Classifications

• • G—PHYSICS
  • G01—MEASURING; TESTING
  • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
  • G01N33/00—Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
  • G01N33/48—Biological material, e.g. blood, urine; Haemocytometers
  • G01N33/50—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
  • G01N33/53—Immunoassay; Biospecific binding assay; Materials therefor
  • G01N33/543—Immunoassay; Biospecific binding assay; Materials therefor with an insoluble carrier for immobilising immunochemicals
  • G01N33/54366—Apparatus specially adapted for solid-phase testing
  • G01N33/54373—Apparatus specially adapted for solid-phase testing involving physiochemical end-point determination, e.g. wave-guides, FETS, gratings
• • C—CHEMISTRY; METALLURGY
  • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
  • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
  • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
  • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
  • C12Q1/6876—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
  • C12Q1/6883—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material
• • G—PHYSICS
  • G01—MEASURING; TESTING
  • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
  • G01N27/00—Investigating or analysing materials by the use of electric, electrochemical, or magnetic means
  • G01N27/02—Investigating or analysing materials by the use of electric, electrochemical, or magnetic means by investigating impedance
  • G01N27/026—Dielectric impedance spectroscopy
• • G—PHYSICS
  • G01—MEASURING; TESTING
  • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
  • G01N27/00—Investigating or analysing materials by the use of electric, electrochemical, or magnetic means
  • G01N27/26—Investigating or analysing materials by the use of electric, electrochemical, or magnetic means by investigating electrochemical variables; by using electrolysis or electrophoresis
  • G01N27/28—Electrolytic cell components
  • G01N27/30—Electrodes, e.g. test electrodes; Half-cells
  • G01N27/327—Biochemical electrodes, e.g. electrical or mechanical details for in vitro measurements
  • G01N27/3275—Sensing specific biomolecules, e.g. nucleic acid strands, based on an electrode surface reaction
  • G01N27/3277—Sensing specific biomolecules, e.g. nucleic acid strands, based on an electrode surface reaction being a redox reaction, e.g. detection by cyclic voltammetry
• • G—PHYSICS
  • G01—MEASURING; TESTING
  • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
  • G01N33/00—Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
  • G01N33/48—Biological material, e.g. blood, urine; Haemocytometers
  • G01N33/50—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
  • G01N33/58—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing involving labelled substances
  • G01N33/582—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing involving labelled substances with fluorescent label
• • G—PHYSICS
  • G01—MEASURING; TESTING
  • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
  • G01N33/00—Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
  • G01N33/48—Biological material, e.g. blood, urine; Haemocytometers
  • G01N33/50—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
  • G01N33/58—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing involving labelled substances
  • G01N33/585—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing involving labelled substances with a particulate label, e.g. coloured latex
• • C—CHEMISTRY; METALLURGY
  • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
  • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
  • C12Q2600/00—Oligonucleotides characterized by their use
  • C12Q2600/118—Prognosis of disease development

Definitions

• the present invention relates to methods for detecting an analyte using enhanced electrochemical impedance spectroscopy (EIS) techniques to obtain data on the analyte.
• EIS electrochemical impedance spectroscopy
• the method is advantageous since it may result in enhanced speed over known EIS assay methods, and therefore may improve time to result (TTR) and facilitate development of such assays in the near patient environment.
• analyte is labelled, usually with a fluorescent label, which can be detected, for example by fluorescence detection, in order to identify the analyte.
• nanoparticles have been used as the labels. These labels will potentially work for any system that permits labelling and involves binding, thus may be useful in a live cell system, as well as proteins and nucleic acids.
• the nanoparticles have been found to overcome a number of limitations of more traditional fluorescent labels including cost, ease of use, sensitivity and selectivity (Fritzsche W, Taton T A, Nanotechnology 14 (2003) R63-R73 "Metal nanoparticles as labels for heterogeneous, chip-based DNA detection”).
• Nanoparticles have been used in a number of different DNA detection methods including optical detection, electrical detection, electrochemical detection and gravimetric detection (Fritzsche W, Taton T A, Nanotechnology 14 (2003) R63-R73 "Metal nanoparticles as labels for heterogeneous, chip-based DNA detection”).
