 7.4 for 2.5 hrs, pH was adjusted to 10 by adding 46.7 μL Na2CO3 (100 mM);
        Total of 186.7 μL sample (per concentration) and 25% sample dilution occurred in the process of adjusting to pH 10
        30 μL sample was added to each chip in triplicates all at once and incubate (for 10 mins) and washed at two different washing stations simultaneously.
    
    


The following volumes of each component were added: buffer 100 μL; GK 5 μL; G3PO 5 μL; CK 5 μL; phosphocreatine (30 mM) 5 μL; glycerol (2 mM) 5 μL; ATP 15 μL; ADHP 5 μL; and HRP 5 μL
E-Chip Experiment
Average Peak current ratio and Area ratio were analyzed for all ten concentrations to obtain standard error on the full dose response curve. No initial testing was done and the chips were washed eight times with Ethanol, four times with water and incubated with target solution of 10 mins right away. Upon 10 min of incubation, chips were washed four times with water and two times with LiClO4 and tested with 1M LiClO4 testing solution.
Example 4
NADH Amplification Protocol
The following buffers were used: 0.5×HEPES, pH 7.4 (29 mM Maltoside), 1:200 benzonase, 1:2000 phosphatase inhibitor cocktail (0.5×), which was modified as follows: 2.5 mM NaF, 3 μM sodium orthovanadate, 500 μM sodium pyrophosphate decahydrate, 500 μM beta-Glycerolphosphate, 2.5 mM NaN3, and 100 μM zinc acetate.
Desired concentrations in well/tube were as follows:













Solution
Concentration








NADH oxidase
5 ng/μL



Ethanol
4%



ADH
80 ng/μL



FAD
10 μM



NADH
3 μM, 1 μM, 300 nM, 100 nM,




30 nM, 10 nM, 3 nM, 1 nM, 0.3 nM









NADH oxidase was prepared by adding 1.45 μL of stock per 100 μL of total NADH reaction solution. Ethanol was prepared by adding 4 μl 100% ethanol per 100 μL NADH reaction solution. ADH (4 μg/μL) was prepared by adding 2.4 mg/600 μL in water and 20% glycerol, and 2 μL of this solution was added per 100 μL of reaction sample.
FAD was prepared by dissolving 5.8 mg in 1000 μL nanopure water to give 7.5 mM stock. 7.5 mM stock was used to make 1 mM stock by adding 13.3 μL of 7.5 mM stock and diluting up to 100 μL. Finally, 1 μL of 1 mM stock was added per 100 μL reaction.
NADH was prepared to a final concentration of 1 μM, 300 nM, 100 nM, 30 nM, 10 nM, 3 nM, 1 nM, 0.3 nM, 0.1 nM, and 0.03 nM.
Each reaction had the following concentration per well:


















buffer with

NADH



NADH



inhibitor

sample
Alcohol
FAD
ADH
oxidase



cocktail and
Buffer
(3 μM-0.03 nM)
100%
1 mM
4 μg/μL
0.344 μg/μL


sample
benzonase
(μL)
(μL)
(μL)
(μL)
(μL)
(μL)






















1
HEPES
100
1
4
1
2
1.45


2
HEPES
100
1
4
1
2
1.45


3
HEPES
100
1
4
1
2
1.45


4
HEPES
100
1
4
1
2
1.45


5
HEPES
100
1
4
1
2
1.45


6
HEPES
100
1
4
1
2
1.45


7
HEPES
100
1
4
1
2
1.45


8
HEPES
100
1
4
1
2
1.45


9
HEPES
100
1
4
1
2
1.45


10
HEPES
100
1
4
1
2
1.45


11
HEPES
100
0
4
1
2
1.45









Each component was added to a 96 well plate and incubated for 2 hours. After 2 hrs 90 μL from each reaction sample was taken and pH adjusted to pH 10 by adding 30 μL 400 mM carbonate solution. 30 μL was then incubated on e-chips in triplicates.
E-chip materials consist of













EAM 2 (1 mg/1 mL EtOH):






 


Target Incubation
1x PBS, 100 mM NaHCO3 pH 10


Buffer:



Testing Buffer:
1M LiClO4•3H2O


Washing Buffer:
Nanopure water


Electrodes:
External Quasi and platinum wire





EAM 2 (PB65_33)



















