CN113945720B - PDGF-BB identification method based on aptamer probe and kit for detecting PDGF-BB - Google Patents
PDGF-BB identification method based on aptamer probe and kit for detecting PDGF-BB Download PDFInfo
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Abstract
The invention provides a PDGF-BB identification method based on a nucleic acid aptamer probe, which comprises the following steps: immunoreacting PDGF-BB in the sample with a nucleic acid aptamer probe, wherein the nucleotide sequence of the nucleic acid aptamer probe comprises a sequence shown as SEQ ID NO. 1. The nucleic acid aptamer with the nucleotide sequence shown in SEQ ID NO.1 shows outstanding specificity and affinity to PDGF-BB, and the nucleic acid aptamer with the sequence shown in SEQ ID NO.1 is used as a nucleic acid aptamer probe for targeting PDGF-BB, so that PDGF-BB antigen protein can be sensitively, accurately and rapidly identified and stably combined, and false positive can be avoided.
Description
Technical Field
The invention belongs to the technical field of biology, and particularly relates to a PDGF-BB identification method based on a nucleic acid aptamer probe and a kit for detecting PDGF-BB.
Background
Platelet Derived Growth Factor (PDGF) is a potent mitogen and important pro-tumor angiogenic growth factor that can be produced by a variety of blood cells, tissue cells and some tumor cells. The current research on PDGF expression and detection in tumor cells has become one of the hot spots in the biomedical research field.
PDGF-BB is the most active subtype of platelet-derived growth factor in the PDGF family. At present, a common recognition method of PDGF-BB is enzyme-linked immunoassay (ELISA), and the basic principle of the method is as follows: ① The antigen or antibody is bound to the surface of a solid support and maintained in its immunological activity. ② The antigen or antibody is linked with an enzyme to form an enzyme-labeled antigen or antibody, which retains both its immunological activity and the enzymatic activity. In the measurement, a specimen to be tested (an antibody or an antigen to be measured therein) and an enzyme-labeled antigen or antibody are reacted with the antigen or antibody on the surface of the solid carrier in different steps. The antigen-antibody complex formed on the solid phase carrier is separated from other substances by a washing method, and finally the enzyme bound on the solid phase carrier is in a certain proportion with the amount of the detected substances in the specimen. After the substrate of the enzyme reaction is added, the substrate is catalyzed by the enzyme to become a colored product, and the amount of the product is directly related to the amount of the detected substance in the sample, so that the color reaction can be qualitatively or quantitatively analyzed according to the existence of the color reaction.
The aptamer is an artificially synthesized nucleic acid capable of specifically binding to a target molecule, and has a stable secondary structure. The mode of the nucleic acid aptamer recognition molecule is similar to that of an antibody, but compared with a protein antibody, the nucleic acid aptamer has more advantages, such as no limitation of immune conditions and immunogenicity, can be artificially synthesized in vitro, is simple and quick to prepare, is reversible in denaturation and renaturation, can be modified, and is easy to store for a long time, transport at room temperature and the like. More importantly, the target molecules of the aptamer are more extensive and can be proteins, nucleic acids, small peptides, amino acids, organic matters, metal ions and the like. In addition, the nucleic acid aptamer has the following advantages, such as: stable chemical property, no report of immunogenicity or toxicity, high affinity, strong specificity and easy modification. These properties make the aptamer widely used in the field of biomedical research an indispensable powerful tool.
Disclosure of Invention
The invention aims to provide a PDGF-BB identification method based on a nucleic acid aptamer probe and a kit for detecting PDGF-BB, so as to improve the sensitivity and accuracy of PDGF-BB detection.
According to one aspect of the present invention, there is provided a PDGF-BB recognition method based on a nucleic acid aptamer probe: immunoreacting PDGF-BB in the sample with a nucleic acid aptamer probe, wherein the nucleotide sequence of the nucleic acid aptamer probe comprises a sequence shown as SEQ ID NO. 1.
Preferably, PDGF-BB in the sample is sequentially immunoreacted with the antibody and the aptamer probe, respectively, to form a sandwich structure of the antibody-protein-aptamer.
Preferably, after forming the sandwich structure, excess nucleic acid aptamer probes not bound to PDGF-BB are washed away, PCR amplification is performed on the nucleic acid aptamer probes involved in constructing the sandwich structure, and the result of PCR amplification is used to characterize PDGF-BB in the sample.