• the use of gold nanoparticles in the detection of DNA hybridization based on electrochemical stripping detection of the colloidal gold tag has been successful (Wang J, Xu D, Kawde A, Poslky R, Analytical Chemistry (2001), 73, 5576-5581 "Metal Nanoparticle-Based Electrochemical Stripping Potentiometric Detection of DNA hybridization”).
• nanoparticle labelling has been combined with electrophoresis in detecting DNA (see WO 2009/112537).
• the electrophoresis is employed to speed up binding of the DNA to complementary probes on an electrode surface.
• the method is advantageous since it may result in enhanced speed and sensitivity over known assay methods.
• EIS electrochemical impedance spectroscopy
• AC impedance measurements also often called electrochemical impedance spectroscopy, or EIS
• EIS electrochemical impedance spectroscopy
• Changes in such impedance spectra have been shown to provide a method for sensitive label-free measurement of probe-target binding in specific surface films on electrodes, particularly when using interdigitated electrodes (IDE) such as interdigitated microelectrodes (IME) or interdigitated nanoelectrodes (INE).
• IDE interdigitated electrodes
• IME interdigitated microelectrodes
• INE interdigitated nanoelectrodes
• the impedance response of IDEs has been considered theoretically and analysis is typically carried out using appropriate electrical equivalent circuits, fitting to the response over a wide frequency range to give parameters for equivalent electrical circuit elements (resistors, capacitors, Warburg elements, etc.) from which characteristic physical parameters (e.g. diffusion coefficients, concentrations, layer thicknesses) indicative of changes in electrochemical response can be extracted. Furthermore, sequential measurement at each frequency is usually employed. Together these factors add to the relatively large time- to-results discussed above, because they contribute to extended analysis and measurement times.
• EIS methods especially label-free methods, are typically slow, and do not provide satisfactory time to result for use in a near patient environment setting required in the present invention.
• the present invention provides a method for detecting an analyte, which method comprises:
• EIS electrochemical impedance spectrometry
• This first aspect of the invention preferably utilises statistical analysis to determine a set of frequencies to be superposed and applied in step (a).
• Statistical methods for determining frequencies in this manner are well known in the art, and the skilled person may employ any known method to determine the set of frequencies to use in the present methods. Such methods can, for example, be found in "Statistical methods in Experimental physics" (2nd Editition) by World Scientific Publications Co. Pte. Ltd. Singapore. Ed. By F. James (2006) ISBN 981-256795.
• Other methods of determining the set of frequencies may be employed if desired. For example, for a particular system (e.g. specific electro de/solution/analyte combination) an empirical method may be employed in advance to find a set of frequencies that will suffice as a standard for that particular system. The standard may then be employed in that system without calculating the required frequencies on every occasion the method is performed. Any other method may also be employed, either in real time or in advance, provided that it produces a viable set of frequencies to employ and does not adversely affect T
• the set should include at least the minimum number of frequencies required to be sufficient to distinguish the presence of the analyte using EIS. Additional frequencies to the minimum may of course be employed, if desired.
• the method may in some embodiments, either in addition to the set of frequencies or in place of the set of frequencies, involve determination of other parameter(s) that in themselves will define a set of frequencies, and thus aid in achieving detection of the presence and/or quantity of the analyte.
• the frequencies and/or parameters are selected with a view to providing the fastest time to result through data analysis.
• the set of frequencies and/or parameters is sufficient to distinguish the presence or absence of the analyte.
• the specification of the set of frequencies is not particularly limited, and they may be defined as a set of specific individual frequencies, a set of frequencies within a range, and/or a single frequency with spacings from it, which define further frequencies in the set.
• the analysis of the results of the EIS measurements using the superposed frequencies is preferably statistical and does not need to employ an equivalent circuit method of analysis, which typically enables faster discrimination.
• the equivalent circuit method, and any other method is not precluded provided that TTR is not adversely affected.
• FFT Fast Fourier transform
• Such FFT techniques are well known in the art, and the skilled person may employ any such technique in the present invention, as desired.
• information on the analyte presence or absence may be obtained from the EIS data, and more preferably the quantity of the analyte present may also be determined.