To a 0° C. solution of compound 6 (0.215 g, 0.75 mmol) in DCM (10 mL) was added sodium borohydride (0.114 g, 3.00 mmol). MeOH (6 mL) was added slowly over 15 min. The reaction was stirred and warmed to room temperature for 1 h. The reaction was concentrated under reduced pressure and the crude residue was dissolved in EtOAc (100 mL), washed with brine (3×100 mL), dried over Na2SO4, filtered, and concentrated under reduced pressure to a crude solid. Purification by column chromatography yielded 7 as an orange solid (197 mg, 0.68 mmol, 91%).
A solution of compound 7 (0.535 g, 1.86 mmol) and sodium azide (0.726 g, 11.2 mmol) in AcOH (35 mL) was stirred at 60° C. for 20 h. The reaction was diluted with EtOAc (200 mL), washed with NaHCO3 (aq) (3×100 mL), dried over Na2SO4, filtered, and concentrated under reduced pressure to a crude brown oil. Purification by column chromatography yielded 8 as an orange oil (0.441 g, 1.41 mmol, 76%).
A solution of compound 8 (0.430 g, 1.37 mmol) and triphenylphosphine (0.431 g, 1.64 mmol) in THF (25 mL) was stirred at 60° C. for 20 h. The reaction was concentrated under reduce pressure to a crude oil which was purified by column chromatography to yield 9 as a dark orange oil (0.371 g, 1.29 mmol, 94%).
A solution of 11-mercaptoundecanoic acid (2.70 g, 12.4 mmol), trityl chloride (4.14 g, 14.8 mmol), and DIPEA (5.17 mmol, 28.7 mmol) in toluene (40 mL) was stirred at room temperature for 20 h. The reaction was concentrated under reduced pressure and the crude residue was dissolved in DCM (100 mL), washed with H2O (3×100 mL), dried over Na2SO4, filtered, and concentrated under reduced pressure to a crude yellow oil. Purification by column chromatography yielded 10 as a white solid (4.14 g, 73%).
To a 0° C. solution of compound 9 (0.355 g, 1.24 mmol) and 10 (0.571 g, 1.24 mmol) in DCM (30 mL) was added 1-[3-(dimethylamino)propyl]-3-ethylcarbodiimide HCl (0.249 g, 1.30 mmol). After stirring for 5 h the reaction was concentrated under reduced pressure to a crude brown oil. Purification by column chromatography yielded 11 as a viscous orange oil (0.724 g, 0.99 mmol, 80%).
To a solution of compound 11 (0.720 g, 0.99 mmol) in EtOH (30 mL) was added a solution of potassium hydroxide (0.333 g, 5.93 mmol) in H2O (3 mL). The reaction was heated to 70° C. After stirring for 24 h, the reaction was concentrated under reduced pressure to crude residue. The crude residue was dissolved in H2O (100 mL), acidified to pH=4.0, extracted with DCM (4×100 mL), dried over Na2SO4, filtered, and concentrated under reduced pressure to an orange oil. The orange oil was purified by column chromatography to yield 12 as a golden yellow solid (0.589 g, 0.84 mmol, 85%).
To a solution of compound 12 (0.456 g, 0.65 mmol) in THF (30 mL) was added diphenylphosphoryl azide (168 μL, 0.78 mmol) followed by triethylamine (136 μL, 0.98 mmol). The reaction was stirred for 20 h and concentrated under reduced pressure to a crude red oil. Purification by column chromatography yielded 13 as a red/orange solid (0.400 g, 0.55 mmol, 85%).
To a solution of compound 13 (0.298 g, 0.41 mmol) and 14 (0.106 g, 0.45 mmol) in toluene (30 mL) was added di-n-butyltin dilaurate (12 μL, 0.002 mmol). The reaction was stirred at 100° C. for 4 h and concentrated under reduced pressure to a crude brown oil. Purification by column chromatography yielded 15 as a golden yellow oil (0.305 g, 0.33 mmol, 80%).




To a solution of compound 15 (0.134 g, 0.14 mmol) in DCM (2 mL) was added a solution of trifluoroacetic acid (200 μL), triethylsilane (115 μL, 0.72 mmol) in DCM (2 mL). The reaction was stirred at room temperature for 3 h and concentrated under reduced pressure to a crude brown oil. Purification by column chromatography yielded 2 as a yellow solid (0.072 g, 0.10 mmol, 72%).
For all chips, the following procedure was performed to deposit the SAM. Chips were rinsed again with EtOH and dried with argon. Accessory parts (gasket, tubs) were cleaned by washing machine, rinsed with EtOH and air-dried. Bases were cleaned by hand. 200 μL of the deposition solution prepared above was added to each chip, and chips were incubated overnight in EtOH incubation chamber. Following overnight incubation, chips removed from containers. The chips were then washed as follows: 8×EtOH, 4× nanopure water.
Each chip was incubated as designated in table below. Buffer used for the samples was complete lysis buffer with modified Phosphatase inhibitor with zinc acetate and sodium azide. The samples were pH adjusted to pH 10 with 400 mM of carbonate in 1:4 ratio. Each concentration was run in triplicates on chips. After target incubation of 10 mins the chips were washed 4× water, 2×LiClO4, and tested.














