Parallel Evaluation of Melting Temperatures of DNAs in the Arrayed Droplets through the Fluorescence from DNA Intercalators.

Parallel evaluation of melting temperatures (Tm's) of DNA molecules in multiple floating droplets (20 µm in diameter) was demonstrated. The Tm values were evaluated from the melting curves which were observed through the fluorescence from the DNA intercalators. The Tm values measured in the droplets corresponded well to those measured in the bulk, indicating the validity of the measurement. The parallel evaluation of Tm's was realized by observing melting curves of DNAs in the different droplets at the same time using the "droplet guide", which guided and fixed the floating droplets to the designated points in the observing plane. This demonstration would pave the way for the improvement of the precision of droplet digital PCR (ddPCR), whose state-of-the-art ascribes color and intensity of fluorescence to the base sequence of DNA in the droplet.

KRAS genotyping by digital PCR combined with melting curve analysis.

Digital PCR (dPCR) has been developed as a method that can quantify nucleic acids more sensitively than real-time PCR. However, dPCR exhibits large fluctuations in the fluorescence intensity of the compartment, resulting in low accuracy. The main cause is most likely due to insufficient PCR. In this study, we proposed a new method that combines dPCR with melting curve analysis and applied that method to KRAS genotyping. Since the melting temperature (Tm) of the PCR product hardly depends on the amplification efficiency, genotyping accuracy is improved by using the Tm value. The results showed that the peaks of the distribution of the Tm values of DNA in the wells were 68.7, 66.3, and 62.6 °C for wild-type KRAS, the G12R mutant, and the G12D mutant, respectively, and the standard deviation of the Tm values was 0.2 °C for each genotype. This result indicates that the proposed method is capable of discriminating between the wild-type sequence and the two mutants. To the best of our knowledge, this is the first demonstration of the genotyping of single mutations by combining melting curve analysis and dPCR. The application of this approach could be useful for the quantification and genotyping of cancer-related genes in low-abundance samples.

Development of bioluminescent pyrophosphate assay using pyruvate phosphate dikinase and its application to single-nucleotide polymorphism analysis.

DNA analysis is an important technology with respect to diagnosis of infectious disease and tailored medication. In this study, we developed a novel bioluminescent assay for pyrophosphate, and it was applied to single-nucleotide polymorphism (SNP) analysis using one-base extension reaction. The principle of this method is as follows. A specific primer within each aliquot possessing a short 3' end of the base of interest was hybridized to the single-stranded DNA template. Subsequently, (exo-)Klenow DNA polymerase and one of either alpha-thio-dATP, dTTP, dGTP, or dCTP were added and incubated for 1 min. Pyrophosphate released by DNA polymerase is converted to ATP by pyruvate phosphate dikinase (PPDK), and the concentration of ATP is determined using the firefly luciferase reaction. This method, which does not require expensive equipment, can be used to rapidly monitor one point mutation in the gene.

Detection of DNA hybridization and extension reactions by an extended-gate field-effect transistor: characterizations of immobilized DNA-probes and role of applying a superimposed high-frequency voltage onto a reference electrode.

As we have already shown in a previous publication [Kamahori, M., Ihige, Y., Shimoda, M., 2007. Anal. Sci. 23, 75-79], an extended-gate field-effect transistor (FET) sensor with a gold electrode, on which both DNA probes and 6-hydroxyl-1-hexanethiol (6-HHT) molecules are immobilized, can detect DNA hybridization and extension reactions by applying a superimposed high-frequency voltage to a reference electrode. However, kinetic parameters such as the dissociation constant (K(d)(s)) and the apparent DNA-probe concentration (C(probe)(s)) on a surface were not clarified. In addition, the role of applying the superimposed high-frequency voltage was not considered in detail. In this study, the values of K(d)(s) and C(probe)(s) were estimated using a method involving single-base extension reaction combined with bioluminescence detection. The value of K(d)(s) on the surface was 0.38 microM, which was about six times that in a liquid phase. The value of C(probe)(s), which expressed the upper detection limit for the solid phase reaction, was 0.079 microM at a DNA-probe density of 2.6 x 10(12)molecules/cm(2). We found that applying the superimposed high-frequency voltage accelerated the DNA molecules to reach the gold surface. Also, the distance between the DNA-probes immobilized on the gold surface was controlled to be over 6 nm by applying a method of competitive reaction with DNA probes and 6-HHT molecules. This space was sufficient to enable the immobilized DNA-probes to lie down on the 6-HHT monolayer in the space between them. Thus, the FET sensor could detect DNA hybridization and extension reactions by applying a superimposed high-frequency voltage to the DNA-probes density-controlling gold surface.