• the invention confirms that EIS biosensing and discrimination can be achieved using a small number of points over a restricted range of frequency (in Example 1 (see below) seven points over one decade of frequency), which enables the simultaneous application of a multiwaveform (in Example 1, a multisine) EIS perturbation containing the necessary frequencies, with fast Fourier transform (FFT) analysis used to extract the necessary information.
• FFT fast Fourier transform
• any analyte may be detected in the present invention, and the method of detection will depend on the type of analyte involved. Some analytes may bind to the electrode directly, whilst others (e.g. DNA) may bind to a probe or complementary molecule on the surface of the electrode.
• the set of frequencies employed in the invention will depend on the type of binding occurring for each particular system under investigation, as well as the physical nature of the system itself (electrode type, electrode composition, electrode dimensions, analyte composition, solvent/liquid medium type, electrolyte etc.). For similar systems, standard frequency sets may be employed, and for new systems or analytes a real-time statistical calculation may be employed, as explained above.
• the present invention further provides a method for detecting an analyte, which method comprises:
• the EIS measurements are measurements of electron transfer resistance, R e t.
• R e t electron transfer resistance
• one parameter particularly sensitive to probe film formation and probe-target hybridisation is the electron transfer resistance, R ⁇ , of a redox couple present in the system (e.g. [Fe(CN) 6 ] 3" 4" ).
• This parameter is well known in the art, and may be calculated from the width of the semicircular feature in a Nyquist plot of the EIS spectra.
• This aspect of the present invention provides an IDE measurement protocol to enable in situ kinetic measurement of the EIS response for analyte binding, either with the electrode surface or via probe-analyte hybridisation. In common with the employment of multiple superposed frequencies, it leads to much shorter EIS measurement time. Also in common with the first aspect, any analyte may be detected, and the specifics of the method of detection will depend on the type of analyte involved. Some analytes may bind to the electrode directly, whilst others may bind to a probe or complementary molecule on the surface of the electrode. The exact nature of the data will depend on the type of binding envisaged for each particular system under investigation.
• both oxidation states of the redox probe e.g. ferricyanade and ferrocyanide
• the redox probe e.g. ferricyanade and ferrocyanide
• the currently known EIS protocol measures the approach to equilibrium of electrode/analyte binding (or analyte/probe binding as in the case where a probe is attached to the electrode). This results in a change (typically increase) in the EIS signal to a constant value, indicative of equilibration.
• the time for equilibration and equilibrium EIS signal are determined in real time, leading to optimum equilibrium measurement.
• the time to result is slow, since complete equilibration is required before a result can be determined, and this is often a lengthy process, controlled by the rates of analyte binding and release.
• the rate of increase of the EIS signal is used and analysed to determine the concentration of analyte in solution; as electrode/analyte binding (or probe/analyte binding) is measured kinetically. This can be achieved with a much more rapid TTR, of minutes or less, and full equilibrium does not need to be reached.
• the EIS data preferably comprises data parameters derived from the complex impedance (x + iy). These parameters are well known to the person skilled in the art and may be selected from one or more of the following:
• the number of superimposed frequencies employed in the invention is not especially limited, provided that they are suitable for analysis using EIS to give the identity and/or quantity of the analyte to the required accuracy.
• the minimum number of superimposed frequencies is from 2-20. More preferably the minimum number of superimposed frequencies is at least 3-10, i.e. at least 3, at least 4, at least 5, at least 6, at least 7, at least 8, at least 9 or at least 10. Most preferably the number of superimposed frequencies is about 7.
• the invention further provides a method for detecting an analyte, which method comprises: a) applying an alternating voltage to the analyte;
• the type of EIS measurements employed are not especially limited. However, preferably the EIS measurements are measurements of electron transfer resistance, Ret. Typically the EIS measurements are measurements calculated from finding the width of the semicircular feature in a Nyquist plot, and in general can be calculated using this approach.
• the present method takes place in a liquid medium.
• the liquid medium is selected so as to aid in the process.
• An acidic medium is preferred, and preferably the liquid medium comprises H 2 S0 4 .
• Figure 1 shows typical Nyquist plots of EIS data from Macro gold (small Z values) and interdigitated micro (IME) electrodes.