Solution



Macro Chip No.
NADH



















1
1
μM



2
300
nM



3
100
nM



4
30
nM



5
10
nM



6
3
nM



7
1
nM



8
0.3
nM



9
0.1
nM



10
0.03
nM



11
0
nM









Example 5
TSH Protein Measurement
The reagents used were as follows: anti-TSH loaded magnetic beads (capture, MP), 10 μg/μL MP; TSH antigen, 1 mU/mL; biotin-anti-TSH conjugate (Secondary), 0.85 mg/mL; Alkaline Phosphatase-Streptavidin conjugate (SA-AP), 1.5 mg/mL; FADP, 10 mM; Apo-DAAO enzyme (DAAO), 3.9 mg/mL-100 μM; D-Proline, 1 M; TBS, 20× (1 M Tris); PBS, 20× (1 M PO4); BSA, 10% filtered solution; Tween20, 10% filtered solution; and Sodium Carbonate, 400 mM.
E-chip materials consist of













EAM (1 mg/1 mL EtOH):






 


Target Incubation
1x PBS, 100 mM NaHCO3 pH 10


Buffer:



Testing Buffer:
1M LiClO4•3H2O


Washing Buffer:
Nanopure water


Electrodes:
External Quasi and platinum wire









Clinical serum samples with known TSH content were obtained from the NorthShore core facility and diluted as shown below:














TSH (μIU/mL)


Sample ID
Dilution (%)
after dilution

















142
1.25
0.13473


144
1.25
0.47359


145
12.50
0.74813


146
1.25
0.05525


147
12.50
0.54663









Magnetic bead binding assay similar in structure to previous magnetic bead assays. Targets consisted of serial dilution of recombinant TSH antigen, and serial dilution concentrations were: 30, 3, 0.3, 0.03, and 0 μIU/mL, in binding buffer (1×PBS, 1% BSA, 0.3% tween). Magnetic bead stocks with capture antibody were pre-washed and pre-blocked at 10 μg/μL. Stock in PBS was diluted 50-fold; and added 100 μL to each tube (20 μg/tube). Pellet beads and remove buffer before adding target. TSH antigen was serial diluted to 30, 3, 0.3, 0.03, and 0 by making 3.16-fold serial dilutions. After removing buffer from beads, 100 μL of each target dilution was added to individual tubes, vortexed quickly to mix after each target dilution is added, and incubated for 30 minutes on shaker (200-300 rpm).
Antibody solution (4 ng/μL) was prepared in binding buffer with enough for 100 μL per tube. Beads were washed by pelleting against magnetic bar, removing supernatant and adding 500 μL of wash buffer, then vortexed briefly and spined down to avoid droplet formation on the walls of the tube. Beads were pelleted against magnetic bar and remove wash buffer, and 100 μL of antibody solution was added to each tube. The solution was vortexed quickly to mix and incubated for 15 minutes at room temperature on shaker (200-300 rpm).
SA-AP solution of 1 mL at 22.5 ng/μL was prepared in binding buffer (BB). Beads were washed by pelleting against magnet, and wash buffer was removed. The solution was briefly vortexed to mix, then it was spun down. Beads were pelleted against the bar magnet and wash buffer was removed. 100 μL of SA-AP solution was added to each tube, and vortexed quickly to mix and incubated for 10 minutes at room temperature on shaker (200-300 rpm).
Beads were washed 4 times as described above. Following washes in wash buffer, 100 μL TBS pH 8.5 was added, and the beads in the buffer were carefully transferred to clean tubes. FADP solution of 20 μM was prepared by adding 2 μL of 10 mM FADP stock to 1 mL of TBS pH 8.5. Beads were pelleted against bar magnet and removed for final incubation. 95 μL of substrate solution was added to each tube, and vortexed quickly to mix and incubated for 30 minutes on shaker (200-300 rpm). During the incubation, E-chips were prepared by washing 8× with ethanol and 4× with nanopure water.
After incubation is complete, beads were pelleted on magnet and 90 μL of substrate solution was moved to a new tube to stop FADP conversion. 10×DAAO solution was prepared by making 2 μM DAAO enzyme and 350 mM D-proline in TBS pH 8.5 buffer. 10×DAAO solution was added to each tube to start reaction, and start of each reaction was staggered by 15 seconds, vortexed briefly each addition and incubated 5 minutes in the tubes. pH was adjusted to 10. 14.28 μL of 400 μM sodium carbonate was added to 100 μL, and added in the same order as the DAAO and again waited 15 seconds between tubes to maintain constant incubation time across tubes; and vortexed briefly after each addition.
The water was aspirated from E-chips. 36 μL of pH adjusted solution was added to each of three replicate chips. Volume was added quickly to replicates and each target dilution was stagger to maintain constant E-Chip incubation time across samples. Samples were incubated for 10 minutes. After incubation, solution from E-Chips was aspirated and washed 4× with water and 2× with 1 M LiClO4. The chips were tested on CHI multiplexer with a 0.5 V/s scan rate.
Data Analysis
Data Analysis was performed in Matlab using the EDAS executable version. The peak current ratio (i2/i1-2) was determined from the bottom curve of each voltammogram.
Results
The standard curved generated in this experiment had a higher signal than in previous experiments, where a shortened protocol with reduced incubation times was used to check consistency in signal between the old and new bead lots. The standard curve had a small error at each TSH dose that increased slightly at higher doses of TSH. The signals from the clinical samples (142, 144, 145, 147, 146) all fell within the range of the standard curve and are shown in FIG. 23. The signal increases with increasing TSH value as determined by Northshore.
It is to be understood that the examples and embodiments described herein are for illustrative purposes only. Unless clearly excluded by the context, all embodiments disclosed for one aspect of the invention can be combined with embodiments disclosed for other aspects of the invention, in any suitable combination. It will be apparent to those skilled in the art that various modifications and variations can be made to the present invention without departing from the scope of the invention. Thus, it is intended that the present invention cover the modifications and variations of this invention provided they come within the scope of the appended claims and their equivalents.