A novel enzyme immunoassay based on potentiometric measurement of molecular adsorption events by an extended-gate field-effect transistor sensor.

We developed a novel enzyme immunoassay based on a potentiometric measurement of molecular adsorption events by using an extended-gate field-effect transistor (FET) sensor. The adsorbing rate of a thiol compound on a gold surface was found to depend on the concentration of the compound. To construct an electrochemical enzyme immunoassay system by using the sensor, the enzyme chemistry of acetylcholinesterase (AChE) to generate a thiol compound was used and combined with the enzyme-linked immunosorbent assays (ELISA). After the AChE-catalyzed reaction, the amount of the antigen was obtained by detecting the adsorbing rate of the generated thiol compound on the gold electrode using the FET sensor. The measurement stability was also found to improve when a high frequency voltage of 10 kHz or more was superimposed to the reference electrode. The signal corresponding to a range between 1 and 250 pg/mL of Interleukin 1 beta was obtained by the FET sensor when a voltage of 1 MHz was superimposed onto the reference electrode. The FET sensor based ELISA used in this measurement technique can successfully detect Interleukin 1 beta at concentrations as low as 1 pg/mL.

DNA detection by an extended-gate FET sensor with a high-frequency voltage superimposed onto a reference electrode.

An extended-gate field-effect-transistor (FET) sensor with a gold-sensing electrode, to which a gold-thiol bond could easily be applied, was developed for DNA detection. Because the gold electrode is located in a different area from the FET, it can be operated without a light-shielding box by masking only the FET. However, when the FET sensor is used in an aqueous solution, fluctuation of the interface potential on the gold surface occurs, which results in decreased sensitivity. In DNA detection, 1 h or more was required to stabilize the drain current of the FET sensor after dipping it into the solution. To improve the sensitivity by reducing the fluctuation, we devised a measurement technique using a high-frequency voltage superimposed onto a reference electrode. With a superimposed high frequency voltage of over 1 kHz, the time required to stabilize the drain current of the FET sensor after dipping it in the solution was not only shortened to 5 min, but the fluctuation of the drain current was also reduced. As a result of applying this method, the FET sensor could successfully detect DNA hybridization and the extension reaction.

Far-ultraviolet absorbance detection of sugars and peptides by high-performance liquid chromatography.

A far-ultraviolet (FUV)-absorbance detector with a transmission flow cell was developed and applied to detect absorbance of sugars and peptides by HPLC. The main inherent limitation of FUV-absorbance detection is the strong absorptions of solvents and atmospheric oxygen in the optical system as well as dissolved oxygen in the solvent. High absorptivity of the solvent and oxygen decreases transmission-light intensity in the flow cell and hinders the absorbance measurement. To solve the above drawbacks, the transmission-light intensity in the flow cell was increased by introducing a new optical system and a nitrogen-purging unit to remove the atmospheric oxygen. The optical system has a photodiode for detecting the reference light at a position of the minus-first-order diffracted light. In addition, acetonitrile and water were selected as usable solvents because of their low absorptivity in the FUV region. As a result of these implementations, the detectable wavelength of the FUV-absorbance detector (with a flow cell having an effective optical path length of 0.5mm) can be extended down to 175nm. Three sugars (glucose, fructose, and sucrose) were successfully detected with the FUV-absorbance detector. These detection results reveal that the absorption peak of sugar in liquid phase lies at around 178nm. The detection limit (S/N=3) in absorbance with a 0.5-mm flow cell at 180nm was 21µAU, which corresponds to 33, 60 and 60µM (198, 360, and 360pmol) for fructose, glucose, and sucrose, respectively. Also, the peptide Met-enkephalin could be detected with a high sensitivity at 190nm. The estimated detection limit (S/N=3) for Met-enkephalin is 29nM (0.29pmol), which is eight times lower than that at 220nm.

