CN112575067A - Method for detecting structure-specific nuclease FEN1 by using DNA ligation reaction and rolling circle amplification combined biosensor - Google Patents
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Abstract
The invention discloses a method for detecting structure-specific nuclease FEN1 by a biosensor combining DNA ligation reaction and rolling circle amplification, which comprises the steps of mixing and incubating a dumbbell-shaped DNA probe with a 5' end sequence fragment, a test sample and a reaction buffer solution, then adding T4DNA ligase and the reaction buffer solution into the solution, incubating, dropping a primer and RCA mixture into the obtained sample to start RCA reaction, measuring the fluorescence of the obtained sample, finally detecting the fluorescence values of the test sample with different concentrations, drawing a relation graph between the concentration and the fluorescence intensity, detecting the fluorescence value of the sample to be detected, and substituting the relation graph to calculate the concentration of FEN 1. The FEN1 detection method has the advantages of high sensitivity, strong selectivity and low cost, and can realize high-efficiency detection of FEN1 in tumors.
Description
Technical Field
The invention relates to a method for detecting a certain target object by a biosensor, in particular to a method for detecting structure-specific nuclease FEN1 by the biosensor combining DNA ligation reaction and rolling circle amplification.
Background
The key role of biomarkers in diagnosis and prognosis has been generally accepted, and the advantage of accurate detection is also of great significance in the development of sophisticated medicine. FEN1(Flap endinecrase 1) plays an important role in the process of DNA replication and repair, and cancer cells are vigorous in vitality, and tend to replicate rapidly in the human body, resulting in over-expression of DNA polymerase and thus FEN 1. Therefore, the specific detection of FEN1 can accurately locate cancer cells for subsequent treatment, and has great significance. However, currently, the development of an analysis technique for detecting FEN1 is still weak, and various conventional detection methods including Western blot and ELISA cannot meet clinical requirements, so that the invention of a new detection technique capable of improving performance and reducing cost is highly required.
From the programmability of functional nucleic acid and DNA nanotechnology, the conformation and function of DNA can be reasonably designed for recognition, catalysis and calculation. Among them, the important application is that the performance of the biosensor is greatly improved by using amplification technologies such as Rolling Circle Amplification (RCA), exponential isothermal amplification (EXPAR), Recombinase Polymerase Amplification (RPA), and the like.
Disclosure of Invention
The purpose of the invention is as follows: the invention aims to provide a method for detecting a structure-specific nuclease FEN1 by using a biosensor combining DNA ligation reaction and rolling circle amplification, which can specifically recognize a target object FEN1 and enhance the sensitivity and accuracy of detection.
The technical scheme is as follows: the method for detecting the structure-specific nuclease FEN1 by using the DNA ligation reaction and rolling circle amplification combined biosensor comprises the following steps:
(a) mixing the dumbbell-shaped DNA probe with the 5' end sequence fragment, a test sample and a reaction buffer solution, and incubating for 20-40min at 35-40 ℃;
(b) adding T4DNA ligase and the reaction buffer solution in the step (a) into the final solution obtained in the step (a), and incubating for 35-45min at the temperature of 20-25 ℃;
(c) dropping the primer and rolling circle amplification mixture into the final solution obtained in (b) to start the rolling circle amplification reaction;
(d) performing rapid and high-flux detection on the final solution obtained in the step (c) on a plate reader, and performing excitation and emission between 450 and 550 nm;
(e) measuring the fluorescence of the final solution obtained in (c) with a fluorescence spectrometer;
(f) repeating the steps, detecting the fluorescence values of the test samples with different concentrations, and calculating the relation between the FEN1 concentration and the fluorescence intensity by drawing a relational graph;
(g) and (e) taking the sample to be tested as a test sample, performing the steps (a) - (e), comparing the measured fluorescence value with the relation graph obtained in the step (f), and calculating the concentration of FEN1 in the sample to be tested.