According to another aspect of the present invention, there is provided a kit for detecting PDGF-BB, comprising a solid phase carrier and a nucleic acid aptamer probe, wherein the surface of the solid phase carrier is coated with a capture antibody targeting PDGF-BB, and the nucleotide sequence of the nucleic acid aptamer probe comprises the sequence shown in SEQ ID NO. 1.
Preferably, the prepared material also comprises a washing solution, wherein the washing solution is phosphate buffer solution containing 0.5% of Tween 20 and 0.1 mol/L.
Preferably, the wash liquor contains 0.05% sodium azide.
Preferably, the pH of the wash solution=7.2.
Preferably, the material provided therewith further comprises Taq-DNA polymerase, PCR reaction buffer, dNTPs and primers, the primers being complementary to a portion of the nucleotide sequence of the aptamer.
The invention adopts the nucleic acid aptamer as a probe to be applied to the recognition detection of PDGF-BB, and compared with protein antibodies targeting PDGF-BB, the nucleic acid aptamer probe is based on the structural characteristics of DNA: the preparation is simple and quick, the molecular weight is small, the chemical property is stable, and the modification is easy to carry out; the method is suitable for PCR amplification, and the antigen protein is qualitatively and quantitatively detected by performing PCR amplification, so that the detection scheme is more various and more convenient than the traditional method for detecting the antibody by using proteins. In the development process, a considerable part of the nucleic acid aptamer targeting PDGF-BB is found to be combined with antigen proteins, and can be combined with a capture antibody or a solid-phase carrier for fixing the capture antibody in a targeting manner, so that false positive occurs. However, among the nucleic acid aptamers obtained by screening, the nucleic acid aptamer with the nucleotide sequence shown in SEQ ID NO.1 shows outstanding specificity and affinity to PDGF-BB, and the nucleic acid aptamer with the nucleotide sequence shown in SEQ ID NO.1 is used as a nucleic acid aptamer probe for targeting PDGF-BB, so that PDGF-BB antigen protein can be sensitively, accurately and rapidly identified and stably combined, and false positive can be avoided.
Preferably, the primers comprise an upstream primer and a downstream primer, the sequence of the upstream primer is shown as SEQ ID NO.2, and the sequence of the downstream primer is shown as SEQ ID NO.3
Optionally, the prepared material also comprises PDGF-BB protein standard substance, substrate chromogenic liquid, stop solution and chromogenic substrate labeled streptavidin, and the aptamer probe is a nucleotide sequence labeled by biotin.
Drawings
FIG. 1 is a secondary structure diagram of the nucleic acid aptamer obtained in example 1;
FIG. 2 is an experimental illustration of the construction of a standard curve in example 2;
FIG. 3 shows Ct values corresponding to the gradient concentration standard sample and the control sample in example 2;
FIG. 4 is a standard graph constructed in example 2.
Detailed Description
In order that those skilled in the art will better understand the present invention, a technical solution of the embodiments of the present invention will be clearly and completely described below, and it is apparent that the described embodiments are only some embodiments of the present invention, not all embodiments.
Example 1
Acquisition of PDGF-B nucleic acid aptamer
Screening of nucleic acid aptamers the screening of nucleic acid aptamers was performed using capillary electrophoresis SELEX technique (SYSTEMATIC EVOLUTIONOF LIGANDS BY EXPONENTIAL ENRICHMENT):
Mixing nucleic acid with PDGF-B antigen, running the mixed solution formed by the mixing on CE (high performance capillary electrophoresis-laser induced fluorescence detection), and separating and collecting nucleic acid molecules (DNA-protein complexes) bound to PDGF-B antigen; passing the DNA-protein complex through the capillary at different rates, wherein the DNA-protein complex can be identified by fluorescent detection techniques as it passes through a window in the capillary, collecting DNA through a complex peak and PCR amplifying; we then used Lambda exonuclease to generate ssDNA; the above procedure was repeated 3-10 times. Negative selection was performed in a similar manner using non-specific proteins, but collected DNA that did not bind to the antigen. After selection, the DNA was sequenced using NGS to identify individual sequences. Finally, the aptamer binding to PDGF-B is found.