• Figure 2 shows plots of real component (x), imaginary component (y), modulus (r), angle ( ⁇ ), Principal component 1 , and Principal component 2 against frequencies for the data for positive controls and immobilised probes for both macro and interdigitated electrodes.
• Figure 3 shows the EIS response of gold protein macroelectrodes (6700 pM antibody) from normal single sine sequential EIS measurement with approximately 23 seconds simultaneous FFT analysis (black - recording time over two minutes; red - 5 multisine EIS measurement over 9 seconds; blue - 15 multisine EIS measurement every 9 seconds).
• Figure 4 shows a comparison of the Nyquist plots of modified gold electrode with 69-mer HCV DNA probe and blocked with 1 mM MCH (diamonds), and hybridization with 1 ⁇ of complementary target (ITI 025) (squares).
• the impedance measurements were carried out in 2xSSC containing 10 mM [Fe(CN) 6 ] 3" and 10 mM [Fe(CN) 6 ] 4" (plus probe or target) at an applied dc potential between the electrodes in the IDE pair of 0 V.
• Figure 5 shows a comparison of the Nyquist plots of modified gold electrode with 69-mer HCV DNA probe and blocked with 1 mM MCH (diamonds), hybridization with 1 ⁇ of non complementary target (ITI 012) (squares), hybridization with 1 nM (triangles) and 50 nM (circles) complementary target (ITI 025).
• the impedance measurements were done in 2xSSC containing 10 mM [Fe(CN) 6 ] 3" and 10 mM [Fe(CN) 6 ] 4" (plus probe or target) at an applied dc potential between the electrodes in the IDE pair of 0 V.
• Figure 6 shows versus time EIS measurements during probe (thiol-DNA) layer formation (diamonds), after blocking with MCH (squares), during hybridization with 1 ⁇ complementary target (triangles) and washing after hybridization (circles).
• Figure 7 shows fluorescence measurement after EIS measurement of complementary target (50 nM) binding and 20 nM QD incubation; PMT setting 180.
• Figure 8 shows a schematic of EIS measurement of impedimetric protease activity.
• a protease e.g. MMP8 or 9
• their respective substrate peptide
• A AC impedance
• the system displays an initial impedance behaviour described in the schematic graph in (A).
• the incubation of the system with a sample containing the desired protease (B) will lead to a shortening of the immobilised peptide leading to a changed impedance signal, e.g. a reduced Ret value as indicated in the schematic graph in (C).
• TTR fast time to result
• the analyte for detection in both aspects of the present method is not especially limited, but is preferably a biomolecule.
• the analyte is selected from a cell, a protein, a polypeptide, a peptide, a peptide fragment, an amino acid, DNA and RNA.
• the method of the present invention is particularly useful for DNA and RNA detection.
• the method of the present invention may be used to detect either a single analyte or a plurality of different analytes simultaneously.
• the method of the present invention is a label-free method, i.e. there is no requirement to label the analyte in order to aid in detection.
• labels may be employed.
• each different analyte may be labelled with one or more different labels relatable to the analyte.
• multiple analytes may be detected by spatial separation, such as by arraying a set of probes for the analytes on a surface. Detection of a plurality of different analytes is also known as multiplexing.
• the analyte is investigated in solution or suspension in a liquid medium.
• the liquid medium is not particularly limited provided that it is suitable for analysis using EIS.
• the liquid medium comprises an electrolyte to facilitate the EIS measurement.
• the electrolyte is a solvent or buffer containing inert ions e.g. PBS; typically redox active species are then added at much lower concentrations.
• the electrolyte is not particularly limited, and may include any electrolyte known in the art. However electrolytes containing transition metal redox systems are preferred, such as Fe(II)/Fe(III) electrolyte systems. [Fe(CN) 6 ] 3" 4" is particularly preferred.
• each label has a different oxidation potential for the electrochemical detection method and, therefore, produces different signal peaks in the data obtained.
• metal nanoparticles are used as labels for different analytes (see below) different metals with different oxidation potentials may be used for each analyte.
• the alternating potential applied to the electrode is not especially limited, and depends upon the medium employed.