A gel-free SNP genotyping method: bioluminometric assay coupled with modified primer extension reactions (BAMPER) directly from double-stranded PCR products.

Inexpensive, high-throughput genotyping methods are needed for analyzing human genetic variations. We have successfully applied the regular bioluminometric assay coupled with modified primer extension reactions (BAMPER) method to single-nucleotide polymorphism (SNP) typing as well as the allele frequency determination for various SNPs. This method includes the production of single-strand target DNA from a genome and a primer extension reaction coupled with inorganic pyrophosphate (PPi) detection by a bioluminometric assay. It is an efficient way to get accurate allele frequencies for various SNPs, while single-strand DNA preparation is labor intensive. The procedure can be simplified in the typing of SNPs. We demonstrate that a modified BAMPER method in which we need not prepare a single-strand DNA can be carried out in one tube. A PCR product is directly used as a template for SNP typing in the new BAMPER method. Generally, tremendous amounts of PPi are produced in a PCR process, as well as many residual dNTPs, and residual PCR primers remain in the PCR products, which cause a large background signal in a bioluminometric assay. Here, shrimp alkaline phosphatase (SAP) and E. coli exonuclease I were used to degrade these components prior to BAMPER detection. The specific primer extension reactions in BAMPER were carried out under thermocycle conditions. The primers were extended to produce large amounts of PPi only when their bases at 3'-termini were complementary to the target. The extension products, PPis, were converted to ATP to be analyzed using the luciferin-luciferase detection system. We successfully demonstrated that PCR products can be directly genotyped by BAMPER in one tube for SNPs with various GC contents. As all reactions can be carried out in a single tube, the method will be useful for realizing a fully automated genotyping system.

Molecule counting with alkanethiol and DNA immobilized on gold microplates for extended gate FET.

Several molecule counting methods based on electrochemical characterization of alkanethiol and thiolated single-stranded oligonucleotide (HS-ssDNA) immobilized on gold microplates, which were used as extended gates of field effect transistors (FETs), have been investigated in this paper. The surface density of alkanethiol and DNA monolayers on gold microplates were quantitatively evaluated from the reductive desorption charge by using cyclic voltammetry (CV) and fast CV (FCV) methods in strong alkali solution. Typically, the surface density of 6-hydroxy-1-hexanethiol (6-HHT) was evaluated to be 4.639 molecules/nm(2), and the 28 base-pair dsDNA about 1.226-4.849 molecules/100 nm(2) on Au microplates after post-treatment with 6-HHT. The behaviors on surface potential and capacitance of different aminoalkanethiols on Au microplates were measured in 0.1 mol/L Na2SO4 and 10 mmol/L Tris-HCl (pH=7.4) solutions, indicating that the surface potential increases and the double-layer capacitance decreases with the length of carbon chain increased for the thiol monolayers, which obey a physics relationship for a capacitor. Comparably, a simple sensing method based on the electronic signals of biochemical reaction events on DNA immobilization and hybridization at the Au surface of the extended gate FET (EGFET) was developed, with which the surface density of the hybridized dsDNA on the gold surface of the EGFET was evaluated to be 1.36 molecules per 100 nm(2), showing that the EGFET is a promising sensing biochip for DNA molecule counting.

Direct detection of enzyme-catalyzed products by FET sensor with ferrocene-modified electrode.