The sequence of the aptamer obtained in this example is:
TCCCACGCATTCTCCACATCATAAGCTGAGCATCTTAGATCCCCGTCAA GGGCAGCGTAA CCT TTCTGTCCTTCCGTCAC(SEQ ID NO.1),
The secondary mechanism is shown in figure 1.
Example 2
1. Kit for constructing and detecting PDGF-BB
The kit for detecting PDGF-BB is prepared from the following materials:
ELISA plate: the surface is coated with a capture antibody, the capture antibody is anti-PDGF-BB monoclonal antibody, and the capture antibody is blocked by using phosphate buffer solution with pH=7.2 and 0.1mol/L containing 5% skimmed milk powder as blocking solution;
nucleic acid aptamer probe: the nucleotide sequence of the nucleic acid aptamer probe is SEQ ID NO.1;
Capture antibody dilution: 15mM phosphate buffer, pH=7.4, containing 0.5% casein, 2-4% sucrose, 150mM NaCl, 0.2% Tween 20;
Sample dilution: 15mM phosphate buffer containing 2-4% sucrose, 150mM NaCl, 0.2% Tween 20, pH=6.5;
washing liquid: 0.1M phosphate buffer containing 0.5% tween 20,0.05% sodium azide, ph=7.2.
Taq-DNA polymerase;
PCR reaction buffer;
dNTP;
Primer: the sequence of the upstream primer is TCCCACGCATTCTCCACATCATA (SEQ ID NO. 2), and the sequence of the downstream primer is GTGACGGAAGGACAGAAAGGTT (SEQ ID NO. 2);
SYBR Green Mix
PDGF-BB protein standard solution.
2. Use of kit for detecting PDGF-BB
The PDGF-BB quantitative detection is carried out by using the kit for detecting PDGF-BB provided by the implementation, and the following steps are carried out:
step one: and respectively adding a PDGF-BB protein standard substance and a sample to be detected which are subjected to gradient dilution into the micropores of the ELISA plate, adding 100 mu L of sample into each hole, repeating each sample, reacting for 40 minutes at 37 ℃, and washing the ELISA plate.
Step two: adding a nucleic acid aptamer probe into the microwells of the ELISA plate, incubating for 40 minutes, and washing the ELISA plate.
The operations of washing the ELISA plates in the first and second steps are performed by using the prepared washing liquid to wash the ELISA plates on the plate washer for 5 times, 10 minutes. In other embodiments, the washing solution configured by the enzyme-linked immunosorbent assay kit can be used for carrying out the washing operation commonly used in the field according to the actual situation, and the washing operation is not limited to the plate washing by a plate washer.
Step three: PCR amplification of standards
(1) PCR amplification was performed using 5. Mu.L of aptamer probe bound to PDGF-BB protein standard, and the total volume of the reaction system was 50. Mu.L, with the following amplification conditions: firstly, carrying out 3mins at 94 ℃, and carrying out recycling amplification 30 times at 94 ℃ for 10s and at 55 ℃ for 25 s;
(2) Adding 5 mu L of PCR reaction solution after amplification of the 1 st time into a new system, and repeating the PCR amplification operation of the 1 st time;
(3) Recovering the aptamer probe.
Step four: PCR amplification of samples
(1) PCR amplification was performed using 5. Mu.L of aptamer probe that bound PDGF-BB protein in the sample, and the total volume of the reaction system was 50. Mu.L, with the following amplification conditions: firstly, carrying out 3mins at 94 ℃, and carrying out recycling amplification 30 times at 94 ℃ for 10s and at 55 ℃ for 25 s;
(2) Adding 5 mu L of PCR reaction solution after amplification of the 1 st time into a new system, and repeating the PCR amplification operation of the 1 st time;
(3) Recovering the aptamer probe.
The standard curve is constructed as follows:
(1) A standard sample containing a concentration gradient antigen and a control sample containing no antigen were set up in such a manner that 40 μl of VEGF standard was added to a clean centrifuge tube containing 360 μl of diluent to prepare 1000pg/ml of standard solution, the 1000pg/ml of standard solution was diluted to further formulate other concentrations of standard sample, and finally an equal amount of the accounting aptamer (SEQ ID No. 1) was added to the standard sample and the control sample, respectively.