The method, the dumbbell-shaped DNA probe with the free end in the step (a) has the sequence:
italicized letters indicate the free 5' terminal sequence and underlined letters indicate the binding region of the primer.
The method, the concentration range of the dumbbell-shaped DNA probe in the step (a) is 5-15 nM.
The method, the reaction buffer solution in the step (a) contains KCl, Tris-HCl, (NH)4)2SO4、MgSO4The solution of (1).
The method, the concentration range of the T4DNA ligase in the step (b) is 3-7U/. mu.L.
In the method, the sequence of the primer in the step (c) is as follows:
the method, wherein the RCA mixture in step (c) comprises phi29DNA polymerase, dNTPs, phi29 reaction buffer and SGI.
The method, step (d), is characterized by excitation and emission at 497nm and 530nm, respectively.
The method, wherein the fluorescence spectrometer measures fluorescence at a wavelength λ 497nm in step (e).
The reaction principle of the present invention is shown in FIG. 1.
Has the advantages that: compared with the prior art, the invention has the following remarkable advantages: (1) the method fully utilizes the characteristic that 5 ' groups are left after FEN1 cuts sequence segments, ensures that T4DNA ligase can connect adjacent 3 ' 5 ' groups to generate closed dumbbell-shaped DNA, thereby carrying out rolling circle amplification and signal amplification and improving the sensitivity of FEN1 detection. (2) The method integrates a signal amplification technology in the detection of FEN1 for the first time, combines functional nucleic acid editing with biomarkers to realize the improvement of sensitivity, and the detection limit of the method reaches the level of femtoltar. (3) The whole process of the biosensor mainly comprises sample addition and constant temperature culture, and has the advantages of simplicity, convenience and practicability; in addition, all enzymes, reagents and oligonucleotides have a mature source, thereby avoiding instability caused by self-synthesis of nanomaterials. (4) The method not only provides a better method for realizing identification and signal amplification of FEN1, but also provides a more effective research means for oncology research related to FEN 1.
Drawings
FIG. 1 is a schematic diagram of the present invention;
FIG. 2A is a graph of the relationship between ligation time and fluorescence of the total reaction; FIG. 2B is a graph showing the relationship between RCA reaction time and fluorescence of the total reaction;
FIG. 3A is a fluorescence spectrum of a sensing system with different concentrations of FEN1 added; FIG. 3B is a linear relationship between FEN1 concentration and fluorescence signal; FIG. 3C shows the selectivity of the method to FEN 1; FIG. 3D is a comparison of the quantification of FEN1 in tumor samples given by this method and a commercial ELISA kit.
Detailed Description
Drugs and reagents: oligonucleotides were synthesized and purified by biological engineering (shanghai, china). T4DNA ligase, phi29DNA polymerase, dNTP, SYBR Green I (SGI) and chemical reagents for buffer preparation were obtained from Biotechnology engineering (Shanghai, China). FEN1 is supplied by BBI (Shanghai, China). Ultrapure water was prepared by the Milli-Q system of Millipore (Mass.) and pretreated with diethyl pyrocarbonate (DEPC, BBI, Shanghai, China) in water to inactivate DNase and RNase before use in DNA-related experiments. Tumor samples given by the commercial ELISA kit are provided by biomanik.
Example 1
Condition optimization experiment of the detection method of the invention
The specific method comprises the following steps:
1) mixing 10 mul of designed dumbbell-shaped DNA probe with 5' end sequence fragment and 10nM concentration, 10 mul of test sample and 30 mul of reaction buffer solution, and incubating for 20-40min at 35-40 ℃. Then, 1. mu.L, 5U/. mu. L T4DNA ligase and 1 Xreaction buffer were added to the solution and incubated at 22 ℃ for 40 min. The reaction buffer solution is: 15mM KCl, 30mM Tris-HCl, 15mM (NH)4)2SO4、3mM MgSO4pH 8.8. 10. mu.L of the test sample is a solution which may contain the target, and the solvent is water or a buffer.