## Claims

1. A method for detecting a target analyte in a test sample, said method comprising:
(a) contacting a target specific enzyme, a recycling enzyme and a peroxide-generating enzyme with said target sample under conditions wherein a peroxide is generated in the presence of said target analyte to form an assay mixture;
(b) contacting the assay mixture with a first solid support comprising an electrode comprising a covalently attached electroactive moiety (EAM) having a first E0, said EAM comprising a transition metal complex comprising a self-immolative moiety (SIM) and a peroxide sensitive moiety (PSM), wherein said peroxide reacts with said PSM to release said SIM from said EAM and result in said EAM having a second E0;
(c) measuring the electrochemical properties of said EAM at the first E0 and at the second E0; and
(d) detecting for the presence or concentration of said target analyte from said electrochemical properties.

2. A method for detecting a target analyte in a test sample, said method comprising:
(a) contacting said test sample with a first complex comprising a labeled target analyte pre-bound to a binding ligand, with said test sample under conditions wherein said target analyte from said test sample, if present, displaces said labeled target from said first complex forming a second complex, wherein said labeled target analyte is labeled with a first member of a specific binding pair;
(b) contacting said second complex with an intermediary enzyme of a peroxide generating system comprising a labeled linker forming a third complex, wherein said labeled linker is labeled with a second member of said specific binding pair;
(c) isolating said third complex;
(d) contacting said third complex with a substrate for said intermediary enzyme of peroxide-generating system under conditions such that product(s) are generated to form a first assay mixture;
(e) contacting a peroxide-generating enzyme and optionally a recycling enzyme with first assay mixture under conditions wherein peroxide is generated to form a second assay mixture;
(f) contacting the second, assay mixture with a first solid support comprising an electrode comprising a covalently attached electroactive moiety (EAM) having a first E0, said EAM comprising a transition metal complex comprising a self-immolative moiety (SIM) and a peroxide sensitive moiety (PSM), wherein said peroxide reacts with said PSM to release said SIM from said EAM and result in said EAM having a second E0;
(g) measuring the electrochemical properties of said EAM at the first E0 and at the second E0; and
(h) detecting for the presence or the concentration of said target analyte from said electrochemical properties.

