The present invention relates to a method, a device and a program for detecting a degree of nucleic acid hybridization.
Hybridization is often used to detect nucleic acids (such as deoxyribonucleic acid (DNA) or ribonucleic acid (RNA)) that have specific sequences. Nucleic acids hybridize to probes that have sequences complementary to sequences of the nucleic acids. The degree of nucleic acid hybridization can be quantitatively analyzed using an electrochemical approach.
NPL 1 describes an example of a method for quantitatively analyzing a degree of nucleic acid hybridization using an electrochemical approach. In this case, a sample containing microRNA (miRNA) is used in cyclic voltammetry (CV) to obtain a pre-hybridization voltammogram (oxidation wave and reduction wave) and a post-hybridization voltammogram (oxidation wave and reduction wave). When the peak current value I0 for the pre-hybridization voltammogram (a pre-hybridization oxidation wave voltammogram has a peak current value I0 at potential Ep0) and the current value I for the potential Ep0 of the post-hybridization oxidation wave voltammogram are measured for identical work electrodes, the current value I is smaller than the peak current value I0. Therefore, the ratio I/I0 of the current value I with respect to the peak current value I0 can function as an indicator for quantitative analysis of a degree of nucleic acid hybridization.
The present inventors have investigated methods of quantitatively analyzing a degree of nucleic acid hybridization using a novel indicator which is different from the indicator described in NPL 1 (the relationship between the peak current value I0 and current value I). When the peak current value I0 and current value I are essentially equal (such as when the amounts of nucleic acids in each sample are very small or when virtually no hybridization has taken place), for example, it is difficult to accurately calculate the relationship (for example, the ratio or difference) between the peak current value I0 and current value I, and it is difficult to use the relationship between the peak current value I0 and current value I for high-precision quantitative analysis of a degree of nucleic acid hybridization. Also, when it is difficult to accurately measure the peak current value I0 (such as when the voltammogram near the peak current value I0 is not steep, thus resulting in a wide range of potentials in which the peak current value I0 and current values near the peak current value I0 are obtained, and making it difficult to establish a unique potential Ep0), it becomes difficult to accurately calculate the relationship (for example, the ratio or difference) between the peak current value I0 and current value I, and it is difficult to use the relationship between the peak current value I0 and current value I for high-precision quantitative analysis of a degree of nucleic acid hybridization.
One object of the invention is to obtain a novel indicator for quantitative analysis of a degree of nucleic acid hybridization. Other objects of the invention will become apparent from the description throughout the present specification.
One aspect of the invention is a method for detecting a degree of nucleic acid hybridization using a first oxidation wave and a second oxidation wave, wherein:
the method includes calculating the potential difference between a first potential at which, in the first oxidation wave, a first current value is obtained in a range below the potential for the peak current value of the first oxidation wave, and a second potential at which, in the second oxidation wave, a first current value is obtained in a range below the potential for the peak current value of the second oxidation wave.
Another aspect of the invention is a device for detecting a degree of nucleic acid hybridization using a first oxidation wave and a second oxidation wave, wherein:
the device comprises a calculator which calculates the potential difference between a first potential at which, in the first oxidation wave, a first current value is obtained in a range below the potential for the peak current value of the first oxidation wave, and a second potential at which, in the second oxidation wave, a first current value is obtained in a range below the potential for the peak current value of the second oxidation wave.
Yet another aspect of the invention is a program that causes a computer to function as a device for detecting a degree of nucleic acid hybridization using a first oxidation wave and a second oxidation wave, wherein:
the program causes the computer to:
calculate the potential difference between a first potential at which, in the first oxidation wave, a first current value is obtained in a range below the potential for the peak current value of the first oxidation wave, and a second potential at which, in the second oxidation wave, a first current value is obtained in a range below the potential for the peak current value of the second oxidation wave.
According to the aforementioned aspects of the invention it is possible to obtain a novel indicator for quantitative analysis of a degree of nucleic acid hybridization.
Embodiments of the invention will now be described with reference to the accompanying drawings. In all of the diagrams, corresponding constituent elements are indicated using like reference numerals and will not be redundantly explained.