2) Primers and 5 μ of LRCA mix (2U phi29DNA polymerase, 1 mdNTPs, 1 XPhi 29 reaction buffer and 1 XPGI) were added dropwise to 1) resulting sample to initiate rolling circle amplification RCA reaction. Primer sequences and 1) template sequences are shown in the following table:
TABLE 1 DNA sequence of this method
Italicized letters indicate the free 5' terminal sequence and underlined letters indicate the binding region of the primer.
3) And then carrying out rapid and high-flux detection on a Synergy H-1 plate reader, and respectively carrying out excitation and emission at 497nm and 530 nm. The fluorescence of the obtained sample was measured by an F-7100 fluorescence spectrometer at a wavelength of λ 497nm, and the fluorescence value was recorded.
The ligation time of T4 ligase and the time of RCA reaction in step 1) and step 2) were varied, and the fluorescence intensity was observed to confirm the optimum reaction time for both reactions. The specific operation is as follows: (1) 5pM FEN1 was incubated with dumbbell DNA with 5' sequence fragment for 30 minutes, then 5U T4DNA ligase was added and incubated at 22 ℃ for various time intervals. Thereafter, the RCA reaction was performed by adding the RCA premix, and incubated at 37 ℃ for 30 minutes. (2) 5pM FEN1 was incubated with dumbbell DNA with 5' sequence fragment for 30min, then 5U T4DNA ligase was added and incubated at 22 ℃ for 40 min. Thereafter, RCA premix was added for RCA reaction and incubated at 37 ℃ for various time intervals. The change in fluorescence was recorded and observed. The relationship between the ligation time and fluorescence intensity of T4 ligase is shown in FIG. 2A, and it can be seen that the optimal ligation time is around 40 min. FIG. 2B shows the relationship between the time of the RCA reaction and the fluorescence intensity, and it can be seen that the optimum RCA reaction time was about 30 min.
Example 2
The test sample in step 1) of example 1 was replaced with FEN1 of different concentration, and other conditions were not changed, and steps 1) -3) of example 1 were repeated to detect fluorescence. The specific configuration method of the FEN1 with different concentrations comprises the following steps: FEN1 standard was diluted with reaction buffer to give FEN1 solutions at concentrations of 0, 20, 100, 500, 1000, 2000, 3000, 5000, 8000 fM.
The fluorescence spectra of the sensing system at corresponding different concentrations of FEN1 were plotted as shown in fig. 3A. The linear relationship between FEN1 concentration and fluorescence signal was plotted as shown in FIG. 3B. Fitting was performed on a linear basis, yielding a linear range of 20-8000fM, with a detection limit of 15fM according to the calculation rule for signal-to-noise ratio of 3.
Example 3
Selectivity test of the detection method of the present invention
The test sample in step 1) of example 1 is replaced by T3 DNA ligase, Exo III, Bst DNA pol, BSA, HAS, histone and IFN-gamma with corresponding concentration, other conditions are not changed, and steps 1) -3) of example 1 are repeated to detect fluorescence, so that the selectivity result of detecting the target FEN1 by the method of the invention is obtained, as shown in FIG. 3C. It can be seen from fig. 3C that the method of the present invention has good selectivity to the target FEN 1.
Example 4
Comparison of the quantitative results of FEN1 in tumor samples given by the method of the invention and a commercial ELISA kit, the detection method was performed according to the instructions provided by the Biomatik kit, as shown in FIG. 3D.
Example 5
Recovery rate test of the detection method of the present invention
The sample is changed into HeLa cells, the target molecules with the same amount are added into the sample, the sample adding detection is carried out, other conditions are not changed, and the steps 1) -3) in the example 1 are repeated, so that the recovery rate of the method in the actual sample is obtained, and the result is shown in Table 2. It can be seen that the recovery rate of the present detection method is good.