(2) Data was collected using qPCR to characterize the amount of antigen contained in each sample by outputting Ct values, where lower Ct values represent higher antigen concentrations; when the DNA is amplified, an additional fluorescent signal is generated, each cycle resulting in approximately doubling of the DNA, and the Ct value represents the number of cycles required for the sample to pass the fluorescence threshold; thus, higher levels of DNA (directly related to the amount of antigen in the sample) will result in lower Ct values.
(3) Calculating average Ct of each group of triplicate standard samples and control samples; subtracting the Ct value of each sample from the control to obtain a Ct value difference between the control and the sample; the Ct values of the standard sample and the control sample obtained according to the above steps and corresponding to the gradient concentrations are shown in fig. 3, and in fig. 3, the intensity of the ordinate is the Ct value corresponding to the sample. The linear relationship obtained by fitting the standard curve with the concentration as x-coordinate and the Ct value difference as y-coordinate is shown in fig. 4.
The minimum detection limit of PDGF-BB is calculated to be 0.2pg/mL, and therefore, the IFN-gamma recognition method provided by the invention can effectively improve the detection sensitivity of PDGF-BB, and the kit related to the recognition method can reach the minimum detection limit which is obviously lower than that of the kit for detecting PDGF-BB at present.
The above embodiments are only for illustrating the technical solution of the present invention and not for limiting the scope of the present invention, and although the present invention has been described in detail with reference to the preferred embodiments, it should be understood by those skilled in the art that the technical solution of the present invention may be modified or substituted without departing from the spirit and scope of the technical solution of the present invention.
SEQUENCE LISTING
<110> Rebauo biotechnology Co., ltd
<120> PDGF-BB identification method based on nucleic acid aptamer probe and kit for detecting PDGF-BB
<160> 3
<170> PatentIn version 3.5
<210> 1
<211> 80
<212> DNA
<213> Artificial sequence
<400> 1
tcccacgcat tctccacatc ataagctgag catcttagat ccccgtcaag ggcagcgtaa 60
cctttctgtc cttccgtcac 80
<210> 2
<211> 23
<212> DNA
<213> Artificial sequence
<400> 2
tcccacgcat tctccacatc ata 23
<210> 3
<211> 22
<212> DNA
<213> Artificial sequence
<400> 3
gtgacggaag gacagaaagg tt 22
Claims (7)
1. A method for identifying PDGF-BB non-diagnostic purposes based on aptamer probes, comprising:
Respectively and sequentially immunoreacting PDGF-BB in a sample with an antibody and a nucleic acid aptamer probe to form a sandwich structure of the antibody-protein-nucleic acid aptamer, wherein the nucleotide sequence of the nucleic acid aptamer probe is shown as SEQ ID NO. 1;
Washing away excess of said aptamer probe that has not bound PDGF-BB after formation of said sandwich structure;
and carrying out PCR amplification on the nucleic acid aptamer probes participating in constructing the sandwich structure, and utilizing the PCR amplification result to characterize PDGF-BB in the sample.
2. A kit for detecting PDGF-BB, characterized by: the prepared material comprises a solid phase carrier and a nucleic acid aptamer probe, wherein the surface of the solid phase carrier is coated with a capture antibody targeting PDGF-BB, and the nucleotide sequence of the nucleic acid aptamer probe is shown as SEQ ID NO. 1.
3. The kit for detecting PDGF-BB of claim 2 wherein: the prepared material also comprises a washing liquid, wherein the washing liquid is phosphate buffer solution containing 0.5% of Tween 20 and 0.1 mol/L.
4. The kit for detecting PDGF-BB of claim 3 wherein: the wash liquor contained 0.05% sodium azide.
5. The kit for detecting PDGF-BB of claim 4 wherein: the pH of the wash solution=7.2.
6. The kit for detecting PDGF-BB of claim 3 wherein: the prepared material also comprises Taq-DNA polymerase, PCR reaction buffer solution, dNTPs and primers, wherein the primers are complementary with partial nucleotide sequences of the nucleic acid aptamer.
7. The kit for detecting PDGF-BB of claim 6 wherein: the primer comprises an upstream primer and a downstream primer, the sequence of the upstream primer is shown as SEQ ID NO.2, and the sequence of the downstream primer is shown as SEQ ID NO. 3.
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