An FET-based biosensor with a ferrocene-modified gold electrode detects the enzyme-produced electrons by using mediators that transfer the electrons from the enzyme to the sensor. Since an extended-gate FET sensor with a light-shielding mask can be operated without a light-shielding box, a small portable instrument will soon be realised. However, when the FET sensor detected enzyme-catalyzed products with the mediators under light conditions, measurements fluctuated due to photo-reduction of the mediators, resulting in decreased sensitivity. To improve sensitivity by reducing the fluctuation, we developed a procedure for directly detecting enzyme-catalyzed products without using the mediators. The key technique used in this procedure was a measurement technique using our developed potential-keeping method, in which the modified electrode of the FET sensor was oxidised by ferricyanide solution to make its surface the same high potential every time, and this high potential was kept until measurement because of the high input impedance of the FET structure. After this method was applied, the interfacial potential of the gold electrode decreased depending on the amount of enzyme-catalyzed products due to the ferrocene molecules immobilised on the gold electrode directly reacting with the products. The results obtained in light conditions indicated that model compounds of the products were detected from 10 µM to 10 mM with the Nernstian response of 59.2 mV/decade. Also, this method was applied to pesticide detection by using the enzyme inhibition by pesticide, and 5 ppb of diazinon was successfully detected by using only a sensor chip.

Extended-gate FET-based enzyme sensor with ferrocenyl-alkanethiol modified gold sensing electrode.

We developed a field-effect transistor (FET)-based enzyme sensor that detects an enzyme-catalyzed redox-reaction event as an interfacial potential change on an 11-ferrocenyl-1-undecanethiol (11-FUT) modified gold electrode. While the sensitivity of ion-sensitive FET (ISFET)-based enzyme sensors that detect an enzyme-catalyzed reaction as a local pH change are strongly affected by the buffer conditions such as pH and buffer capacity, the sensitivity of the proposed FET-based enzyme sensor is not affected by them in principle. The FET-based enzyme sensor consists of a detection part, which is an extended-gate FET sensor with an 11-FUT immobilized gold electrode, and an enzyme reaction part. The FET sensor detected the redox reaction of hexacyanoferrate ions, which are standard redox reagents of an enzymatic assay in blood tests, as a change in the interfacial potential of the 11-FUT modified gold electrode in accordance with the Nernstian response at a slope of 59 mV/decade at 25 degrees C. Also, the FET sensor had a dynamic range of more than five orders and showed no sensitivity to pH. A FET-based enzyme sensor for measuring cholesterol level was constructed by adding an enzyme reaction part, which contained cholesterol dehydrogenase and hexacyanoferrate (II)/(III) ions, on the 11-FUT modified gold electrode. Since the sensitivity of the FET sensor based on potentiometric detection was independent of the sample volume, the sample volume was easily reduced to 2.5 microL while maintaining the sensitivity. The FET-based enzyme sensor successfully detected a serum cholesterol level from 33 to 233 mg/dL at the Nernstian slope of 57 mV/decade.

Enzyme immunoassay using a reusable extended-gate field-effect-transistor sensor with a ferrocenylalkanethiol-modified gold electrode.

A reusable extended-gate field-effect transistor (FET) sensor with an 11-ferrocenyl-1-undecanethiol (11-FUT) modified gold electrode was developed for applying to enzyme immunoassay. It was found that the 11-FUT modified FET sensor detected a thiol compound 50 times or more repeatedly after a treatment with a 5% hydrogen peroxide solution. The gate-voltage shift of the FET sensor showed a fairly good linearity (R(2) = 0.998) within a range from 10(-2) to 10(-6) M on the concentration of 6-hydroxyl-1-hexanethiol, which is a thiol compound, at a Nernstian response of 58.5 mV/decade. The FET-based immunoassay was constructed by combining the 11-FUT modified-FET sensor with the enzyme-linked immunosorbent assay (ELISA), in which the enzyme chemistry of acetylcholinesterase (AChE) was used to generate a thiol compound. The 11-FUT modified FET sensor with an AC voltage at 1 MHz superimposed onto the reference electrode detected the AChE-catalyzed product corresponding to a serum concentration of interleukin 1beta from 10 to 5000 pg/mL. In addition, all measurements were successfully performed by using the same FET-sensor chip after a treatment with a 5% hydrogen peroxide solution.