In the following explanation, the calculator 100, determiner 110 and memory 120 are shown not as hardware unit configurations but rather as functional unit blocks. The calculator 100, determiner 110 and memory 120 are provided by an optional combination of hardware and software, which may essentially be any type of computer CPU, a memory, a program that forms the constituent elements in the diagram that are loaded into the memory, a storage medium such as a hard disk that stores the program, and a network connection interface. A variety of different modified examples for the method and device are possible.
With this configuration it is possible to obtain a novel indicator for quantitative analysis of the degree of nucleic acid hybridization. Specifically, this configuration allows the potential difference ΔE to be calculated by the calculator 100. As explained below, the potential difference ΔE can serve as an indicator for quantitative analysis of the degree of nucleic acid hybridization.
Moreover, this configuration does not require calculation of the relationship (for example, the ratio or difference) between the peak current value I0 and current value I, even when the peak current value I0 of the first oxidation wave O1 and the current value I of the second oxidation wave O2 (the second oxidation wave O2 has a second current value (current value I) at the potential Ep0 for the peak current value I0 of the first oxidation wave O1), are essentially equal. Thus, even when the peak current value I0 of the first oxidation wave O1 and the current value I of the second oxidation wave O2 are essentially equal, it is possible to quantitatively analyze the degree of nucleic acid hybridization to a high degree of precision.
According to one example, the potential difference ΔE can be calculated even when the peak current value I0 of the first oxidation wave O1 and the current value I of the second oxidation wave O2 are essentially equal, such as when the current value I of the second oxidation wave O2 is 90% to 110% of the peak current value I0 of the first oxidation wave O1.
In addition, with the aforementioned configuration it is not necessary to calculate the relationship (for example, the ratio or difference) between the peak current value I0 and current value I, even when it is difficult to accurately measure the peak current value I0 of the first oxidation wave O1 (such as when the first oxidation wave O1 near the peak current value I0 is not steep, thus resulting in a wide range of potentials in which the peak current value I0 and current values near the peak current value I0 are obtained, and making it difficult to establish a unique potential Ep0). Thus, even when it is difficult to accurately measure the peak current value I0, it is still possible to quantitatively analyze the degree of nucleic acid hybridization to a high degree of precision.
In the example shown in
According to another example, the measurement system 20 may measure each voltammogram by a method other than CV, such as differential pulse voltammetry (DPV). In this example as well, each voltammogram includes an oxidation wave. The potential difference ΔE can therefore be calculated by the same method as explained using
The measurement system 20 has an electrode (work electrode) for measurement of the voltammogram C1 and voltammogram C2. The measurement system 20 may also have multiple electrodes (multiple work electrodes). In this case the calculator 100 will be able to calculate multiple potential differences ΔE respectively for the multiple electrodes. The calculator 100 may statistically process the multiple potential differences ΔE, by calculating the median or average for the multiple potential differences ΔE, for example.
In the example shown in
In the example shown in
According to another example, each oxidation wave may represent measurement results for other type of nucleic acid than miRNA. For example, it may represent measurement results for DNA or it may represent measurement results for other RNA than miRNA.
The user of the device 10 may appropriately determine the first current value I1 depending on different conditions (such as the first oxidation wave O1 and the second oxidation wave O2).
According to one example, the first current value I1 may be selected from a range of current values in which variation (such as standard deviation) in the potential difference ΔE is kept to within a fixed range, and for example, it may be 10% to 90% of the peak current value I0 of the first oxidation wave O1 (a potential difference ΔE of within 10% to 90% of the peak current value I0 of the first oxidation wave O1, for example, is kept to within a fixed range from the mean value for the potential difference ΔE at 10% to 90% of the peak current value I0 of the first oxidation wave O1, at any current value). The calculator 100 may also calculate the potential difference ΔE for a plurality of current value ratios I1/I0 (for example, current value ratios I1/I0 of 0.20, 0.30 and 0.40). The calculator 100 may statistically process the multiple potential differences ΔE, such as calculating the median or average for the multiple potential differences ΔE.