• the largest possible amplitude for EIS is fixed by the solvent limits (for water around 2V, giving a rms amplitude of around 1-2V).
• the potential may be from +1.0 to +2.0 V, and preferably from +1.2 V to +1.8 V.
• both oxidised and reduced species are present and this typically results in the use of less than 250mV amplitude.
• the alternating voltage applied between electrodes is of amplitude about lOmV root mean squared (rms). This enables the response to be linearised for e.g. equivalent circuit analysis. Higher amplitude responses can be used (and if statistical methods are to be employed to extract characteristic signals, they could be different/ advantageous) .
• the electrical detection method is carried out on a chip.
• the optical and electrical detection may be carried on one chip when the analyte(s) have been labelled with the different labels simultaneously.
• the analyte(s) may then be combined after labelling for optical and electrical detection on one chip or optical and electrical detection may be carried out separately on two separate chips.
• the analyte(s) is nucleic acid and the labelling step is performed using labelled primers and primer extension using labelled nucleosides.
• the labelled extended primer may be hybridised to a probe for optical and electrical detection. This is particularly advantageous because it allows the label(s) for electrical detection to be positioned in close proximity to the electrode for detection.
• the amount of analyte present can be quantified by voltammetry.
• Quantitative data can be obtained from the signal peaks by integration, i.e. determining the area under the graph for each signal peak produced.
• labels are employed, in particular when multiplexing is desirable.
• the labels referred to are not especially limited, but are preferably selected from nanoparticles, single molecules, intrinsic components of the target such as specific nucleotides or amino acids, and chemiluminescent enzymes. Suitable chemiluminescent enzymes include HRP and alkaline phosphatise. Fluorescent labels are particularly preferred, since optical detection of the labels is readily combined with the electrochemical methods of the invention.
• the labels are nanoparticles.
• Nanoparticles are particularly advantageous in these embodiments of the present invention because they operate successfully in electrical detection methods.
• the proximity of the nanoparticles to the surface is not especially important, which makes the assay more flexible.
• the nanoparticles comprise a collection of molecules because this gives rise to greater signal in optical and electrical detection methods than when single molecules are used.
• the nanoparticles are selected from metals, metal nanoshells, metal binary compounds and quantum dots.
• preferred metals or other elements are gold, silver, copper, cadmium, selenium, palladium and platinum.
• preferred metal binary and other compounds include CdSe, ZnS, CdTe, CdS, PbS, PbSe, Hgl, ZnTe, GaAs, HgS, CdAs, CdP, ZnP, AgS, InP, GaP, GalnP, and InGaN.
• Metal nanoshells are sphere nanoparticles comprising a core nanoparticle surrounded by a thin metal shell.
• Examples of metal nanoshells are a core of gold sulphide or silica surrounded by a thin gold shell.
• Quantum dots are semiconductor nanocrystals, which are highly light-absorbing, luminescent nanoparticles (West J, Halas N, Annual Review of Biomedical Engineering, 2003, 5: 285-292 "Engineered Nanomaterials for Biophotonics Applications: Improving Sensing, Imaging and Therapeutics”).
• quantum dots are CdSe, ZnS, CdTe, CdS, PbS, PbSe, Hgl, ZnTe, GaAs, HgS, CdAs, CdP, ZnP, AgS, InP, GaP, GalnP, and InGaN nanocrystals.
• Any of the above labels may be attached to an antibody.
• the size of the labels is preferably less than 200 nm in diameter, more preferably less than 100 nm in diameter, still more preferably 2-50 nm in diameter, still more preferably 5-50 nm in diameter, still more preferably 10-30 nm in diameter, most preferably 15-25 nm.
• each different analyte is labelled with one or more different labels relatable to the analyte.
• the labels may be different due to their composition and/or type.
• the labels may be different metal nanoparticles.
• the nanoparticles are metal nanoshells, the dimensions of the core and shell layers may be varied to produce different labels.
• the labels have different physical properties, for example size, shape and surface roughness.
• the labels may have the same composition and/or type and different physical properties.
• the different labels for the different analytes are preferably distinguishable from one another in the optical detection method and the electrical detection method.