3. The method according to claim 2, wherein said specific binding pair is biotin/streptavidin.

4. A method for detecting a target analyte in a test sample, said method comprising:
(a) contacting a first binding ligand with said test sample under conditions wherein said first binding ligand binds said target analyte, if present, in said test sample to form a first complex;
(b) contacting said first complex with a second binding ligand under conditions wherein said first complex and said second binding ligand bind to form a second complex, wherein said second binding ligand comprises an intermediary enzyme of a peroxide-generating system;
(c) isolating said second complex;
(d) contacting said second complex with a substrate for said intermediary enzyme of peroxide-generating system under conditions such that products are generated to form a first assay mixture;
(e) contacting a peroxide-generating enzyme and optionally a recycling enzyme with a first assay mixture under conditions wherein peroxide is generated to form a second assay mixture;
(f) contacting the second assay mixture with a first solid support comprising an electrode comprising a covalently attached electroactive moiety (EAM) having a first E0, said EAM comprising a transition metal complex comprising a self-immolative moiety (SIM) and a peroxide sensitive moiety (PSM), wherein said peroxide reacts with said PSM to release said SIM from said EAM and result in said EAM having a second E0;
(g) measuring the electrochemical properties of said EAM at the first E0 and at the second E0; and
(h) detecting for the presence or the concentration of said target analyte from said electrochemical properties.

5. The method according to claim 4, wherein the target analyte is a protein.

6. The method according to any of claim 2 or 4, wherein said binding ligand is attached to a second solid support.

7. A method according to claim 6, wherein said second solid support is chosen from the group consisting of microparticles, magnetic microparticles, beads, and microchannels.

8. A method according to any of claim 2 or 4, wherein said electrode further comprises a self-assembled monolayer (SAM).

9. The method according to any of claim 2 or 4, wherein the target analyte is a small molecule.

10. The method according to any of claim 2 or 4, wherein said product(s) is a substrate for said peroxide generating enzyme.

11. The method according to any of claim 2 or 4, further comprising the presence of a substrate for said peroxide generating enzyme and wherein said product(s) is a cofactor for said peroxide-generating enzyme.

12. The method according to claim 11, wherein said recycling enzyme is included to recycle said cofactor.

13. A method according to claim 1, wherein said target analyte is reduced Nicotinamide Adenine Dinucleotide (NADH).

14. A method according to claim 13, wherein said recycling enzyme is Alcohol Dehydrogenase (ADH), said target specific enzyme is NADH Oxidase, and said peroxide generating enzyme is NADH oxidase.

15. A method according to claim 1, wherein said target analyte is Adenosine Triphosphate (ATP).

16. A method according to claim 15, wherein said target specific enzyme is Glycerol Kinase (GK), said recycling enzyme is Creatine Kinase (CK) or Glycerol 3-Phosphate Dehydrogenase (GPDH), and said peroxide generating enzyme is Glycerol-3-Phosphate Oxidase (G3PO).

17. The method according to any of claim 2 or 4, wherein said intermediary enzyme of a peroxide generating system is alkaline phosphatase (AP) or any other dephosphorylating enzyme.

18. The method according to any of claim 2 or 4, wherein said peroxide-generating enzyme is selected from the group consisting of D-amino acid oxidase (DAAO), or any flavin dependent oxidoreductase enzyme.

19. The method according to any of claim 2 or 4, wherein said peroxide-generating enzyme is NADH Oxidase and said optional recycling enzyme is Alcohol Dehydrogenase (ADH).

20. A method according to any of claim 2 or 4, where the target analyte is testosterone.

21. A method according to any of claims 2 or 4, wherein said first binding ligand and said second binding ligand are independently chosen from the group consisting of monoclonal antibodies, fragments of monoclonal antibodies, polyclonal antibodies, fragments of polyclonal antibodies, proteins, and peptides.

22. A method according to any of claim 2 or 4, wherein said EAM comprises a transition metal.

23. A method according to claim 22, wherein said transition metal is chosen from the group consisting of iron, ruthenium and osmium.

24. A method according to any of claim 2 or 4, wherein said EAM is chosen from the group consisting of ferrocene and substituted ferrocene.

25. A method according to claim 2, wherein the target analyte is a nucleic acid.

26. A method according to claim 4, wherein the target analyte is a nucleic acid.

27. A method according to claim 25, wherein the binding ligand is a nucleic acid.

28. A method according to claim 26, wherein the first binding ligand is a nucleic acid.

29. The method according to claim 1, wherein the target analyte is a small molecule.