TABLE 2 detection results of HeLa cells detected by the sensor prepared by the present invention
Claims (9)
1. A method for detecting a structure-specific nuclease FEN1 by using a biosensor combining a DNA ligation reaction and rolling circle amplification is characterized by comprising the following steps:
(a) mixing the dumbbell-shaped DNA probe with the 5' end sequence fragment, a test sample and a reaction buffer solution, and incubating for 20-40min at 35-40 ℃;
(b) adding T4DNA ligase and the reaction buffer solution in the step (a) into the final solution obtained in the step (a), and incubating for 35-45min at the temperature of 20-25 ℃;
(c) dropping the primer and rolling circle amplification mixture into the final solution obtained in (b) to start the rolling circle amplification reaction;
(d) performing rapid and high-flux detection on the final solution obtained in the step (c) on a plate reader, and performing excitation and emission between 450 and 550 nm;
(e) measuring the fluorescence of the final solution obtained in (c) with a fluorescence spectrometer;
(f) repeating the steps, detecting the fluorescence values of the test samples with different concentrations, and calculating the relation between the FEN1 concentration and the fluorescence intensity by drawing a relational graph;
(g) and (e) taking the sample to be tested as a test sample, performing the steps (a) - (e), comparing the measured fluorescence value with the relation graph obtained in the step (f), and calculating the concentration of FEN1 in the sample to be tested.
2. The method according to claim 1, wherein the dumbbell DNA probe with free ends in step (a) has the sequence:
italicized letters indicate the free 5' terminal sequence and underlined letters indicate the binding region of the primer.
3. The method according to claim 1, wherein the concentration of the dumbbell DNA probe in step (a) is in the range of 5 to 15 nM.
4. The method of claim 1, wherein the reaction buffer in step (a) is a solution containing KCl, Tris-HCl, (NH)4)2SO4、MgSO4The solution of (1).
5. The method according to claim 1, wherein the concentration of T4DNA ligase in step (b) is in the range of 3-7U/. mu.L.
6. The method of claim 1, wherein the primer of step (c) has a sequence of:
7. the method of claim 1, wherein the RCA mixture in step (c) comprises phi29DNA polymerase, dNTPs, phi29 reaction buffer, and SGI.
8. The method according to claim 1, wherein in step (d) the excitation and emission are performed at 497nm and 530nm, respectively.
9. The method of claim 1, wherein the fluorescence spectrometer measures fluorescence at a wavelength of λ 497nm in step (e).
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Cited By (3)
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| CN109750088A (en) * | 2019-03-22 | 2019-05-14 | 重庆医科大学 | Sensor based on TdT-RCA and its application in dnmt rna detection |
| CN113355400A (en) * | 2021-04-06 | 2021-09-07 | 南京师范大学 | Cadmium ion detection method based on T3 DNA ligase |
| CN114410793A (en) * | 2022-02-16 | 2022-04-29 | 山东师范大学 | Method for detecting FEN1 activity by label-free fluorescence |
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| AU9341701A (en) * | 1996-11-29 | 2002-01-17 | Third Wave Technologies, Inc. | Fen-1 endonucleases, mixtures and cleavage methods |
| WO2013003630A2 (en) * | 2011-06-28 | 2013-01-03 | Igor Kutyavin | Methods and compositions for enrichment of nucleic acids in mixtures of highly homologous sequences |
| CN108823315A (en) * | 2018-07-24 | 2018-11-16 | 重庆医科大学附属第二医院 | Detect the application that the reagent of fen1 gene expression dose is invaded in the reagent of transfer in preparation for diagnosing and predicting liver cancer |
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| CN113355400B (en) * | 2021-04-06 | 2023-08-22 | 南京师范大学 | Cadmium ion detection method based on T3 DNA ligase |
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| CN114410793B (en) * | 2022-02-16 | 2024-03-08 | 山东师范大学 | Method for detecting FEN1 activity by label-free fluorescence |
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