• the labels may have different frequencies of emission, different scattering signals and different oxidation potentials.
• the method typically comprises a further initial step of labelling the analyte with one or more labels to form the labelled analyte.
• the means for labelling the analyte are not particularly limited and many suitable methods are well known in the art.
• the analyte is DNA or RNA it may be labelled by enzymatic extension of label-bound primers, post-hybridization labelling at ligand or reactive sites or "sandwich” hybridization of unlabelled target and label-oligonucleotide conjugate probe (Fritzsche W, Taton T A, Nanotechnology 14 (2003) R63-R73 "Metal nanoparticles as labels for heterogeneous, chip-based DNA detection").
• oligonucleotides to nanoparticles
• thiol-modified and disulfide-modified oligonucleotides spontaneously bind to gold nanoparticles surfaces, di- and tri-sulphide modified conjugates, oligothiol-nanoparticle conjugates and oligonucleotide conjugates from Nanoprobes' phosphine-modified nanoparticles (see figure 2 of Fritzsche W, Taton T A, Nanotechnology 14 (2003) R63-R73 "Metal nanoparticles as labels for heterogeneous, chip-based DNA detection").
• both DNA or RNA strands may be biotinylated.
• the biotinylated target strand may be hybridized to oligonucleotide probe-coated magnetic beads. Streptavidin- coated gold nanoparticles may then bind to the captured target strand (Wang J, Xu D, Kawde A, Poslky R, Analytical Chemistry (2001), 73, 5576-5581 "Metal Nanoparticle-Based Electrochemical Stripping Potentiometric Detection of DNA hybridization”).
• the magnetic beads allow magnetic removal of non-hybridized DNA.
• the EIS methods of the present invention may be employed in many different specific methods. However, they are particularly suited to protease detection, such as impedimetric protease activity detection.
• Figure 8 shows a schematic which demonstrates how this may operate.
• To measure the activity of a protease its substrate (a particular peptide) is immobilised on an electrode or device suitable to measure AC impedance (A), such as the devices used in the methods of the present invention.
• A AC impedance
• the system displays an initial impedance behaviour described in the schematic graph in (A).
• the incubation of the system with a sample containing the desired protease (B) will lead to a shortening of the immobilised peptide leading to a changed impedance signal, e.g. a reduced Re t value as indicated in the schematic graph in (C).
• a changed impedance signal e.g. a reduced Re t value as indicated in the schematic graph in (C).
• the advantage of this aspect of the invention is that no additional reagents need to be introduced in the test to measure the protease activity.
• the system has the potential to be multiplexed as many proteases could be measured in the same sample and reaction space.
• the system also is potentially much faster than conventional systems as kinetic impedance measurements can be done in a multiplexed manner.
• proteases may be detected, and the type of protease is not especially limited. However, in some embodiments, proteases associated with wounds are employed. Typically these proteases are ones which are present in wounds that are not healing. Two proteases that are of particular interest are MM8 and MM9.
• any EIS set-up may be employed.
• the electrodes, electrolytes, liquid medium, analytes (and probes if they are to be used) that will be involved in the final analysis will be employed to ensure that the parameters are as close to optimal as possible.
• the DNA probes were purified by passing them through a MicroSpinTM G-25 column (Amersham Biosciences, Buckinghamshire, UK) after cleavage of the disulfide protected nucleotides with 5 mM of TCEP solution.
• Figure 2 shows that for both large (macro) and small (interdigitated micro) electrodes, the real component and modulus provide similar information and best discriminate the EIS signal from the positive controls and immobilised probes, particularly at the lower end of the frequency range.
• the imaginary component best discriminates the EIS signal in the middle of the frequency range.
• the present invention selects the most useful range of frequency and smallest number of measurements that best discriminates between the different EIS data for all experimental conditions, and does not require employing fitting models such as equivalent circuits.
• Statistical analysis in this Example determined a 7-point optimal frequency range for both macro gold and interdigitated micro electrodes (IME) using the fold change between the EIS signal of the positive control and the immobilised probes.
• IME interdigitated micro electrodes
• Table 1 Summary results for 7-point optimal frequency range (in Hz) for Macro Electrode and Interdigitated Micro Electrode based on complementary hybridisation vs. immobilised probe without target comparison.