The reason for the potential difference ΔE produced in
The potential of an electrode (work electrode) in a measurement system 20 can fall due to a negative overall charge ΔQ produced by the hybridized target nucleic acid. During measurement of the oxidation wave, an electrical double layer of capacitance C is formed in the work electrode. The reduction in potential of the work electrode can be estimated as ΔQ/C. Therefore, the post-hybridization oxidation wave (the second oxidation wave O2 in the example shown in
The device 10 includes a determiner 110. The determiner 110 determines the degree of nucleic acid hybridization based on the potential difference ΔE. As explained above regarding the reason for the potential difference ΔE, the degree of nucleic acid hybridization is greater with a larger potential difference ΔE and lower with a smaller potential difference ΔE. The determiner 110 therefore determines that the degree of nucleic acid hybridization is greater with a larger potential difference ΔE and the degree of nucleic acid hybridization is lower with a smaller potential difference ΔE.
The device 10 also includes a memory 120. As explained below for
The reference data indicates degrees of nucleic acid hybridization (ΔH1, ΔH2, ΔH3, . . . in the right column of
The bus 11 is a data transmission line for sending and receiving of data between the processor 12, memory 13, storage device 14 and network interface 15. However, the method of connection between the processor 12, memory 13, storage device 14 and network interface 15 is not limited to being a bus connection.
The processor 12 is a computing device such as a CPU (Central Processing Unit) or GPU (Graphics Processing Unit). The memory 13 is a main memory unit such as a RAM (Random Access Memory) or ROM (Read Only Memory). The storage device 14 is an auxiliary storage device such as an HDD (Hard Disk Drive), SSD (Solid State Drive) or memory card.
The storage device 14 stores a program module that carries out the functions of the device 10 (for the calculator 100, determiner 110 or memory 120). The processor 12 executes each program module by reading from a memory 13, and carries out the function corresponding to each program module.
The network interface 15 is an interface for connection of the device 10 with a communication network such as a LAN (Local Area Network) or WAN (Wide Area Network). The device 10 is able to communicate with the measurement system 20 by connection to the communication network via the network interface 15. The device 10 may be connected to the measurement system 20 through a wireless network or it may be connected to the measurement system 20 through a wired network. According to another example, data obtained at the measurement system 20 (for example, the voltammogram C1 and the voltammogram C2 shown in
As shown in
The example shown in
As shown in
The potential difference ′ΔE for the first reduction wave R1 and the second reduction wave R2 can be estimated as the degree of shift from the pre-hybridization reduction wave (the first reduction wave R1 in the example shown in
In the graph shown in
For each of 74 different measurement systems 20 (work electrodes) in the example shown in
First oxidation wave O1: Oxidation wave before miRNA hybridization (measuring solution: 0.25 mM phosphate buffer+0.5 mM NaClO4, marker: 1 mM [Fe(CN)6]4−)
Second oxidation wave O2: Oxidation wave after miRNA hybridization (measuring solution: 0.25 mM phosphate buffer+0.5 mM NaClO4, marker: 1 mM [Fe(CN)6]4−)
CV sweep rate: 500 mV/sec
First current value I1: 3 nA (approximately 20% of peak current value I0 for each first oxidation wave O1)
The median of the current value ratio I/I0 was 1.0205. This shows that the current value I of the second oxidation wave O2 was essentially equivalent to the peak current value I0 of the first oxidation wave O1. It can therefore be difficult to quantitatively analyze the degree of nucleic acid hybridization to a high degree of precision using the current value ratio I/I0.
The median of the potential difference ΔE was 35 mV. A potential difference ΔE on this level can be considered to be distinctly apparent. It is therefore concluded that the degree of nucleic acid hybridization can be quantitatively analyzed to high precision using the potential difference ΔE.
Embodiments of the invention have been described above with reference to the accompanying drawings, but it is to be understood that these are merely examples of the invention, and that other constructions may be employed as well.
The present application claims priority based on Japanese Patent Application No. 2018-183439, which was filed on Sep. 28, 2018 and the entirety of the disclosure of which is incorporated herein by reference.
Number | Date | Country | Kind |
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2018-183439 | Sep 2018 | JP | national |
Filing Document | Filing Date | Country | Kind |
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PCT/JP2019/034380 | 9/2/2019 | WO | 00 |