• the modulus data and real component give a very similar range of optimal frequencies for EIS measurement, spanning around a decade of frequency.
• the imaginary component gives optimal signals at slightly higher frequencies than that for real and modulus data, again spanning a decade of frequencies.
• the very large changes in the electrode dimensions from macro to IME have had little effect on the optimum frequency range for measurement, consistent with the response being largely independent of electrode area, which simplifies EIS measurement.
• Differential analysis of complementary versus mock hybridisation using fold-change gave a similar optimal frequency range to that of complementary hybridisation vs. immobilised probe signals (Table 2), confirming that the same measurement range can be used.
• Table 2 7-point optimal frequency range in Hz for Macro Gold Electrode based on complementary versus mock hybridisation comparison.
• FIG. 3 shows a comparison of the EIS Nyquist plot for the previously used method of sequential application of single sines to the measured responses for 5 multisine (over one decade of frequency) and 15 multisine (over two decades of frequency) EIS measurements for a protein macroelectrode experimental system.
• Experimental data collection, analysis and display was achieved on a PC in several minutes for sequential application, around 7 seconds for 5 sines and around 23 seconds for 15 sines.
• the component frequencies for this multisine experiment have been selected to span the frequency range determined by statistical analysis, which spans the semicircular charge transfer feature in the EIS Nyquist plot shown.
• the extremely close correspondence of all data indicates that the multisine EIS approach leads to more rapid EIS parameter extraction compatible with EIS measurement and analysis (and hence a TTR) of seconds, without compromising the accuracy of measurement.
• the DNA probes were purified by passing them through a MicroSpinTM G-25 column (Amersham Biosciences, Buckinghamshire, UK) after cleavage of the disulfide protected nucleotides with 5 mM of TCEP solution.
• thiol-DNA probe layers were immersed in a 10 ⁇ DNA solution in 2xSSC buffer and l O mM of each of [Fe(CN) 6 ] 3" and [Fe(CN) 6 ] 4" (10 mM [Fe(CN) 6 ] 3" 4" ) at room temperature.
• the EIS measurement was started as soon as the electrode was immersed in the DNA solution and was left to run for 3-4 h.
• the electrode EIS signal was measured again in 10 mM [Fe(CN) 6 ] 3" 4_ 2xSSC buffer to check for changes after the blocking step.
• the electrodes were then immersed in the target (complementary or not) DNA dissolved in 2xSSC and containing 10 mM [Fe(CN) 6 ] 3" 4" to allow EIS measurements, again at 0 V DC.
• Figure 4 shows typical impedance plots of these 69-mer thiol-DNA modified probe electrodes, before and after hybridisation with 1 ⁇ of complementary target (ITI 025).
• the high frequency semicircle is the common feature for both macro and IDE electrodes, and gives information on the charge transfer through the probe film layer at the electrode surface.
• the diameter of this high frequency semicircle increases, as expected, due to complementary target-probe binding in the probe layer, whilst the lower frequency diffusion feature remains essentially unchanged, indicating (as expected) little effect on diffusion between the electrodes.
• Figure 5 shows another example of IDEs prepared in the same way.
• Figure 6 now shows typical EIS measurements made in real time: the parameter sensitive to probe film formation and probe-target hybridisation is the electron transfer resistance, Re t , for [Fe(CN) 6 ] 3"/4" , which has been calculated from finding the width of the semicircular feature in the Nyquist plot of each of the EIS spectra. This has been plotted (as Ret for electron transfer) as function of time in this Figure.
• the kinetic technique is then used to monitor probe-target binding in the solution containing complementary target and ferri/ferrocyanide.
• an immediate increase in Ret is seen due to complementary target-probe binding.
• the initial response is immediate, with the first point showing an increase in Ret and with the value more than doubling within the first hour.
• This method enables the measurement of EIS response kinetically every few seconds (see multisine IDF).
• the rate of increase in probe-target binding would typically be expected to be first order in (and certainly dependent on) target concentration; therefore analysis of the rate of rise of EIS is then possible on the seconds to minutes timescale to give target concentration.

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